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Sample records for proposed ancestral photosystem

  1. Photosystem II

    ScienceCinema

    James Barber

    2016-07-12

    James Barber, Ernst Chain Professor of Biochemistry at Imperial College, London, gives a BSA Distinguished Lecture titled, "The Structure and Function of Photosystem II: The Water-Splitting Enzyme of Photosynthesis."

  2. Are palaeoscolecids ancestral ecdysozoans?

    PubMed

    Harvey, Thomas H P; Dong, Xiping; Donoghue, Philip C J

    2010-01-01

    The reconstruction of ancestors is a central aim of comparative anatomy and evolutionary developmental biology, not least in attempts to understand the relationship between developmental and organismal evolution. Inferences based on living taxa can and should be tested against the fossil record, which provides an independent and direct view onto historical character combinations. Here, we consider the nature of the last common ancestor of living ecdysozoans through a detailed analysis of palaeoscolecids, an early and extinct group of introvert-bearing worms that have been proposed to be ancestral ecdysozoans. In a review of palaeoscolecid anatomy, including newly resolved details of the internal and external cuticle structure, we identify specific characters shared with various living nematoid and scalidophoran worms, but not with panarthropods. Considered within a formal cladistic context, these characters provide most overall support for a stem-priapulid affinity, meaning that palaeoscolecids are far-removed from the ecdysozoan ancestor. We conclude that previous interpretations in which palaeoscolecids occupy a deeper position in the ecdysozoan tree lack particular morphological support and rely instead on a paucity of preserved characters. This bears out a more general point that fossil taxa may appear plesiomorphic merely because they preserve only plesiomorphies, rather than the mélange of primitive and derived characters anticipated of organisms properly allocated to a position deep within animal phylogeny. PMID:20433458

  3. Structure of photosystem I.

    PubMed

    Fromme, P; Jordan, P; Krauss, N

    2001-10-30

    In plants and cyanobacteria, the primary step in oxygenic photosynthesis, the light induced charge separation, is driven by two large membrane intrinsic protein complexes, the photosystems I and II. Photosystem I catalyses the light driven electron transfer from plastocyanin/cytochrome c(6) on the lumenal side of the membrane to ferredoxin/flavodoxin at the stromal side by a chain of electron carriers. Photosystem I of Synechococcus elongatus consists of 12 protein subunits, 96 chlorophyll a molecules, 22 carotenoids, three [4Fe4S] clusters and two phylloquinones. Furthermore, it has been discovered that four lipids are intrinsic components of photosystem I. Photosystem I exists as a trimer in the native membrane with a molecular mass of 1068 kDa for the whole complex. The X-ray structure of photosystem I at a resolution of 2.5 A shows the location of the individual subunits and cofactors and provides new information on the protein-cofactor interactions. [P. Jordan, P. Fromme, H.T. Witt, O. Klukas, W. Saenger, N. Krauss, Nature 411 (2001) 909-917]. In this review, biochemical data and results of biophysical investigations are discussed with respect to the X-ray crystallographic structure in order to give an overview of the structure and function of this large membrane protein.

  4. Photosystem II: evolutionary perspectives.

    PubMed Central

    Rutherford, A W; Faller, P

    2003-01-01

    Based on the current model of its structure and function, photosystem II (PSII) seems to have evolved from an ancestor that was homodimeric in terms of its protein core and contained a special pair of chlorophylls as the photo-oxidizable cofactor. It is proposed that the key event in the evolution of PSII was a mutation that resulted in the separation of the two pigments that made up the special chlorophyll pair, making them into two chlorophylls that were neither special nor paired. These ordinary chlorophylls, along with the two adjacent monomeric chlorophylls, were very oxidizing: a property proposed to be intrinsic to monomeric chlorophylls in the environment provided by reaction centre (RC) proteins. It seems likely that other (mainly electrostatic) changes in the environments of the pigments probably tuned their redox potentials further but these changes would have been minor compared with the redox jump imposed by splitting of the special pair. This sudden increase in redox potential allowed the development of oxygen evolution. The highly oxidizing homodimeric RC would probably have been not only inefficient in terms of photochemistry and charge storage but also wasteful in terms of protein or pigments undergoing damage due to the oxidative chemistry. These problems would have constituted selective pressures in favour of the lop-sided, heterodimeric system that exists as PSII today, in which the highly oxidized species are limited to only one side of the heterodimer: the sacrificial, rapidly turned-over D1 protein. It is also suggested that one reason for maintaining an oxidizable tyrosine, TyrD, on the D2 side of the RC, is that the proton associated with its tyrosyl radical, has an electrostatic role in confining P(+) to the expendable D1 side. PMID:12594932

  5. Ancestral reconstruction of tick lineages.

    PubMed

    Mans, Ben J; de Castro, Minique H; Pienaar, Ronel; de Klerk, Daniel; Gaven, Philasande; Genu, Siyamcela; Latif, Abdalla A

    2016-06-01

    Ancestral reconstruction in its fullest sense aims to describe the complete evolutionary history of a lineage. This depends on accurate phylogenies and an understanding of the key characters of each parental lineage. An attempt is made to delineate our current knowledge with regard to the ancestral reconstruction of the tick (Ixodida) lineage. Tick characters may be assigned to Core of Life, Lineages of Life or Edges of Life phenomena depending on how far back these characters may be assigned in the evolutionary Tree of Life. These include housekeeping genes, sub-cellular systems, heme processing (Core of Life), development, moulting, appendages, nervous and organ systems, homeostasis, respiration (Lineages of Life), specific adaptations to a blood-feeding lifestyle, including the complexities of salivary gland secretions and tick-host interactions (Edges of Life). The phylogenetic relationships of lineages, their origins and importance in ancestral reconstruction are discussed. Uncertainties with respect to systematic relationships, ancestral reconstruction and the challenges faced in comparative transcriptomics (next-generation sequencing approaches) are highlighted. While almost 150 years of information regarding tick biology have been assembled, progress in recent years indicates that we are in the infancy of understanding tick evolution. Even so, broad reconstructions can be made with relation to biological features associated with various lineages. Conservation of characters shared with sister and parent lineages are evident, but appreciable differences are present in the tick lineage indicating modification with descent, as expected for Darwinian evolutionary theory. Many of these differences can be related to the hematophagous lifestyle of ticks. PMID:26868413

  6. Adaptive Memory: Ancestral Priorities and the Mnemonic Value of Survival Processing

    ERIC Educational Resources Information Center

    Nairne, James S.; Pandeirada, Josefa N. S.

    2010-01-01

    Evolutionary psychologists often propose that humans carry around "stone-age" brains, along with a toolkit of cognitive adaptations designed originally to solve hunter-gatherer problems. This perspective predicts that optimal cognitive performance might sometimes be induced by ancestrally-based problems, those present in ancestral environments,…

  7. Material science lesson from the biological photosystem

    NASA Astrophysics Data System (ADS)

    Kim, Younghye; Lee, Jun Ho; Ha, Heonjin; Im, Sang Won; Nam, Ki Tae

    2016-08-01

    Inspired by photosynthesis, artificial systems for a sustainable energy supply are being designed. Each sequential energy conversion process from light to biomass in natural photosynthesis is a valuable model for an energy collection, transport and conversion system. Notwithstanding the numerous lessons of nature that provide inspiration for new developments, the features of natural photosynthesis need to be reengineered to meet man's demands. This review describes recent strategies toward adapting key lessons from natural photosynthesis to artificial systems. We focus on the underlying material science in photosynthesis that combines photosystems as pivotal functional materials and a range of materials into an integrated system. Finally, a perspective on the future development of photosynthesis mimetic energy systems is proposed.

  8. Ancestral gene synteny reconstruction improves extant species scaffolding

    PubMed Central

    2015-01-01

    We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ARt-DeCo that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to handle dozens of complete genomes, including genes with complex histories, by using gene phylogenies reconciled with a species tree, that is, annotated with speciation, duplication and loss events. Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. We compare our method with a previously published one that follows the same goal on a small number of genomes with universal unicopy genes. Then we test it on the whole Ensembl database, by proposing partial ancestral genome structures, as well as a more complete scaffolding for many partially assembled genomes on 69 eukaryote species. We carefully analyze a couple of extant adjacencies proposed by our method, and show that they are indeed real links in the extant genomes, that were missing in the current assembly. On a reduced data set of 39 eutherian mammals, we estimate the precision and sensitivity of ARt-DeCo by simulating a fragmentation in some well assembled genomes, and measure how many adjacencies are recovered. We find a very high precision, while the sensitivity depends on the quality of the data and on the proximity of closely related genomes. PMID:26450761

  9. Evidence that cytochrome b{sub 559} protects photosystem II against photoinhibition

    SciTech Connect

    Poulson, M.; Samson, G.; Whitmarsh, J.

    1995-08-29

    Light that exceeds the photosynthetic capacity of a plant can impair the ability of photosystem II to oxidize water. The light-induced inhibition is initiated by inopportune electron transport reactions that create damaging redox states. There is evidence that secondary electron transport pathways within the photosystem II reaction center can protect against potentially damaging redox states. Experiments using thylakoid membranes poised at different ambient redox potentials demonstrate that light-induced damage to photosystem II can be controlled by a redox component within the reaction center. The rate of photoinhibition is slow when the redox component is oxidized, but increases by more than 10-fold when the redox. component is reduced. Here, using spinach thylakoid membranes, we provide evidence that the redox component is cytochrome b{sub 559}, an intrinsic heme protein of the photosystem II reaction center. The results support a model in which the low-potential (LP) form of cytochrome b{sub 559} protects photosystem II by deactivating a rarely formed, but hazardous redox state of photosystem II, namely, P680/Pheo{sup -}/Q{sub A}{sup -}. Cytochrome b{sub 559}LP is proposed to deactivate this potentially lethal redox state by accepting electrons from reduced pheophytin.

  10. Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa.

    PubMed

    Cheng, Feng; Mandáková, Terezie; Wu, Jian; Xie, Qi; Lysak, Martin A; Wang, Xiaowu

    2013-05-01

    The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers. PMID:23653472

  11. Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa.

    PubMed

    Cheng, Feng; Mandáková, Terezie; Wu, Jian; Xie, Qi; Lysak, Martin A; Wang, Xiaowu

    2013-05-01

    The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers.

  12. Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

    PubMed Central

    2015-01-01

    Background We propose the computational reconstruction of a whole bacterial ancestral genome at the nucleotide scale, and its validation by a sequence of ancient DNA. This rare possibility is offered by an ancient sequence of the late middle ages plague agent. It has been hypothesized to be ancestral to extant Yersinia pestis strains based on the pattern of nucleotide substitutions. But the dynamics of indels, duplications, insertion sequences and rearrangements has impacted all genomes much more than the substitution process, which makes the ancestral reconstruction task challenging. Results We use a set of gene families from 13 Yersinia species, construct reconciled phylogenies for all of them, and determine gene orders in ancestral species. Gene trees integrate information from the sequence, the species tree and gene order. We reconstruct ancestral sequences for ancestral genic and intergenic regions, providing nearly a complete genome sequence for the ancestor, containing a chromosome and three plasmids. Conclusion The comparison of the ancestral and ancient sequences provides a unique opportunity to assess the quality of ancestral genome reconstruction methods. But the quality of the sequencing and assembly of the ancient sequence can also be questioned by this comparison. PMID:26450112

  13. Recreating a functional ancestral archosaur visual pigment.

    PubMed

    Chang, Belinda S W; Jönsson, Karolina; Kazmi, Manija A; Donoghue, Michael J; Sakmar, Thomas P

    2002-09-01

    The ancestors of the archosaurs, a major branch of the diapsid reptiles, originated more than 240 MYA near the dawn of the Triassic Period. We used maximum likelihood phylogenetic ancestral reconstruction methods and explored different models of evolution for inferring the amino acid sequence of a putative ancestral archosaur visual pigment. Three different types of maximum likelihood models were used: nucleotide-based, amino acid-based, and codon-based models. Where possible, within each type of model, likelihood ratio tests were used to determine which model best fit the data. Ancestral reconstructions of the ancestral archosaur node using the best-fitting models of each type were found to be in agreement, except for three amino acid residues at which one reconstruction differed from the other two. To determine if these ancestral pigments would be functionally active, the corresponding genes were chemically synthesized and then expressed in a mammalian cell line in tissue culture. The expressed artificial genes were all found to bind to 11-cis-retinal to yield stable photoactive pigments with lambda(max) values of about 508 nm, which is slightly redshifted relative to that of extant vertebrate pigments. The ancestral archosaur pigments also activated the retinal G protein transducin, as measured in a fluorescence assay. Our results show that ancestral genes from ancient organisms can be reconstructed de novo and tested for function using a combination of phylogenetic and biochemical methods. PMID:12200476

  14. Recreating a functional ancestral archosaur visual pigment.

    PubMed

    Chang, Belinda S W; Jönsson, Karolina; Kazmi, Manija A; Donoghue, Michael J; Sakmar, Thomas P

    2002-09-01

    The ancestors of the archosaurs, a major branch of the diapsid reptiles, originated more than 240 MYA near the dawn of the Triassic Period. We used maximum likelihood phylogenetic ancestral reconstruction methods and explored different models of evolution for inferring the amino acid sequence of a putative ancestral archosaur visual pigment. Three different types of maximum likelihood models were used: nucleotide-based, amino acid-based, and codon-based models. Where possible, within each type of model, likelihood ratio tests were used to determine which model best fit the data. Ancestral reconstructions of the ancestral archosaur node using the best-fitting models of each type were found to be in agreement, except for three amino acid residues at which one reconstruction differed from the other two. To determine if these ancestral pigments would be functionally active, the corresponding genes were chemically synthesized and then expressed in a mammalian cell line in tissue culture. The expressed artificial genes were all found to bind to 11-cis-retinal to yield stable photoactive pigments with lambda(max) values of about 508 nm, which is slightly redshifted relative to that of extant vertebrate pigments. The ancestral archosaur pigments also activated the retinal G protein transducin, as measured in a fluorescence assay. Our results show that ancestral genes from ancient organisms can be reconstructed de novo and tested for function using a combination of phylogenetic and biochemical methods.

  15. Light harvesting in photosystem II.

    PubMed

    van Amerongen, Herbert; Croce, Roberta

    2013-10-01

    Water oxidation in photosynthesis takes place in photosystem II (PSII). This photosystem is built around a reaction center (RC) where sunlight-induced charge separation occurs. This RC consists of various polypeptides that bind only a few chromophores or pigments, next to several other cofactors. It can handle far more photons than the ones absorbed by its own pigments and therefore, additional excitations are provided by the surrounding light-harvesting complexes or antennae. The RC is located in the PSII core that also contains the inner light-harvesting complexes CP43 and CP47, harboring 13 and 16 chlorophyll pigments, respectively. The core is surrounded by outer light-harvesting complexes (Lhcs), together forming the so-called supercomplexes, at least in plants. These PSII supercomplexes are complemented by some "extra" Lhcs, but their exact location in the thylakoid membrane is unknown. The whole system consists of many subunits and appears to be modular, i.e., both its composition and organization depend on environmental conditions, especially on the quality and intensity of the light. In this review, we will provide a short overview of the relation between the structure and organization of pigment-protein complexes in PSII, ranging from individual complexes to entire membranes and experimental and theoretical results on excitation energy transfer and charge separation. It will become clear that time-resolved fluorescence data can provide invaluable information about the organization and functioning of thylakoid membranes. At the end, an overview will be given of unanswered questions that should be addressed in the near future.

  16. The ancestral eutherian karyotype is present in Xenarthra.

    PubMed

    Svartman, Marta; Stone, Gary; Stanyon, Roscoe

    2006-07-01

    Molecular studies have led recently to the proposal of a new super-ordinal arrangement of the 18 extant Eutherian orders. From the four proposed super-orders, Afrotheria and Xenarthra were considered the most basal. Chromosome-painting studies with human probes in these two mammalian groups are thus key in the quest to establish the ancestral Eutherian karyotype. Although a reasonable amount of chromosome-painting data with human probes have already been obtained for Afrotheria, no Xenarthra species has been thoroughly analyzed with this approach. We hybridized human chromosome probes to metaphases of species (Dasypus novemcinctus, Tamandua tetradactyla, and Choloepus hoffmanii) representing three of the four Xenarthra families. Our data allowed us to review the current hypotheses for the ancestral Eutherian karyotype, which range from 2n = 44 to 2n = 48. One of the species studied, the two-toed sloth C. hoffmanii (2n = 50), showed a chromosome complement strikingly similar to the proposed 2n = 48 ancestral Eutherian karyotype, strongly reinforcing it.

  17. Ancestral Rocky Mountian Tectonics: A Sedimentary Record of Ancestral Front Range and Uncompahgre Exhumation

    NASA Astrophysics Data System (ADS)

    Smith, T. M.; Saylor, J. E.; Lapen, T. J.

    2015-12-01

    The Ancestral Rocky Mountains (ARM) encompass multiple crustal provinces with characteristic crystallization ages across the central and western US. Two driving mechanisms have been proposed to explain ARM deformation. (1) Ouachita-Marathon collision SE of the ARM uplifts has been linked to an E-to-W sequence of uplift and is consistent with proposed disruption of a larger Paradox-Central Colorado Trough Basin by exhumation of the Uncompahgre Uplift. Initial exhumation of the Amarillo-Wichita Uplift to the east would provide a unique ~530 Ma signal absent from source areas to the SW, and result in initial exhumation of the Ancestral Front Range. (2) Alternatively, deformation due to flat slab subduction along a hypothesized plate boundary to the SW suggests a SW-to-NE younging of exhumation. This hypothesis suggests a SW-derived Grenville signature, and would trigger uplift of the Uncompahgre first. We analyzed depositional environments, sediment dispersal patterns, and sediment and basement zircon U-Pb and (U-Th)/He ages in 3 locations in the Paradox Basin and Central Colorado Trough (CCT). The Paradox Basin exhibits an up-section transition in fluvial style that suggests a decrease in overbank stability and increased lateral migration. Similarly, the CCT records a long-term progradation of depositional environments from marginal marine to fluvial, indicating that sediment supply in both basins outpaced accommodation. Preliminary provenance results indicate little to no input from the Amarillo-Wichita uplift in either basin despite uniformly westward sediment dispersal systems in both basins. Results also show that the Uncompahgre Uplift was the source for sediment throughout Paradox Basin deposition. These observations are inconsistent with the predictions of scenario 1 above. Rather, they suggest either a synchronous response to tectonic stress across the ARM provinces or an SW-to-NE pattern of deformation.

  18. Electron spin resonance studies of urea-ferricyanide inactivated spinach photosystem I particles

    SciTech Connect

    Golbeck, J.H.; Warden, J.T.

    1981-09-01

    The photosystem I acceptor system of a subchloroplast particle from spinach was investigated by optical and electron spin resonance (ESR) spectroscopy following graduated inactivation of the bound iron-sulfur proteins by urea-ferricyanide. The chemical analysis of iron and sulfur and the ESR properties of centers A, B, and X are consistent with the participation of three iron-sulfur centers in photosystem I. A differential decrease in centers A, B, and X is observed under conditions which induce S= ..-->.. S/sup 0/ conversion in the bound iron-sulfur proteins. Center B is shown to be the most susceptible, while center X is the least susceptible component to oxidative denaturation. Stepwise inactivation experiments suggest that electron transport in photosystem I does not occur sequentially from X ..-->.. B ..-->.. A since there is quantitative photoreduction of center A in the absence of center B. We propose that center A is directly reduced by X.

  19. Unraveling photosystems. Final technical report

    SciTech Connect

    1997-09-01

    This report highlights four main points. (1) A residue substitution in phosphoribulokinase of Synechocystis PCC 6803 renders the mutant light-sensitive. The authors isolated a light-sensitive mutant (BRLS) of the photosynthetic cyanobacterium Synechocystis 6803 that does not survive exposure to bright light; 70% of BRLS cells die upon exposure to light of > 3000 lux for 2 hr. (2) Excitation energy transfer from phycocyanin to chlorophyll in an apcA-defective mutant of Synechocystis sp. PCC 6803. A greenish mutant of the normally bule-green cyanobacterium Synechocystis sp. PC 6803, designated UV6p, was isolated and characterized. UV6p possesses functional photosystems I and II but lacks normal light harvesting phycobilisomes because allophycocyanin is absent and core-specific linker proteins are almost entirely absent. (3) Deletion of the psbG1 gene of the cyanobacterium Synechocystis sp. PCC 6803 leads to the activation of the cryptic psbG2 gene. The genes psbG1 and psbG2 in cyanobacterium Synechocystis sp. PCC 6803 are homologous. The psbG1 gene is located on the chromosome and is part of the ndhC-psbG1-ORF157 operon, while psbG2 is located on a plasmid and is not flanked by equivalent ndhC or ORF157 genes. (4) Deletion of the structural gene for the NADH-dehydrogenase subunit 4 of Synechocystis 6803 alters respiratory properties. Chloroplasts and cyanobacteria contain genes encoding polypeptides homologous to some subunits of the mitochondrial respiratory NADH-ubiquinol oxidoreductase complex (NADH dehydrogenase). Nothing is known of the role of the NADH dehydrogenase complex in photosynthesis, respiration, or other functions in chloroplasts, and little is known about their specific roles in the perhaps 42 subunits of this complex in the mitochondrion.

  20. Electron transport and photophosphorylation by Photosystem I in vivo in plants and cyanobacteria.

    PubMed

    Fork, D C; Herbert, S K

    1993-06-01

    Recently, a number of techniques, some of them relatively new and many often used in combination, have given a clearer picture of the dynamic role of electron transport in Photosystem I of photosynthesis and of coupled cyclic photophosphorylation. For example, the photoacoustic technique has detected cyclic electron transport in vivo in all the major algal groups and in leaves of higher plants. Spectroscopic measurements of the Photosystem I reaction center and of the changes in light scattering associated with thylakoid membrane energization also indicate that cyclic photophosphorylation occurs in living plants and cyanobacteria, particularly under stressful conditions.In cyanobacteria, the path of cyclic electron transport has recently been proposed to include an NAD(P)H dehydrogenase, a complex that may also participate in respiratory electron transport. Photosynthesis and respiration may share common electron carriers in eukaryotes also. Chlororespiration, the uptake of O2 in the dark by chloroplasts, is inhibited by excitation of Photosystem I, which diverts electrons away from the chlororespiratory chain into the photosynthetic electron transport chain. Chlororespiration in N-starved Chlamydomonas increases ten fold over that of the control, perhaps because carbohydrates and NAD(P)H are oxidized and ATP produced by this process.The regulation of energy distribution to the photosystems and of cyclic and non-cyclic phosphorylation via state 1 to state 2 transitions may involve the cytochrome b 6-f complex. An increased demand for ATP lowers the transthylakoid pH gradient, activates the b 6-f complex, stimulates phosphorylation of the light-harvesting chlorophyll-protein complex of Photosystem II and decreases energy input to Photosystem II upon induction of state 2. The resulting increase in the absorption by Photosystem I favors cyclic electron flow and ATP production over linear electron flow to NADP and 'poises' the system by slowing down the flow of

  1. Structure of Photosystems I and II.

    PubMed

    Fromme, Petra; Grotjohann, Ingo

    2008-01-01

    Photosynthesis is the major process that converts solar energy into chemical energy on Earth. Two and a half billion years ago, the ancestors of cyanobacteria were able to use water as electron source for the photosynthetic process, thereby evolving oxygen and changing the atmosphere of our planet Earth. Two large membrane protein complexes, Photosystems I and II, catalyze the primary step in this energy conversion, the light-induced charge separation across the photosynthetic membrane. This chapter describes and compares the structure of two Photosystems and discusses their function in respect to the mechanism of light harvesting, electron transfer and water splitting.

  2. Phylogenomics of primates and their ancestral populations

    PubMed Central

    Siepel, Adam

    2009-01-01

    Genome assemblies are now available for nine primate species, and large-scale sequencing projects are underway or approved for six others. An explicitly evolutionary and phylogenetic approach to comparative genomics, called phylogenomics, will be essential in unlocking the valuable information about evolutionary history and genomic function that is contained within these genomes. However, most phylogenomic analyses so far have ignored the effects of variation in ancestral populations on patterns of sequence divergence. These effects can be pronounced in the primates, owing to large ancestral effective population sizes relative to the intervals between speciation events. In particular, local genealogies can vary considerably across loci, which can produce biases and diminished power in many phylogenomic analyses of interest, including phylogeny reconstruction, the identification of functional elements, and the detection of natural selection. At the same time, this variation in genealogies can be exploited to gain insight into the nature of ancestral populations. In this Perspective, I explore this area of intersection between phylogenetics and population genetics, and its implications for primate phylogenomics. I begin by “lifting the hood” on the conventional tree-like representation of the phylogenetic relationships between species, to expose the population-genetic processes that operate along its branches. Next, I briefly review an emerging literature that makes use of the complex relationships among coalescence, recombination, and speciation to produce inferences about evolutionary histories, ancestral populations, and natural selection. Finally, I discuss remaining challenges and future prospects at this nexus of phylogenetics, population genetics, and genomics. PMID:19801602

  3. Excitation energy transfer in the photosystem I

    SciTech Connect

    Webber, Andrew N

    2012-09-25

    Photosystem I is a multimeric pigment protein complex in plants, green alage and cyanobacteria that functions in series with Photosystem II to use light energy to oxidize water and reduce carbon dioxide. The Photosystem I core complex contains 96 chlorophyll a molecules and 22 carotenoids that are involved in light harvesting and electron transfer. In eucaryotes, PSI also has a peripheral light harvesting complex I (LHCI). The role of specific chlorophylls in excitation and electron transfer are still unresolved. In particular, the role of so-called bridging chlorophylls, located between the bulk antenna and the core electron transfer chain, in the transfer of excitation energy to the reaction center are unknown. During the past funding period, site directed mutagenesis has been used to create mutants that effect the physical properties of these key chlorophylls, and to explore how this alters the function of the photosystem. Studying these mutants using ultrafast absorption spectroscopy has led to a better understanding of the process by which excitation energy is transferred from the antenna chlorophylls to the electron transfer chain chlorophylls, and what the role of connecting chlorophylls and A_0 chlorophylls is in this process. We have also used these mutants to investigate whch of the central group of six chlorophylls are involved in the primary steps of charge separation and electron transfer.

  4. Regulation of photosystem I light harvesting by zeaxanthin.

    PubMed

    Ballottari, Matteo; Alcocer, Marcelo J P; D'Andrea, Cosimo; Viola, Daniele; Ahn, Tae Kyu; Petrozza, Annamaria; Polli, Dario; Fleming, Graham R; Cerullo, Giulio; Bassi, Roberto

    2014-06-10

    In oxygenic photosynthetic eukaryotes, the hydroxylated carotenoid zeaxanthin is produced from preexisting violaxanthin upon exposure to excess light conditions. Zeaxanthin binding to components of the photosystem II (PSII) antenna system has been investigated thoroughly and shown to help in the dissipation of excess chlorophyll-excited states and scavenging of oxygen radicals. However, the functional consequences of the accumulation of the light-harvesting complex I (LHCI) proteins in the photosystem I (PSI) antenna have remained unclarified so far. In this work we investigated the effect of zeaxanthin binding on photoprotection of PSI-LHCI by comparing preparations isolated from wild-type Arabidopsis thaliana (i.e., with violaxanthin) and those isolated from the A. thaliana nonphotochemical quenching 2 mutant, in which violaxanthin is replaced by zeaxanthin. Time-resolved fluorescence measurements showed that zeaxanthin binding leads to a previously unrecognized quenching effect on PSI-LHCI fluorescence. The efficiency of energy transfer from the LHCI moiety of the complex to the PSI reaction center was down-regulated, and an enhanced PSI resistance to photoinhibition was observed both in vitro and in vivo. Thus, zeaxanthin was shown to be effective in inducing dissipative states in PSI, similar to its well-known effect on PSII. We propose that, upon acclimation to high light, PSI-LHCI changes its light-harvesting efficiency by a zeaxanthin-dependent quenching of the absorbed excitation energy, whereas in PSII the stoichiometry of LHC antenna proteins per reaction center is reduced directly.

  5. Reconstruction of ancestral genomic sequences using likelihood.

    PubMed

    Elias, Isaac; Tuller, Tamir

    2007-03-01

    A challenging task in computational biology is the reconstruction of genomic sequences of extinct ancestors, given the phylogenetic tree and the sequences at the leafs. This task is best solved by calculating the most likely estimate of the ancestral sequences, along with the most likely edge lengths. We deal with this problem and also the variant in which the phylogenetic tree in addition to the ancestral sequences need to be estimated. The latter problem is known to be NP-hard, while the computational complexity of the former is unknown. Currently, all algorithms for solving these problems are heuristics without performance guarantees. The biological importance of these problems calls for developing better algorithms with guarantees of finding either optimal or approximate solutions. We develop approximation, fix parameter tractable (FPT), and fast heuristic algorithms for two variants of the problem; when the phylogenetic tree is known and when it is unknown. The approximation algorithm guarantees a solution with a log-likelihood ratio of 2 relative to the optimal solution. The FPT has a running time which is polynomial in the length of the sequences and exponential in the number of taxa. This makes it useful for calculating the optimal solution for small trees. Moreover, we combine the approximation algorithm and the FPT into an algorithm with arbitrary good approximation guarantee (PTAS). We tested our algorithms on both synthetic and biological data. In particular, we used the FPT for computing the most likely ancestral mitochondrial genomes of hominidae (the great apes), thereby answering an interesting biological question. Moreover, we show how the approximation algorithms find good solutions for reconstructing the ancestral genomes for a set of lentiviruses (relatives of HIV). Supplementary material of this work is available at www.nada.kth.se/~isaac/publications/aml/aml.html.

  6. The ancestral complement system in sea urchins.

    PubMed

    Smith, L C; Clow, L A; Terwilliger, D P

    2001-04-01

    The origin of adaptive immunity in the vertebrates can be traced to the appearance of the ancestral RAG genes in the ancestral jawed vertebrate; however, the innate immune system is more ancient. A central subsystem within innate immunity is the complement system, which has been identified throughout and seems to be restricted to the deuterostomes. The evolutionary history of complement can be traced from the sea urchins (members of the echinoderm phylum), which have a simplified system homologous to the alternative pathway, through the agnathans (hagfish and lamprey) and the elasmobranchs (sharks and rays) to the teleosts (bony fish) and tetrapods, with increases in the numbers of complement components and duplications in complement pathways. Increasing complexity in the complement system parallels increasing complexity in the deuterostome animals. This review focuses on the simplest of the complement systems that is present in the sea urchin. Two components have been identified that show significant homology to vertebrate C3 and factor B (Bf), called SpC3 and SpBf, respectively. Sequence analysis from both molecules reveals their ancestral characteristics. Immune challenge of sea urchins indicates that SpC3 is inducible and is present in coelomic fluid (the body fluids) in relatively high concentrations, while SpBf expression is constitutive and is present in much lower concentrations. Opsonization of foreign cells and particles followed by augmented uptake by phagocytic coelomocytes appears to be a central function for this simpler complement system and important for host defense in the sea urchin. These activities are similar to some of the functions of the homologous proteins in the vertebrate complement system. The selective advantage for the ancestral deuterostome may have been the amplification feedback loop that is still of central importance in the alternative pathway of complement in higher vertebrates. Feedback loop functions would quickly coat

  7. A Comparison Between Plant Photosystem I and Photosystem II Architecture and Functioning

    PubMed Central

    Caffarri, Stefano; Tibiletti, Tania; Jennings, Robert C.; Santabarbara, Stefano

    2014-01-01

    Oxygenic photosynthesis is indispensable both for the development and maintenance of life on earth by converting light energy into chemical energy and by producing molecular oxygen and consuming carbon dioxide. This latter process has been responsible for reducing the CO2 from its very high levels in the primitive atmosphere to the present low levels and thus reducing global temperatures to levels conducive to the development of life. Photosystem I and photosystem II are the two multi-protein complexes that contain the pigments necessary to harvest photons and use light energy to catalyse the primary photosynthetic endergonic reactions producing high energy compounds. Both photosystems are highly organised membrane supercomplexes composed of a core complex, containing the reaction centre where electron transport is initiated, and of a peripheral antenna system, which is important for light harvesting and photosynthetic activity regulation. If on the one hand both the chemical reactions catalysed by the two photosystems and their detailed structure are different, on the other hand they share many similarities. In this review we discuss and compare various aspects of the organisation, functioning and regulation of plant photosystems by comparing them for similarities and differences as obtained by structural, biochemical and spectroscopic investigations. PMID:24678674

  8. Crystal structure of plant photosystem I

    NASA Astrophysics Data System (ADS)

    Ben-Shem, Adam; Frolow, Felix; Nelson, Nathan

    2003-12-01

    Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4Å resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.

  9. Energy transfer from photosystem II to photosystem I in Porphyridium cruentum.

    PubMed

    Ley, A C; Butler, W L

    1977-11-17

    Rates of photooxidation of P-700 by green (560 nm) or blue (438 nm) light were measured in whole cells of porphyridium cruentum which had been frozen to -196 degrees C under conditions in which the Photosystem II reaction centers were either all open (dark adapted cells) or all closed (preilluminated cells). The rate of photooxidation of P-700 at -196 degrees C by green actinic light was approx. 80% faster in the preilluminated cells than in the dark-adapted cells. With blue actinic light, the rates of P-700 photooxidation in the dark-adapted and preilluminated cells were not significantly different. These results are in excellent agreement with predictions based on our previous estimates of energy distribution in the photosynthetic apparatus of Porphyridium cruentum including the yield of energy transfer from Photosystem II to Photosystem I determined from low temperature fluorescence measurements.

  10. In search of ancestral Kilauea volcano

    USGS Publications Warehouse

    Lipman, P.W.; Sisson, T.W.; Ui, T.; Naka, J.

    2000-01-01

    Submersible observations and samples show that the lower south flank of Hawaii, offshore from Kilauea volcano and the active Hilina slump system, consists entirely of compositionally diverse volcaniclastic rocks; pillow lavas are confined to shallow slopes. Submarine-erupted basalt clasts have strongly variable alkalic and transitional basalt compositions (to 41% SiO2, 10.8% alkalies), contrasting with present-day Kilauea tholeiites. The volcaniclastic rocks provide a unique record of ancestral alkalic growth of an archetypal hotspot volcano, including transition to its tholeiitic shield stage, and associated slope-failure events.

  11. Subunit stoichiometry of the chloroplast photosystem I complex

    SciTech Connect

    Bruce, B.D.; Malkin, R.

    1988-05-25

    A native photosystem I (PS I) complex and a PS I core complex depleted of antenna subunits has been isolated from the uniformly /sup 14/C-labeled aquatic higher plant, Lemna. These complexes have been analyzed for their subunit stoichiometry by quantitative sodium dodecyl sulfate-polyacrylamide gel electrophoresis methods. The results for both preparations indicate that one copy of each high molecular mass subunit is present per PS I complex and that a single copy of most low molecular mass subunits is also present. These results suggest that iron-sulfur center X, an early PS I electron acceptor proposed to bind to the high molecular mass subunits, contains a single (4Fe-4S) cluster which is bound to a dimeric structure of high molecular mass subunits, each providing 2 cysteine residues to coordinate this cluster.

  12. Mapping ancestral genomes with massive gene loss: A matrix sandwich problem

    PubMed Central

    Gavranović, Haris; Chauve, Cedric; Salse, Jérôme; Tannier, Eric

    2011-01-01

    Motivation: Ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. Most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of DNA segments present in exactly one exemplar in every considered species. Complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. It follows that some ancestors are inaccessible by these methods, such as the proto–monocotyledon whose evolution involved massive gene loss following a whole genome duplication. Results: We propose a mapping approach based on the combinatorial notion of ‘sandwich consecutive ones matrix’, which explicitly takes gene losses into account. We introduce combinatorial optimization problems related to this concept, and propose a heuristic solver and a lower bound on the optimal solution. We use these results to propose a configuration for the proto-chromosomes of the monocot ancestor, and study the accuracy of this configuration. We also use our method to reconstruct the ancestral boreoeutherian genomes, which illustrates that the framework we propose is not specific to plant paleogenomics but is adapted to reconstruct any ancestral genome from extant genomes with heterogeneous marker content. Availability: Upon request to the authors. Contact: haris.gavranovic@gmail.com; eric.tannier@inria.fr PMID:21685079

  13. State transitions in Chlamydomonas reinhardtii strongly modulate the functional size of photosystem II but not of photosystem I.

    PubMed

    Ünlü, Caner; Drop, Bartlomiej; Croce, Roberta; van Amerongen, Herbert

    2014-03-01

    Plants and green algae optimize photosynthesis in changing light conditions by balancing the amount of light absorbed by photosystems I and II. These photosystems work in series to extract electrons from water and reduce NADP(+) to NADPH. Light-harvesting complexes (LHCs) are held responsible for maintaining the balance by moving from one photosystem to the other in a process called state transitions. In the green alga Chlamydomonas reinhardtii, a photosynthetic model organism, state transitions are thought to involve 80% of the LHCs. Here, we demonstrate with picosecond-fluorescence spectroscopy on C. reinhardtii cells that, although LHCs indeed detach from photosystem II in state 2 conditions, only a fraction attaches to photosystem I. The detached antenna complexes become protected against photodamage via shortening of the excited-state lifetime. It is discussed how the transition from state 1 to state 2 can protect C. reinhardtii in high-light conditions and how this differs from the situation in plants.

  14. Achieving solar overall water splitting with hybrid photosystems of photosystem II and artificial photocatalysts.

    PubMed

    Wang, Wangyin; Chen, Jun; Li, Can; Tian, Wenming

    2014-01-01

    Solar overall water splitting is a promising sustainable approach for solar-to-chemical energy conversion, which harnesses solar irradiation to oxidize water to oxygen and reduce the protons to hydrogen. The water oxidation step is vital but difficult to achieve through inorganic photocatalysis. However, nature offers an efficient light-driven water-oxidizing enzyme, photosystem II (PSII). Here we report an overall water splitting natural-artificial hybrid system, in which the plant PSII and inorganic photocatalysts (for example, Ru/SrTiO3:Rh), coupled with an inorganic electron shuttle [Fe(CN)6(3-)/Fe(CN)6(4-)], are integrated and dispersed in aqueous solutions. The activity of this hybrid photosystem reaches to around 2,489 mol H2 (mol PSII)(-1) h(-1) under visible light irradiation, and solar overall water splitting is also achieved under solar irradiation outdoors. The optical imaging shows that the hybrid photosystems are constructed through the self-assembly of PSII adhered onto the inorganic photocatalyst surface. Our work may provide a prototype of natural-artificial hybrids for developing autonomous solar water splitting system. PMID:25115942

  15. Achieving solar overall water splitting with hybrid photosystems of photosystem II and artificial photocatalysts.

    PubMed

    Wang, Wangyin; Chen, Jun; Li, Can; Tian, Wenming

    2014-08-13

    Solar overall water splitting is a promising sustainable approach for solar-to-chemical energy conversion, which harnesses solar irradiation to oxidize water to oxygen and reduce the protons to hydrogen. The water oxidation step is vital but difficult to achieve through inorganic photocatalysis. However, nature offers an efficient light-driven water-oxidizing enzyme, photosystem II (PSII). Here we report an overall water splitting natural-artificial hybrid system, in which the plant PSII and inorganic photocatalysts (for example, Ru/SrTiO3:Rh), coupled with an inorganic electron shuttle [Fe(CN)6(3-)/Fe(CN)6(4-)], are integrated and dispersed in aqueous solutions. The activity of this hybrid photosystem reaches to around 2,489 mol H2 (mol PSII)(-1) h(-1) under visible light irradiation, and solar overall water splitting is also achieved under solar irradiation outdoors. The optical imaging shows that the hybrid photosystems are constructed through the self-assembly of PSII adhered onto the inorganic photocatalyst surface. Our work may provide a prototype of natural-artificial hybrids for developing autonomous solar water splitting system.

  16. In Vivo Identification of Photosystem II Light Harvesting Complexes Interacting with PHOTOSYSTEM II SUBUNIT S.

    PubMed

    Gerotto, Caterina; Franchin, Cinzia; Arrigoni, Giorgio; Morosinotto, Tomas

    2015-08-01

    Light is the primary energy source for photosynthetic organisms, but in excess, it can generate reactive oxygen species and lead to cell damage. Plants evolved multiple mechanisms to modulate light use efficiency depending on illumination intensity to thrive in a highly dynamic natural environment. One of the main mechanisms for protection from intense illumination is the dissipation of excess excitation energy as heat, a process called nonphotochemical quenching. In plants, nonphotochemical quenching induction depends on the generation of a pH gradient across thylakoid membranes and on the presence of a protein called PHOTOSYSTEM II SUBUNIT S (PSBS). Here, we generated Physcomitrella patens lines expressing histidine-tagged PSBS that were exploited to purify the native protein by affinity chromatography. The mild conditions used in the purification allowed copurifying PSBS with its interactors, which were identified by mass spectrometry analysis to be mainly photosystem II antenna proteins, such as LIGHT-HARVESTING COMPLEX B (LHCB). PSBS interaction with other proteins appears to be promiscuous and not exclusive, although the major proteins copurified with PSBS were components of the LHCII trimers (LHCB3 and LHCBM). These results provide evidence of a physical interaction between specific photosystem II light-harvesting complexes and PSBS in the thylakoids, suggesting that these subunits are major players in heat dissipation of excess energy.

  17. Matrilocal residence is ancestral in Austronesian societies.

    PubMed

    Jordan, Fiona M; Gray, Russell D; Greenhill, Simon J; Mace, Ruth

    2009-06-01

    The nature of social life in human prehistory is elusive, yet knowing how kinship systems evolve is critical for understanding population history and cultural diversity. Post-marital residence rules specify sex-specific dispersal and kin association, influencing the pattern of genetic markers across populations. Cultural phylogenetics allows us to practise 'virtual archaeology' on these aspects of social life that leave no trace in the archaeological record. Here we show that early Austronesian societies practised matrilocal post-marital residence. Using a Markov-chain Monte Carlo comparative method implemented in a Bayesian phylogenetic framework, we estimated the type of residence at each ancestral node in a sample of Austronesian language trees spanning 135 Pacific societies. Matrilocal residence has been hypothesized for proto-Oceanic society (ca 3500 BP), but we find strong evidence that matrilocality was predominant in earlier Austronesian societies ca 5000-4500 BP, at the root of the language family and its early branches. Our results illuminate the divergent patterns of mtDNA and Y-chromosome markers seen in the Pacific. The analysis of present-day cross-cultural data in this way allows us to directly address cultural evolutionary and life-history processes in prehistory.

  18. Competition between the 735 nm fluorescence and the photochemistry of Photosystem I in chloroplasts at low temperature.

    PubMed

    Satoh, K; Butler, W L

    1978-04-11

    Fluorescence emission spectra of chloroplasts, initially frozen to--196 degrees C, were measured at various temperatures as the sample was allowed to warm. The 735 nm emission band attributed to fluorescence from Photosystem I was approx. 10-fold greater at--196 degrees C than at--78 degrees C. The initial rate of photooxidation of P-700 was also measured at--196 degrees C and--78 degrees C and was found to be approximately twice as large at the higher temperature. It is proposed that the 735 nm emission band is fluorescence from a long wavelength form of chlorophyll, C-705, which acts as a trap for excitation energy in the antenna chlorophyl system of Photosystem I. Furthermore, it is proposed that C-705 only forms on cooling to low temperatures and that the temperature dependence of the 735 nm emission is the temperature dependence for the formation of C-705. C-705 and P-700 compete to trap the excitation energy in Photosystem I. It is estimated from the data that at--78 degrees C P-700 traps approx. 20 times more energy than C-705 while, at--196 degrees C, the two traps are approximately equally effective. By analogy, the 695 nm fluorescence which also appears on cooling to--196 degrees C is attributed to traps in Photosystem II which form only on cooling to temperatures near--196 degrees C. PMID:638135

  19. Photoinactivation of photosystem II by flashing light.

    PubMed

    Szilárd, András; Sass, László; Hideg, Eva; Vass, Imre

    2005-06-01

    Inhibition of Photosystem II (PS II) activity by single turnover visible light flashes was studied in thylakoid membranes isolated form spinach. Flash illumination results in decreased oxygen evolving activity of PS II, which effect is most pronounced when the water-oxidizing complex is in the S2 and S3 states, and increases with increasing time delay between the subsequent flashes. By applying the fluorescent spin-trap DanePy, we detected the production of singlet oxygen, whose amount was increasing with increasing flash spacing. These findings were explained in the framework of a model, which assumes that recombination of the S2QB - and S3QB - states generate the triplet state of the reaction center chlorophyll and lead to the production of singlet oxygen.

  20. Applications of Delayed Fluorescence from Photosystem II

    PubMed Central

    Guo, Ya; Tan, Jinglu

    2013-01-01

    While photosystem II (PSII) of plants utilizes light for photosynthesis, part of the absorbed energy may be reverted back and dissipated as long-term fluorescence (delayed fluorescence or DF). Because the generation of DF is coupled with the processes of forward photosynthetic activities, DF contains the information about plant physiological states and plant-environment interactions. This makes DF a potentially powerful biosensing mechanism to measure plant photosynthetic activities and environmental conditions. While DF has attracted the interest of many researchers, some aspects of it are still unknown because of the complexity of photosynthetic system. In order to provide a holistic picture about the usefulness of DF, it is meaningful to summarize the research on DF applications. In this short review, available literature on applications of DF from PSII is summarized. PMID:24351639

  1. Analysis of photosystem II biogenesis in cyanobacteria.

    PubMed

    Heinz, Steffen; Liauw, Pasqual; Nickelsen, Jörg; Nowaczyk, Marc

    2016-03-01

    Photosystem II (PSII), a large multisubunit membrane protein complex found in the thylakoid membranes of cyanobacteria, algae and plants, catalyzes light-driven oxygen evolution from water and reduction of plastoquinone. Biogenesis of PSII requires coordinated assembly of at least 20 protein subunits, as well as incorporation of various organic and inorganic cofactors. The stepwise assembly process is facilitated by numerous protein factors that have been identified in recent years. Further analysis of this process requires the development or refinement of specific methods for the identification of novel assembly factors and, in particular, elucidation of the unique role of each. Here we summarize current knowledge of PSII biogenesis in cyanobacteria, focusing primarily on the impact of methodological advances and innovations. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.

  2. Revisiting the photosystem II repair cycle

    PubMed Central

    Theis, Jasmine; Schroda, Michael

    2016-01-01

    ABSTRACT The ability of photosystem (PS) II to catalyze the light-driven oxidation of water comes along with its vulnerability to oxidative damage, in particular of the D1 core subunit. Photodamaged PSII undergoes repair in a multi-step process involving (i) reversible phosphorylation of PSII core subunits; (ii) monomerization and lateral migration of the PSII core from grana to stroma thylakoids; (iii) partial disassembly of PSII; (iv) proteolytic degradation of damaged D1; (v) replacement of damaged D1 protein with a new copy; (vi) reassembly of PSII monomers and migration back to grana thylakoids for dimerization and supercomplex assembly. Here we review the current knowledge on the PSII repair cycle. PMID:27494214

  3. [The Carnot efficiency and plant photosystems].

    PubMed

    Jennings, R C; Santabarbara, S; Belgio, E; Zucchelli, G

    2014-01-01

    The concept that the Carnot efficiency places an upper limit of 0.60-0.75 on the thermodynamic efficiency of photosynthetic primary photochemistry is examined using the PSI-LHCI preparation. The maximal quantum efficiency was determined approximately 0.99 which yielded a thermodynamic efficiency of 0.96, a value far above that predicted on the basis of the Carnot efficiency. The commonly presented reasoning leading to the Carnot efficiency idea was therefore critically examined. It is concluded that the crucial assumption that the pigment system, under illumination, is in equilibrium with the incident light field, at a black body temperature of Tr, is erroneous, as the temperature of the excited state pigments was experimentally shown to be that of the sample solvent (thermal bath), 280 K in this case. It is concluded that the classical reasoning used to describe the thermodynamics of heat systems is not applicable to "photonic" systems such as plant photosystems.

  4. Revisiting the photosystem II repair cycle.

    PubMed

    Theis, Jasmine; Schroda, Michael

    2016-09-01

    The ability of photosystem (PS) II to catalyze the light-driven oxidation of water comes along with its vulnerability to oxidative damage, in particular of the D1 core subunit. Photodamaged PSII undergoes repair in a multi-step process involving (i) reversible phosphorylation of PSII core subunits; (ii) monomerization and lateral migration of the PSII core from grana to stroma thylakoids; (iii) partial disassembly of PSII; (iv) proteolytic degradation of damaged D1; (v) replacement of damaged D1 protein with a new copy; (vi) reassembly of PSII monomers and migration back to grana thylakoids for dimerization and supercomplex assembly. Here we review the current knowledge on the PSII repair cycle. PMID:27494214

  5. Protein sequences and redox titrations indicate that the electron acceptors in reaction centers from heliobacteria are similar to Photosystem I

    NASA Technical Reports Server (NTRS)

    Trost, J. T.; Brune, D. C.; Blankenship, R. E.

    1992-01-01

    Photosynthetic reaction centers isolated from Heliobacillus mobilis exhibit a single major protein on SDS-PAGE of 47 000 Mr. Attempts to sequence the reaction center polypeptide indicated that the N-terminus is blocked. After enzymatic and chemical cleavage, four peptide fragments were sequenced from the Heliobacillus mobilis apoprotein. Only one of these sequences showed significant specific similarity to any of the protein and deduced protein sequences in the GenBank data base. This fragment is identical with 56% of the residues, including both cysteines, found in highly conserved region that is proposed to bind iron-sulfur center Fx in the Photosystem I reaction center peptide that is the psaB gene product. The similarity to the psaA gene product in this region is 48%. Redox titrations of laser-flash-induced photobleaching with millisecond decay kinetics on isolated reaction centers from Heliobacterium gestii indicate a midpoint potential of -414 mV with n = 2 titration behavior. In membranes, the behavior is intermediate between n = 1 and n = 2, and the apparent midpoint potential is -444 mV. This is compared to the behavior in Photosystem I, where the intermediate electron acceptor A1, thought to be a phylloquinone molecule, has been proposed to undergo a double reduction at low redox potentials in the presence of viologen redox mediators. These results strongly suggest that the acceptor side electron transfer system in reaction centers from heliobacteria is indeed analogous to that found in Photosystem I. The sequence similarities indicate that the divergence of the heliobacteria from the Photosystem I line occurred before the gene duplication and subsequent divergence that lead to the heterodimeric protein core of the Photosystem I reaction center.

  6. Protein sequences and redox titrations indicate that the electron acceptors in reaction centers from heliobacteria are similar to Photosystem I.

    PubMed

    Trost, J T; Brune, D C; Blankenship, R E

    1992-01-01

    Photosynthetic reaction centers isolated from Heliobacillus mobilis exhibit a single major protein on SDS-PAGE of 47 000 Mr. Attempts to sequence the reaction center polypeptide indicated that the N-terminus is blocked. After enzymatic and chemical cleavage, four peptide fragments were sequenced from the Heliobacillus mobilis apoprotein. Only one of these sequences showed significant specific similarity to any of the protein and deduced protein sequences in the GenBank data base. This fragment is identical with 56% of the residues, including both cysteines, found in highly conserved region that is proposed to bind iron-sulfur center Fx in the Photosystem I reaction center peptide that is the psaB gene product. The similarity to the psaA gene product in this region is 48%. Redox titrations of laser-flash-induced photobleaching with millisecond decay kinetics on isolated reaction centers from Heliobacterium gestii indicate a midpoint potential of -414 mV with n = 2 titration behavior. In membranes, the behavior is intermediate between n = 1 and n = 2, and the apparent midpoint potential is -444 mV. This is compared to the behavior in Photosystem I, where the intermediate electron acceptor A1, thought to be a phylloquinone molecule, has been proposed to undergo a double reduction at low redox potentials in the presence of viologen redox mediators. These results strongly suggest that the acceptor side electron transfer system in reaction centers from heliobacteria is indeed analogous to that found in Photosystem I. The sequence similarities indicate that the divergence of the heliobacteria from the Photosystem I line occurred before the gene duplication and subsequent divergence that lead to the heterodimeric protein core of the Photosystem I reaction center.

  7. Ancient eudicot hexaploidy meets ancestral eurosid gene order

    PubMed Central

    2013-01-01

    Background A hexaploidization event over 125 Mya underlies the evolutionary lineage of the majority of flowering plants, including very many species of agricultural importance. Half of these belong to the rosid subgrouping, containing severals whose genome sequences have been published. Although most duplicate and triplicate genes have been lost in all descendants, clear traces of the original chromosome triples can be discerned, their internal contiguity highly conserved in some genomes and very fragmented in others. To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids, including the retention of a small proportion of the duplicate and triplicate genes and the reconstruction of putative ancestral intermediates between the original hexaploid and modern species, in this case the ancestor of the eurosid clade. Results We quantitatively trace the fate of gene triples originating in the hexaploidy across seven core eudicot flowering plants, and fit this to a two-stage model, pre- and post-radiation. We also measure the simultaneous dynamics of duplicate orthologous gene loss in three rosids, as influenced by biological functional class. We propose a new protocol for reconstructing ancestral gene order using only gene adjacency data from pairwise genomic analyses, based on repeating MAXIMUM WEIGHT MATCHING at two levels of resolution, an approach designed to transcend limitations on reconstructed contig size, while still avoiding the ambiguities of a multiplicity of solutions. Applied to three high-quality rosid genomes without subsequent polyploidy events, our automated procedure reconstructs the ancestor of the eurosid clade. Conclusions The gene loss analysis and the ancestor reconstruction present complementary assessments of post-hexaploidization evolution, the first at the level of individual gene families within and across sister genomes and the second at the

  8. The action spectrum of Photosystem II photoinactivation in visible light.

    PubMed

    Zavafer, Alonso; Chow, Wah Soon; Cheah, Mun Hon

    2015-11-01

    Photosynthesis is always accompanied by light induced damage to the Photosystem II (PSII) which is compensated by its subsequent repair. Photoinhibition of PSII is a complex process, balancing between photoinactivation, protective and repair mechanisms. Current understanding of photoinactivation is limited with competing hypotheses where the photosensitiser is either photosynthetic pigments or the Mn4CaO5 cluster itself, with little consensus on the mechanisms and consequences of PSII photoinactivation. The mechanism of photoinactivation should be reflected in the action spectrum of PSII photoinactivation, but there is a great diversity of the action spectra reported thus far. The only consensus is that PSII photoinactivation is greatest in the UV region of the electromagnetic spectrum. In this review, the authors revisit the methods, technical constraints and the different action spectra of PSII photoinactivation reported to date and compare them against the diverse mechanisms proposed. Upon critical examination of the reported action spectra, a hybrid mechanism of photoinactivation, sensitised by both photosynthetic pigments and the Mn4CaO5 appears to be the most plausible rationalisation.

  9. The action spectrum of Photosystem II photoinactivation in visible light.

    PubMed

    Zavafer, Alonso; Chow, Wah Soon; Cheah, Mun Hon

    2015-11-01

    Photosynthesis is always accompanied by light induced damage to the Photosystem II (PSII) which is compensated by its subsequent repair. Photoinhibition of PSII is a complex process, balancing between photoinactivation, protective and repair mechanisms. Current understanding of photoinactivation is limited with competing hypotheses where the photosensitiser is either photosynthetic pigments or the Mn4CaO5 cluster itself, with little consensus on the mechanisms and consequences of PSII photoinactivation. The mechanism of photoinactivation should be reflected in the action spectrum of PSII photoinactivation, but there is a great diversity of the action spectra reported thus far. The only consensus is that PSII photoinactivation is greatest in the UV region of the electromagnetic spectrum. In this review, the authors revisit the methods, technical constraints and the different action spectra of PSII photoinactivation reported to date and compare them against the diverse mechanisms proposed. Upon critical examination of the reported action spectra, a hybrid mechanism of photoinactivation, sensitised by both photosynthetic pigments and the Mn4CaO5 appears to be the most plausible rationalisation. PMID:26298696

  10. Spectral hole burning studies of photosystem II

    SciTech Connect

    Chang, H.C.

    1995-11-01

    Low temperature absorption and hole burning spectroscopies were applied to the D1-D2-cyt b{sub 559} and the CP47 and CP43 antenna protein complexes of Photosystem H from higher plants. Low temperature transient and persistent hole-burning data and theoretical calculations on the kinetics and temperature dependence of the P680 hole profile are presented and provide convincing support for the linker model. Implicit in the linker model is that the 684-nm-absorbing Chl a serve to shuttle energy from the proximal antenna complex to reaction center. The stoichiometry of isolated Photosystem H Reaction Center (PSII RC) in several different preparations is also discussed. The additional Chl a are due to 684-nm-absorbing Chl a, some contamination by the CP47 complex, and non-native Chl a absorbing near 670 nm. In the CP47 protein complex, attention is focused on the lower energy chlorophyll a Q{sub y}-states. High pressure hole-burning studies of PSII RC revealed for the first time a strong pressure effect on the primary electron transfer dynamics. The 4.2 K lifetime of P680*, the primary donor state, increases from 2.0 ps to 7.0 ps as pressure increases from 0.1 to 267 MPa. Importantly, this effect is irreversible (plastic) while the pressure induced effect on the low temperature absorption and non-line narrowed P680 hole spectra are reversible (elastic). Nonadiabatic rate expressions, which take into account the distribution of energy gap values, are used to estimate the linear pressure shift of the acceptor state energy for both the superexchange and two-step mechanisms for primary charge separation. It was found that the pressure dependence could be explained with a linear pressure shift of {approximately} 1 cm{sup -1}/MPa in magnitude for the acceptor state. The results point to the marriage of hole burning and high pressures as having considerable potential for the study of primary transport dynamics in reaction centers and antenna complexes.

  11. Inference of Ancestral Recombination Graphs through Topological Data Analysis

    PubMed Central

    Cámara, Pablo G.; Levine, Arnold J.; Rabadán, Raúl

    2016-01-01

    The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands. PMID:27532298

  12. Ancestral genetic complexity of arachidonic acid metabolism in Metazoa.

    PubMed

    Yuan, Dongjuan; Zou, Qiuqiong; Yu, Ting; Song, Cuikai; Huang, Shengfeng; Chen, Shangwu; Ren, Zhenghua; Xu, Anlong

    2014-09-01

    Eicosanoids play an important role in inducing complex and crucial physiological processes in animals. Eicosanoid biosynthesis in animals is widely reported; however, eicosanoid production in invertebrate tissue is remarkably different to vertebrates and in certain respects remains elusive. We, for the first time, compared the orthologs involved in arachidonic acid (AA) metabolism in 14 species of invertebrates and 3 species of vertebrates. Based on parsimony, a complex AA-metabolic system may have existed in the common ancestor of the Metazoa, and then expanded and diversified through invertebrate lineages. A primary vertebrate-like AA-metabolic system via cyclooxygenase (COX), lipoxygenase (LOX), and cytochrome P450 (CYP) pathways was further identified in the basal chordate, amphioxus. The expression profiling of AA-metabolic enzymes and lipidomic analysis of eicosanoid production in the tissues of amphioxus supported our supposition. Thus, we proposed that the ancestral complexity of AA-metabolic network diversified with the different lineages of invertebrates, adapting with the diversity of body plans and ecological opportunity, and arriving at the vertebrate-like pattern in the basal chordate, amphioxus.

  13. Inference of Ancestral Recombination Graphs through Topological Data Analysis.

    PubMed

    Cámara, Pablo G; Levine, Arnold J; Rabadán, Raúl

    2016-08-01

    The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands. PMID:27532298

  14. Ancestral genetic complexity of arachidonic acid metabolism in Metazoa.

    PubMed

    Yuan, Dongjuan; Zou, Qiuqiong; Yu, Ting; Song, Cuikai; Huang, Shengfeng; Chen, Shangwu; Ren, Zhenghua; Xu, Anlong

    2014-09-01

    Eicosanoids play an important role in inducing complex and crucial physiological processes in animals. Eicosanoid biosynthesis in animals is widely reported; however, eicosanoid production in invertebrate tissue is remarkably different to vertebrates and in certain respects remains elusive. We, for the first time, compared the orthologs involved in arachidonic acid (AA) metabolism in 14 species of invertebrates and 3 species of vertebrates. Based on parsimony, a complex AA-metabolic system may have existed in the common ancestor of the Metazoa, and then expanded and diversified through invertebrate lineages. A primary vertebrate-like AA-metabolic system via cyclooxygenase (COX), lipoxygenase (LOX), and cytochrome P450 (CYP) pathways was further identified in the basal chordate, amphioxus. The expression profiling of AA-metabolic enzymes and lipidomic analysis of eicosanoid production in the tissues of amphioxus supported our supposition. Thus, we proposed that the ancestral complexity of AA-metabolic network diversified with the different lineages of invertebrates, adapting with the diversity of body plans and ecological opportunity, and arriving at the vertebrate-like pattern in the basal chordate, amphioxus. PMID:24801744

  15. Dynamic quenching in single photosystem II supercomplexes.

    PubMed

    Gruber, J Michael; Xu, Pengqi; Chmeliov, Jevgenij; Krüger, Tjaart P J; Alexandre, Maxime T A; Valkunas, Leonas; Croce, Roberta; van Grondelle, Rienk

    2016-10-01

    Photosystem II (PSII) is a huge pigment-protein supercomplex responsible for the primary steps of photosynthesis in green plants. Its light-harvesting antenna exhibits efficient transfer of the absorbed excitation energy to the reaction center and also contains a well-regulated protection mechanism against over-excitation in strong light conditions. The latter is based on conformational changes in antenna complexes that open up excitation decay channels resulting in considerable fluorescence quenching. Meanwhile, fluorescence blinking, observed in single antennas, is likely caused by a similar mechanism. Thus the question arises whether this effect is also present in and relevant to the native supramolecular organization of a fully assembled PSII. To further investigate energy transfer and quenching in single PSII, we performed single-molecule experiments on PSII supercomplexes at 5 °C. Analysis of the fluorescence intensity and mean lifetime allowed us to distinguish detached antennas and specifically analyze PSII supercomplexes. The average fluorescence lifetime in PSII of about 100-150 ps, measured under our extreme excitation conditions, is surprisingly similar to published ensemble lifetime data of photochemical quenching in PSII of a similar size. In our case, this lifetime is nevertheless caused by either one or multiple quenched antennas or by a quencher in the reaction center. The observed reversible light-induced changes in fluorescence intensity on a millisecond timescale are reminiscent of blinking subunits. Our results therefore directly illustrate how environmental control over a fluctuating antenna can regulate light-harvesting in plant photosynthesis. PMID:27604572

  16. Proton transfer pathways in Photosystem II

    NASA Astrophysics Data System (ADS)

    Ishikita, Hiroshi

    2014-03-01

    Using quantum mechanics/molecular mechanics calculations and the 1.9-Å crystal structure of Photosystem II (Umena, Y., Kawakami, K., Shen, J.-R., and Kamiya, N. (2011) Nature 473, 55-60), we investigated the H-bonding environment of the redox active tyrosine, TyrD and obtained insights that help explain its slow redox kinetics and the stability of TyrD radical. The water molecule distal to TyrD, 4 Å away from the phenolic O of TyrD (OTyrD) , corresponds to the presence of the tyrosyl radical state. The water molecule proximal to TyrD, in H-bonding distance to OTyrD, corresponds to the presence of the unoxidised tyrosine. The H+ released upon oxidation of TyrD is transferred to the proximal water, which shifts to the distal position, triggering a concerted proton transfer pathway involving D2-Arg180 and a series of waters, through which the proton reaches the aqueous phase at D2-His61. The water movement linked to the ejection of the proton from the hydrophobic environment near TyrD makes oxidation slow and quasi-irreversible, explaining the great stability of the TyrD radical. A symmetry-related proton pathway associated with TyrZ is pointed out and this is associated with one of the Cl- sites. This may represent a proton pathway functional in the water oxidation cycle.

  17. Photoinduced changes in photosystem II pigments

    NASA Astrophysics Data System (ADS)

    Andreeva, Atanaska S.; Busheva, Mira C.; Stoitchkova, Katerina V.; Tzonova, Iren K.

    2010-11-01

    The photosynthetic apparatus in higher plants performs two seemingly opposing tasks: efficient harvest of sunlight, but also rapid and harmless dissipation of excess light energy as heat to avoid deleterious photodamage. In order to study this process in pigment-protein supercomplexes of photosystem II (PSII), 77 K fluorescence and room temperature resonance Raman (RR) spectroscopy were applied to investigate the changes in structure and spectral properties of the pigments in spinach PSII membranes. The high-light treatment results in a strong quenching of the fluorescence (being largest when the excitation is absorbed by carotenoids) and a red-shift of the main maximum. Decomposition of the fluorescence spectra into four bands revealed intensive quenching of F685 and F695 bands, possible bleaching of chlorophyll a, enhanced extent of light harvesting complexes (LHCII) aggregation and increased energy transfer to aggregated LHCII. The analysis of RR spectra revealed the predominant contribution of ß-carotene (ß-Car) upon 457.8 and 488 nm excitations and lutein (Lut) at 514.5 nm. During prolonged exposure to strong light no significant bleaching of ß-Car and weak photobleaching of Lut is observed. The results will contribute to the efforts to produce more efficient and robust solar cells when exposed to fluctuations in light intensity.

  18. Photoelectrochemistry of photosystem I bound in nafion.

    PubMed

    Baker, David R; Simmerman, Richard F; Sumner, James J; Bruce, Barry D; Lundgren, Cynthia A

    2014-11-18

    Developing a solid state Photosystem I (PSI) modified electrode is attractive for photoelectrochemical applications because of the quantum yield of PSI, which approaches unity in the visible spectrum. Electrodes are constructed using a Nafion film to encapsulate PSI as well as the hole-scavenging redox mediator Os(bpy)2Cl2. The photoactive electrodes generate photocurrents of 4 μA/cm(2) when illuminated with 1.4 mW/cm(2) of 676 nm band-pass filtered light. Methyl viologen (MV(2+)) is present in the electrolyte to scavenge photoelectrons from PSI in the Nafion film and transport charges to the counter electrode. Because MV(2+) is positively charged in both reduced and oxidized states, it is able to diffuse through the cation permeable channels of Nafion. Photocurrent is produced when the working electrode is set to voltages negative of the Os(3+)/Os(2+) redox potential. Charge transfer through the Nafion film and photohole scavenging at the PSI luminal surface by Os(bpy)2Cl2 depends on the reduction of Os redox centers to Os(2+) via hole scavenging from PSI. The optimal film densities of Nafion (10 μg/cm(2) Nafion) and PSI (100 μg/cm(2) PSI) are determined to provide the highest photocurrents. These optimal film densities force films to be thin to allow the majority of PSI to have productive electrical contact with the backing electrode. PMID:25341002

  19. Dynamic quenching in single photosystem II supercomplexes.

    PubMed

    Gruber, J Michael; Xu, Pengqi; Chmeliov, Jevgenij; Krüger, Tjaart P J; Alexandre, Maxime T A; Valkunas, Leonas; Croce, Roberta; van Grondelle, Rienk

    2016-10-01

    Photosystem II (PSII) is a huge pigment-protein supercomplex responsible for the primary steps of photosynthesis in green plants. Its light-harvesting antenna exhibits efficient transfer of the absorbed excitation energy to the reaction center and also contains a well-regulated protection mechanism against over-excitation in strong light conditions. The latter is based on conformational changes in antenna complexes that open up excitation decay channels resulting in considerable fluorescence quenching. Meanwhile, fluorescence blinking, observed in single antennas, is likely caused by a similar mechanism. Thus the question arises whether this effect is also present in and relevant to the native supramolecular organization of a fully assembled PSII. To further investigate energy transfer and quenching in single PSII, we performed single-molecule experiments on PSII supercomplexes at 5 °C. Analysis of the fluorescence intensity and mean lifetime allowed us to distinguish detached antennas and specifically analyze PSII supercomplexes. The average fluorescence lifetime in PSII of about 100-150 ps, measured under our extreme excitation conditions, is surprisingly similar to published ensemble lifetime data of photochemical quenching in PSII of a similar size. In our case, this lifetime is nevertheless caused by either one or multiple quenched antennas or by a quencher in the reaction center. The observed reversible light-induced changes in fluorescence intensity on a millisecond timescale are reminiscent of blinking subunits. Our results therefore directly illustrate how environmental control over a fluctuating antenna can regulate light-harvesting in plant photosynthesis.

  20. Multistep organic synthesis of modular photosystems

    PubMed Central

    2012-01-01

    Summary Quite extensive synthetic achievements vanish in the online supporting information of publications on functional systems. Underappreciated, their value is recognized by experts only. As an example, we here focus in on the recent synthesis of multicomponent photosystems with antiparallel charge-transfer cascades in co-axial hole- and electron-transporting channels. The synthetic steps are described one-by-one, starting with commercial starting materials and moving on to key intermediates, such as asparagusic acid, an intriguing natural product, as well as diphosphonate “feet”, and panchromatic naphthalenediimides (NDIs), to finally reach the target molecules. These products are initiators and propagators for self-organizing surface-initiated polymerization (SOSIP), a new method introduced to secure facile access to complex architectures. Chemoorthogonal to the ring-opening disulfide exchange used for SOSIP, hydrazone exchange is then introduced to achieve stack exchange, which is a “switching” technology invented to drill giant holes into SOSIP architectures and fill them with functional π-stacks of free choice. PMID:23015840

  1. Photosystem II: an enzyme of global significance.

    PubMed

    Barber, J

    2006-11-01

    Photosystem II (PSII) is a multisubunit enzyme embedded in the lipid environment of the thylakoid membranes of plants, algae and cyanobacteria. Powered by light, this enzyme catalyses the chemically and thermodynamically demanding reaction of water splitting. In so doing, it releases dioxygen into the atmosphere and provides the reducing equivalents required for the conversion of CO2 into the organic molecules of life. Recently, a fully refined structure of a 700 kDa cyanobacterial dimeric PSII complex was elucidated by X-ray crystallography which gave organizational and structural details of the 19 subunits (16 intrinsic and three extrinsic) which make up each monomer and provided information about the position and protein environments of 57 different cofactors. The water-splitting site was revealed as a cluster of four Mn ions and a Ca2+ ion surrounded by amino acid side chains, of which six or seven form direct ligands to the metals. The metal cluster was modelled as a cubane-like structure composed of three Mn ions and the Ca2+ linked by oxo-bonds with the fourth Mn attached to the cubane via one of its oxygens. The overall structure of the catalytic site is providing a framework to develop a mechanistic scheme for the water-splitting process, knowledge which could have significant implications for mimicking the reaction in an artificial chemical system. PMID:17052167

  2. Moderate Photoinhibition of Photosystem II Protects Photosystem I from Photodamage at Chilling Stress in Tobacco Leaves.

    PubMed

    Huang, Wei; Yang, Ying-Jie; Hu, Hong; Zhang, Shi-Bao

    2016-01-01

    It has been indicated that photosystem I (PSI) is susceptible to chilling-light stress in tobacco leaves, but the effect of growth light intensity on chilling-induced PSI photoinhibition in tobacco is unclear. We examined the effects of chilling temperature (4°C) associated with moderate light intensity (300 μmol photons m(-2) s(-1)) on the activities of PSI and photosystem II (PSII) in leaves from sun- and shade-grown plants of tobacco (Nicotiana tabacum cv. k326). The sun leaves had a higher activity of alternative electron flow than the shade leaves. After 4 h chilling treatment, the sun leaves showed significantly a higher PSI photoinhibition than the shade leaves. At chilling temperature the sun leaves showed a greater electron flow from PSII to PSI, accompanying with a lower P700 oxidation ratio. When leaves were pre-treated with lincomycin, PSII activity decreased by 42% (sun leaves) and 47% (shade leaves) after 2 h exposure to the chilling-light stress, but PSI activity remained stable during the chilling-light treatment, because the electron flow from PSII to PSI was remarkably depressed. These results indicated that the stronger chilling-induced PSI photoinhibition in the sun leaves was resulted from a greater electron flow from PSII to PSI. Furthermore, moderate PSII photoinhibition depressed electron flow to PSI and then protected PSI activity against further photodamage in chilled tobacco leaves. PMID:26941755

  3. Moderate Photoinhibition of Photosystem II Protects Photosystem I from Photodamage at Chilling Stress in Tobacco Leaves

    PubMed Central

    Huang, Wei; Yang, Ying-Jie; Hu, Hong; Zhang, Shi-Bao

    2016-01-01

    It has been indicated that photosystem I (PSI) is susceptible to chilling-light stress in tobacco leaves, but the effect of growth light intensity on chilling-induced PSI photoinhibition in tobacco is unclear. We examined the effects of chilling temperature (4°C) associated with moderate light intensity (300 μmol photons m-2 s-1) on the activities of PSI and photosystem II (PSII) in leaves from sun- and shade-grown plants of tobacco (Nicotiana tabacum cv. k326). The sun leaves had a higher activity of alternative electron flow than the shade leaves. After 4 h chilling treatment, the sun leaves showed significantly a higher PSI photoinhibition than the shade leaves. At chilling temperature the sun leaves showed a greater electron flow from PSII to PSI, accompanying with a lower P700 oxidation ratio. When leaves were pre-treated with lincomycin, PSII activity decreased by 42% (sun leaves) and 47% (shade leaves) after 2 h exposure to the chilling-light stress, but PSI activity remained stable during the chilling-light treatment, because the electron flow from PSII to PSI was remarkably depressed. These results indicated that the stronger chilling-induced PSI photoinhibition in the sun leaves was resulted from a greater electron flow from PSII to PSI. Furthermore, moderate PSII photoinhibition depressed electron flow to PSI and then protected PSI activity against further photodamage in chilled tobacco leaves. PMID:26941755

  4. Structure Determination and Improved Model of Plant Photosystem I*

    PubMed Central

    Amunts, Alexey; Toporik, Hila; Borovikova, Anna; Nelson, Nathan

    2010-01-01

    Photosystem I functions as a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae, and higher plants. Functionally, Photosystem I captures sunlight and transfers the excitation energy through an intricate and precisely organized antenna system, consisting of a pigment network, to the center of the molecule, where it is used in the transmembrane electron transfer reaction. Our current understanding of the sophisticated mechanisms underlying these processes has profited greatly from elucidation of the crystal structures of the Photosystem I complex. In this report, we describe the developments that ultimately led to enhanced structural information of plant Photosystem I. In addition, we report an improved crystallographic model at 3.3-Å resolution, which allows analysis of the structure in more detail. An improved electron density map yielded identification and tracing of subunit PsaK. The location of an additional ten β-carotenes as well as five chlorophylls and several loop regions, which were previously uninterpretable, are now modeled. This represents the most complete plant Photosystem I structure obtained thus far, revealing the locations of and interactions among 17 protein subunits and 193 non-covalently bound photochemical cofactors. Using the new crystal structure, we examine the network of contacts among the protein subunits from the structural perspective, which provide the basis for elucidating the functional organization of the complex. PMID:19923216

  5. Deficient Photosystem II in Agranal Bundle Sheath Chloroplasts of C4 Plants

    PubMed Central

    Woo, K. C.; Anderson, Jan M.; Boardman, N. K.; Downton, W. J. S.; Osmond, C. B.; Thorne, S. W.

    1970-01-01

    A method is described for separating mesophyll and bundle sheath chloroplasts from the leaves of C4 plants. The agranal bundle sheath chloroplasts are inactive in the Hill reaction, whereas granal bundle sheath and granal mesophyll chloroplasts exhibit normal photosystem II activity. The agranal bundle sheath chloroplasts are deficient in photosystem II; they lack cytochrome b-559 and the fluorescence bands associated with photosystem II. All the chloroplasts exhibit photosystem I activity. PMID:16591853

  6. An experimental phylogeny to benchmark ancestral sequence reconstruction

    PubMed Central

    Randall, Ryan N.; Radford, Caelan E.; Roof, Kelsey A.; Natarajan, Divya K.; Gaucher, Eric A.

    2016-01-01

    Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed many key mechanisms of molecular evolution. One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation. Here we build an experimental phylogeny using the gene of a single red fluorescent protein to address this criticism. The evolved phylogeny consists of 19 operational taxonomic units (leaves) and 17 ancestral bifurcations (nodes) that display a wide variety of fluorescent phenotypes. The 19 leaves then serve as ‘modern' sequences that we subject to ASR analyses using various algorithms and to benchmark against the known ancestral genotypes and ancestral phenotypes. We confirm computer simulations that show all algorithms infer ancient sequences with high accuracy, yet we also reveal wide variation in the phenotypes encoded by incorrectly inferred sequences. Specifically, Bayesian methods incorporating rate variation significantly outperform the maximum parsimony criterion in phenotypic accuracy. Subsampling of extant sequences had minor effect on the inference of ancestral sequences. PMID:27628687

  7. An experimental phylogeny to benchmark ancestral sequence reconstruction.

    PubMed

    Randall, Ryan N; Radford, Caelan E; Roof, Kelsey A; Natarajan, Divya K; Gaucher, Eric A

    2016-01-01

    Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed many key mechanisms of molecular evolution. One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation. Here we build an experimental phylogeny using the gene of a single red fluorescent protein to address this criticism. The evolved phylogeny consists of 19 operational taxonomic units (leaves) and 17 ancestral bifurcations (nodes) that display a wide variety of fluorescent phenotypes. The 19 leaves then serve as 'modern' sequences that we subject to ASR analyses using various algorithms and to benchmark against the known ancestral genotypes and ancestral phenotypes. We confirm computer simulations that show all algorithms infer ancient sequences with high accuracy, yet we also reveal wide variation in the phenotypes encoded by incorrectly inferred sequences. Specifically, Bayesian methods incorporating rate variation significantly outperform the maximum parsimony criterion in phenotypic accuracy. Subsampling of extant sequences had minor effect on the inference of ancestral sequences. PMID:27628687

  8. Phylogeographic ancestral inference using the coalescent model on haplotype trees.

    PubMed

    Manolopoulou, Ioanna; Emerson, Brent C

    2012-06-01

    Phylogeographic ancestral inference is issue frequently arising in population ecology that aims to understand the geographical roots and structure of species. Here, we specifically address relatively small scale mtDNA datasets (typically less than 500 sequences with fewer than 1000 nucleotides), focusing on ancestral location inference. Our approach uses a coalescent modelling framework projected onto haplotype trees in order to reduce computational complexity, at the same time adhering to complex evolutionary processes. Statistical innovations of the last few years have allowed for computationally feasible yet accurate inferences in phylogenetic frameworks. We implement our methods on a set of synthetic datasets and show how, despite high uncertainty in terms of identifying the root haplotype, estimation of the ancestral location naturally encompasses lower uncertainty, allowing us to pinpoint the Maximum A Posteriori estimates for ancestral locations. We exemplify our methods on a set of synthetic datasets and then combine our inference methods with the phylogeographic clustering approach presented in Manolopoulou et al. (2011) on a real dataset from weevils in the Iberian peninsula in order to infer ancestral locations as well as population substructure.

  9. Male androphilia in the ancestral environment. An ethnological analysis.

    PubMed

    VanderLaan, Doug P; Ren, Zhiyuan; Vasey, Paul L

    2013-12-01

    The kin selection hypothesis posits that male androphilia (male sexual attraction to adult males) evolved because androphilic males invest more in kin, thereby enhancing inclusive fitness. Increased kin-directed altruism has been repeatedly documented among a population of transgendered androphilic males, but never among androphilic males in other cultures who adopt gender identities as men. Thus, the kin selection hypothesis may be viable if male androphilia was expressed in the transgendered form in the ancestral past. Using the Standard Cross-Cultural Sample (SCCS), we examined 46 societies in which male androphilia was expressed in the transgendered form (transgendered societies) and 146 comparison societies (non-transgendered societies). We analyzed SCCS variables pertaining to ancestral sociocultural conditions, access to kin, and societal reactions to homosexuality. Our results show that ancestral sociocultural conditions and bilateral and double descent systems were more common in transgendered than in non-transgendered societies. Across the entire sample, descent systems and residence patterns that would presumably facilitate increased access to kin were associated with the presence of ancestral sociocultural conditions. Among transgendered societies, negative societal attitudes toward homosexuality were unlikely. We conclude that the ancestral human sociocultural environment was likely conducive to the expression of the transgendered form of male androphilia. Descent systems, residence patterns, and societal reactions to homosexuality likely facilitated investments in kin by transgendered males. Given that contemporary transgendered male androphiles appear to exhibit elevated kin-directed altruism, these findings further indicate the viability of the kin selection hypothesis.

  10. Structure and dynamics in Photosystem I

    NASA Astrophysics Data System (ADS)

    Jolley, Craig Charles

    Photosystem I (PSI) is a transmembrane protein complex that uses incident light energy to drive an energetically unfavorable electron transfer reaction across a membrane in the early steps of oxygenic photosynthesis. This electron transfer reaction provides energy for the fixing of carbon dioxide and for the subsequent synthesis of nearly all biological material on Earth. Despite the morphological variety of oxygenic photosynthetic organisms---ranging from single-celled aquatic cyanobacteria to large, complex terrestrial plants---the structure and function of PSI are remarkably well-conserved across phyla. PSI has been the subject of extensive interdisciplinary research involving fields ranging from molecular genetics to condensed matter physics, and many aspects of its function still remain unclear. This study presents a variety of theoretical and experimental approaches to aspects of PSI structure and dynamics. An atomic-level structural model of higher plant PSI has been constructed based on recent protein crystal structures, and provides insight into the evolution of eukaryotic PSI. Time-resolved optical spectroscopic studies of PSI supercomplexes from the green freshwater alga Chlamydomonas reinhardtii illustrate how this organism adapts its photosynthetic apparatus to deal with changing environmental conditions and highlight the importance of structure-function relationships in light-harvesting systems. A novel computational approach using constrained geometric simulations has been used to model a portion of the PSI assembly process, shedding some light on how the heterodimeric PSI reaction center evolved from the more ancient homodimeric photosynthetic reaction centers found in green sulfur bacteria and heliobacteria. A new method is also demonstrated in which constrained geometric simulations are used to flexibly fit a high-resolution protein structure to a low-resolution density map obtained with cryo-electron microscopy (cryo-EM) or low-resolution x

  11. Photoprotection of photosystems in fluctuating light intensities.

    PubMed

    Allahverdiyeva, Yagut; Suorsa, Marjaana; Tikkanen, Mikko; Aro, Eva-Mari

    2015-05-01

    Oxygenic photosynthetic organisms experience strong fluctuations in light intensity in their natural terrestrial and aquatic growth environments. Recent studies with both plants and cyanobacteria have revealed that Photosystem (PS) I is the potential target of damage upon abrupt changes in light intensity. Photosynthetic organisms have, however, developed powerful mechanisms in order to protect their photosynthetic apparatus against such potentially hazardous light conditions. Although the electron transfer chain has remained relatively unchanged in both plant chloroplasts and their cyanobacterial ancestors, the photoprotective and regulatory mechanisms of photosynthetic light reactions have experienced conspicuous evolutionary changes. In cyanobacteria, the specific flavodiiron proteins (Flv1 and Flv3) are responsible for safeguarding PSI under rapidly fluctuating light intensities, whilst the thylakoid located terminal oxidases are involved in the protection of PSII during 12h diurnal cycles involving abrupt, square-wave, changes from dark to high light. Higher plants such as Arabidopsis thaliana have evolved different protective mechanisms. In particular, the PGR5 protein controls electron flow during sudden changes in light intensity by allowing the regulation mostly via the Cytochrome b6f complex. Besides the function of PGR5, plants have also acquired other dynamic regulatory mechanisms, among them the STN7-related LHCII protein phosphorylation that is similarly responsible for protection against rapid changes in the light environment. The green alga Chlamydomonas reinhardtii, as an evolutionary intermediate between cyanobacteria and higher plants, probably possesses both protective mechanisms. In this review, evolutionarily different photoprotective mechanisms under fluctuating light conditions are described and their contributions to cyanobacterial and plant photosynthesis are discussed.

  12. Optimization and evolution of light harvesting in photosynthesis: the role of antenna chlorophyll conserved between photosystem II and photosystem I.

    PubMed

    Vasil'ev, Sergej; Bruce, Doug

    2004-11-01

    The efficiency of oxygenic photosynthesis depends on the presence of core antenna chlorophyll closely associated with the photochemical reaction centers of both photosystem II (PSII) and photosystem I (PSI). Although the number and overall arrangement of these chlorophylls in PSII and PSI differ, structural comparison reveals a cluster of 26 conserved chlorophylls in nearly identical positions and orientations. To explore the role of these conserved chlorophylls within PSII and PSI we studied the influence of their orientation on the efficiency of photochemistry in computer simulations. We found that the native orientations of the conserved chlorophylls were not optimal for light harvesting in either photosystem. However, PSII and PSI each contain two highly orientationally optimized antenna chlorophylls, located close to their respective reaction centers, in positions unique to each photosystem. In both photosystems the orientation of these optimized bridging chlorophylls had a much larger impact on photochemical efficiency than the orientation of any of the conserved chlorophylls. The differential optimization of antenna chlorophyll is discussed in the context of competing selection pressures for the evolution of light harvesting in photosynthesis.

  13. The RUBISCO to Photosystem II Ratio Limits the Maximum Photosynthetic Rate in Picocyanobacteria

    PubMed Central

    Zorz, Jackie K.; Allanach, Jessica R.; Murphy, Cole D.; Roodvoets, Mitchell S.; Campbell, Douglas A.; Cockshutt, Amanda M.

    2015-01-01

    Marine Synechococcus and Prochlorococcus are picocyanobacteria predominating in subtropical, oligotrophic marine environments, a niche predicted to expand with climate change. When grown under common low light conditions Synechococcus WH 8102 and Prochlorococcus MED 4 show similar Cytochrome b6f and Photosystem I contents normalized to Photosystem II content, while Prochlorococcus MIT 9313 has twice the Cytochrome b6f content and four times the Photosystem I content of the other strains. Interestingly, the Prochlorococcus strains contain only one third to one half of the RUBISCO catalytic subunits compared to the marine Synechococcus strain. The maximum Photosystem II electron transport rates were similar for the two Prochlorococcus strains but higher for the marine Synechococcus strain. Photosystem II electron transport capacity is highly correlated to the molar ratio of RUBISCO active sites to Photosystem II but not to the ratio of cytochrome b6f to Photosystem II, nor to the ratio of Photosystem I: Photosystem II. Thus, the catalytic capacity for the rate-limiting step of carbon fixation, the ultimate electron sink, appears to limit electron transport rates. The high abundance of Cytochrome b6f and Photosystem I in MIT 9313, combined with the slower flow of electrons away from Photosystem II and the relatively low level of RUBISCO, are consistent with cyclic electron flow around Photosystem I in this strain. PMID:25658887

  14. Carotenoids Assist in Cyanobacterial Photosystem II Assembly and Function

    PubMed Central

    Zakar, Tomas; Laczko-Dobos, Hajnalka; Toth, Tunde N.; Gombos, Zoltan

    2016-01-01

    Carotenoids (carotenes and xanthophylls) are ubiquitous constituents of living organisms. They are protective agents against oxidative stresses and serve as modulators of membrane microviscosity. As antioxidants they can protect photosynthetic organisms from free radicals like reactive oxygen species that originate from water splitting, the first step of photosynthesis. We summarize the structural and functional roles of carotenoids in connection with cyanobacterial Photosystem II. Although carotenoids are hydrophobic molecules, their complexes with proteins also allow cytoplasmic localization. In cyanobacterial cells such complexes are called orange carotenoid proteins, and they protect Photosystem II and Photosystem I by preventing their overexcitation through phycobilisomes (PBS). Recently it has been observed that carotenoids are not only required for the proper functioning, but also for the structural stability of PBSs. PMID:27014318

  15. Binding sites associated with inhibition of photosystem II

    SciTech Connect

    Shipman, L.L.

    1981-01-01

    A variety of experimental and theoretical evidence has been integrated into coherent molecular mechanisms for the action of photosystem II herbicides. Photosystem II herbicides act by inhibiting electron transfers between the first and second plastoquinones on the reducing side of photosystem II. Each herbicide molecule must have a flat polar component with hydrophobic substituents to be active. The hydrophobic substituents serve to partition the molecule into lipid regions of the cell and to fit the hydrophobic region of the herbicide binding site. The flat polar portion of the herbicide is used for electrostatic binding to the polar region of the herbicide binding site. Theoretical calculations have been carried out to investigate the binding of herbicides to model proteinaceous binding sites.

  16. Carotenoids Assist in Cyanobacterial Photosystem II Assembly and Function.

    PubMed

    Zakar, Tomas; Laczko-Dobos, Hajnalka; Toth, Tunde N; Gombos, Zoltan

    2016-01-01

    Carotenoids (carotenes and xanthophylls) are ubiquitous constituents of living organisms. They are protective agents against oxidative stresses and serve as modulators of membrane microviscosity. As antioxidants they can protect photosynthetic organisms from free radicals like reactive oxygen species that originate from water splitting, the first step of photosynthesis. We summarize the structural and functional roles of carotenoids in connection with cyanobacterial Photosystem II. Although carotenoids are hydrophobic molecules, their complexes with proteins also allow cytoplasmic localization. In cyanobacterial cells such complexes are called orange carotenoid proteins, and they protect Photosystem II and Photosystem I by preventing their overexcitation through phycobilisomes (PBS). Recently it has been observed that carotenoids are not only required for the proper functioning, but also for the structural stability of PBSs. PMID:27014318

  17. The structure of photosystem I and evolution of photosynthesis.

    PubMed

    Nelson, Nathan; Ben-Shem, Adam

    2005-09-01

    Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on earth. The primary step in this process--the conversion of sunlight into chemical energy--is driven by four multi-subunit membrane protein complexes named photosystem I, photosystem II, cytochrome b(6)f complex and F-ATPase. Photosystem I generates the most negative redox potential in nature and thus largely determines the global amount of enthalpy in living systems. The recent structural determination of PSI complexes from cyanobacteria and plants sheds light on the evolutionary forces that shaped oxygenic photosynthesis. The fortuitous formation of our solar system in a space plentiful of elements, our distance from the sun and the long time of uninterrupted evolution enabled the perfection of photosynthesis and the evolution of advanced organisms. The available structural information complements the knowledge gained from genomic and proteomic data to illustrate a more precise scenario for the evolution of life systems on earth. PMID:16108066

  18. Whole genome profiling physical map and ancestral annotation of tobacco Hicks Broadleaf.

    PubMed

    Sierro, Nicolas; van Oeveren, Jan; van Eijk, Michiel J T; Martin, Florian; Stormo, Keith E; Peitsch, Manuel C; Ivanov, Nikolai V

    2013-09-01

    Genomics-based breeding of economically important crops such as banana, coffee, cotton, potato, tobacco and wheat is often hampered by genome size, polyploidy and high repeat content. We adapted sequence-based whole-genome profiling (WGP™) technology to obtain insight into the polyploidy of the model plant Nicotiana tabacum (tobacco). N. tabacum is assumed to originate from a hybridization event between ancestors of Nicotiana sylvestris and Nicotiana tomentosiformis approximately 200,000 years ago. This resulted in tobacco having a haploid genome size of 4500 million base pairs, approximately four times larger than the related tomato (Solanum lycopersicum) and potato (Solanum tuberosum) genomes. In this study, a physical map containing 9750 contigs of bacterial artificial chromosomes (BACs) was constructed. The mean contig size was 462 kbp, and the calculated genome coverage equaled the estimated tobacco genome size. We used a method for determination of the ancestral origin of the genome by annotation of WGP sequence tags. This assignment agreed with the ancestral annotation available from the tobacco genetic map, and may be used to investigate the evolution of homoeologous genome segments after polyploidization. The map generated is an essential scaffold for the tobacco genome. We propose the combination of WGP physical mapping technology and tag profiling of ancestral lines as a generally applicable method to elucidate the ancestral origin of genome segments of polyploid species. The physical mapping of genes and their origins will enable application of biotechnology to polyploid plants aimed at accelerating and increasing the precision of breeding for abiotic and biotic stress resistance.

  19. Whole genome profiling physical map and ancestral annotation of tobacco Hicks Broadleaf

    PubMed Central

    Sierro, Nicolas; van Oeveren, Jan; van Eijk, Michiel J T; Martin, Florian; Stormo, Keith E; Peitsch, Manuel C; Ivanov, Nikolai V

    2013-01-01

    Genomics-based breeding of economically important crops such as banana, coffee, cotton, potato, tobacco and wheat is often hampered by genome size, polyploidy and high repeat content. We adapted sequence-based whole-genome profiling (WGP™) technology to obtain insight into the polyploidy of the model plant Nicotiana tabacum (tobacco). N. tabacum is assumed to originate from a hybridization event between ancestors of Nicotiana sylvestris and Nicotiana tomentosiformis approximately 200 000 years ago. This resulted in tobacco having a haploid genome size of 4500 million base pairs, approximately four times larger than the related tomato (Solanum lycopersicum) and potato (Solanum tuberosum) genomes. In this study, a physical map containing 9750 contigs of bacterial artificial chromosomes (BACs) was constructed. The mean contig size was 462 kbp, and the calculated genome coverage equaled the estimated tobacco genome size. We used a method for determination of the ancestral origin of the genome by annotation of WGP sequence tags. This assignment agreed with the ancestral annotation available from the tobacco genetic map, and may be used to investigate the evolution of homoeologous genome segments after polyploidization. The map generated is an essential scaffold for the tobacco genome. We propose the combination of WGP physical mapping technology and tag profiling of ancestral lines as a generally applicable method to elucidate the ancestral origin of genome segments of polyploid species. The physical mapping of genes and their origins will enable application of biotechnology to polyploid plants aimed at accelerating and increasing the precision of breeding for abiotic and biotic stress resistance. PMID:23672264

  20. Unraveling recombination rate evolution using ancestral recombination maps

    PubMed Central

    Munch, Kasper; Schierup, Mikkel H; Mailund, Thomas

    2014-01-01

    Recombination maps of ancestral species can be constructed from comparative analyses of genomes from closely related species, exemplified by a recently published map of the human-chimpanzee ancestor. Such maps resolve differences in recombination rate between species into changes along individual branches in the speciation tree, and allow identification of associated changes in the genomic sequences. We describe how coalescent hidden Markov models are able to call individual recombination events in ancestral species through inference of incomplete lineage sorting along a genomic alignment. In the great apes, speciation events are sufficiently close in time that a map can be inferred for the ancestral species at each internal branch - allowing evolution of recombination rate to be tracked over evolutionary time scales from speciation event to speciation event. We see this approach as a way of characterizing the evolution of recombination rate and the genomic properties that influence it. PMID:25043668

  1. Photosystem II and photosynthetic oxidation of water: an overview.

    PubMed Central

    Goussias, Charilaos; Boussac, Alain; Rutherford, A William

    2002-01-01

    Conceptually, photosystem II, the oxygen-evolving enzyme, can be divided into two parts: the photochemical part and the catalytic part. The photochemical part contains the ultra-fast and ultra-efficient light-induced charge separation and stabilization steps that occur when light is absorbed by chlorophyll. The catalytic part, where water is oxidized, involves a cluster of Mn ions close to a redox-active tyrosine residue. Our current understanding of the catalytic mechanism is mainly based on spectroscopic studies. Here, we present an overview of the current state of knowledge of photosystem II, attempting to delineate the open questions and the directions of current research. PMID:12437876

  2. The Microcephalin Ancestral Allele in a Neanderthal Individual

    PubMed Central

    Lari, Martina; Rizzi, Ermanno; Milani, Lucio; Corti, Giorgio; Balsamo, Carlotta; Vai, Stefania; Catalano, Giulio; Pilli, Elena; Longo, Laura; Condemi, Silvana; Giunti, Paolo; Hänni, Catherine; De Bellis, Gianluca; Orlando, Ludovic; Barbujani, Guido; Caramelli, David

    2010-01-01

    Background The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. Methodology/Principal Findings Here we report the first PCR amplification and high- throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. Conclusions/Significance The MCPH1 genotype of the Monti Lessini (MLS) Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA. PMID:20498832

  3. Reconstructing the ancestral butterfly eye: focus on the opsins.

    PubMed

    Briscoe, Adriana D

    2008-06-01

    The eyes of butterflies are remarkable, because they are nearly as diverse as the colors of wings. Much of eye diversity can be traced to alterations in the number, spectral properties and spatial distribution of the visual pigments. Visual pigments are light-sensitive molecules composed of an opsin protein and a chromophore. Most butterflies have eyes that contain visual pigments with a wavelength of peak absorbance, lambda(max), in the ultraviolet (UV, 300-400 nm), blue (B, 400-500 nm) and long wavelength (LW, 500-600 nm) part of the visible light spectrum, respectively, encoded by distinct UV, B and LW opsin genes. In the compound eye of butterflies, each individual ommatidium is composed of nine photoreceptor cells (R1-9) that generally express only one opsin mRNA per cell, although in some butterfly eyes there are ommatidial subtypes in which two opsins are co-expressed in the same photoreceptor cell. Based on a phylogenetic analysis of opsin cDNAs from the five butterfly families, Papilionidae, Pieridae, Nymphalidae, Lycaenidae and Riodinidae, and comparative analysis of opsin gene expression patterns from four of the five families, I propose a model for the patterning of the ancestral butterfly eye that is most closely aligned with the nymphalid eye. The R1 and R2 cells of the main retina expressed UV-UV-, UV-B- or B-B-absorbing visual pigments while the R3-9 cells expressed a LW-absorbing visual pigment. Visual systems of existing butterflies then underwent an adaptive expansion based on lineage-specific B and LW opsin gene multiplications and on alterations in the spatial expression of opsins within the eye. Understanding the molecular sophistication of butterfly eye complexity is a challenge that, if met, has broad biological implications.

  4. Left-lateral intraplate deformation along the ancestral rocky mountains: Implications for late paleozoic plate motions

    NASA Astrophysics Data System (ADS)

    Budnik, Roy T.

    1986-12-01

    North America underwent synchronous orogenic events during the late Paleozoic along its eastern margin (Alleghanian orogeny), southern margin (Ouachita orogeny), and within the southwestern part of the continent (Ancestral Rocky Mountain orogeny). All three orogenies were initiated in the late Mississippian to early Pennsylvanian, reached the greatest intensity in the middle Pennsylvanian, and ended in the early Permian. The Alleghanian and Ouachita orogenies have been related to the closing of the proto-Atlantic and the collision between North America and South America-Africa: it is here proposed that the Ancestral Rocky Mountains were produced by a collision between eastern North America and Africa. The Ancestral Rockies were formed as the result of reactivation of the Wichita megashear, a preexisting zone of weakness that extends from southern Oklahoma to eastern Utah. Previous plate tectonic models have implied that the megashear was a zone of right-lateral strike-slip faulting and north-northwest-directed compression. However, structural and stratigraphic data from Oklahoma and Texas suggest that the Wichita megashear was a major left-lateral fault zone formed under east-northeast-oriented compression. Palinspastic reconstruction of pre-mid-Devonian strata across the megashear in Texas indicates that 120 to 150 km of left slip occurred during the Desmoinesian (middle Pennsylvanian). The proposed plate tectonic model for the Ancestral Rocky Mountain orogeny includes: (1) movement of the North American plate eastward from a spreading center in the proto-Pacific; (2) closing of the proto-Atlantic Ocean; (3) collision of North America-Europe (Laurussia) and South America-Africa (Gondwana) resulting in the Hercynian, Alleghanian, and Ouachita orogenies; (4) differential movement across the Wichita megashear and formation of a left-lateral strike-slip fault zone (Ancestral Rocky Mountain orogeny) as the result of east-west compression within the North American plate

  5. Inhibition of the Water Oxidizing Complex of Photosystem II and the Reoxidation of the Quinone Acceptor QA− by Pb2+

    PubMed Central

    Belatik, Ahmed; Hotchandani, Surat; Carpentier, Robert

    2013-01-01

    The action of the environmental toxic Pb2+ on photosynthetic electron transport was studied in thylakoid membranes isolated from spinach leaves. Fluorescence and thermoluminescence techniques were performed in order to determine the mode of Pb2+ action in photosystem II (PSII). The invariance of fluorescence characteristics of chlorophyll a (Chl a) and magnesium tetraphenylporphyrin (MgTPP), a molecule structurally analogous to Chl a, in the presence of Pb2+ confirms that Pb cation does not interact directly with chlorophyll molecules in PSII. The results show that Pb interacts with the water oxidation complex thus perturbing charge recombination between the quinone acceptors of PSII and the S2 state of the Mn4Ca cluster. Electron transfer between the quinone acceptors QA and QB is also greatly retarded in the presence of Pb2+. This is proposed to be owing to a transmembrane modification of the acceptor side of the photosystem. PMID:23861859

  6. Photoinhibition of Photosystems I and II Using Chlorophyll Fluorescence Measurements

    ERIC Educational Resources Information Center

    Quiles, Maria Jose

    2005-01-01

    In this study the photoinhibition of photosystems (PS) I and II caused by exposure to high intensity light in oat ("Avena sativa," var Prevision) is measured by the emission of chlorophyll fluorescence in intact leaves adapted to darkness. The maximal quantum yield of PS II was lower in plants grown under high light intensity than in plants grown…

  7. Are survival processing memory advantages based on ancestral priorities?

    PubMed

    Soderstrom, Nicholas C; McCabe, David P

    2011-06-01

    Recent research has suggested that our memory systems are especially tuned to process information according to its survival relevance, and that inducing problems of "ancestral priorities" faced by our ancestors should lead to optimal recall performance (Nairne & Pandeirada, Cognitive Psychology, 2010). The present study investigated the specificity of this idea by comparing an ancestor-consistent scenario and a modern survival scenario that involved threats that were encountered by human ancestors (e.g., predators) or threats from fictitious creatures (i.e., zombies). Participants read one of four survival scenarios in which the environment and the explicit threat were either consistent or inconsistent with ancestrally based problems (i.e., grasslands-predators, grasslands-zombies, city-attackers, city-zombies), or they rated words for pleasantness. After rating words based on their survival relevance (or pleasantness), the participants performed a free recall task. All survival scenarios led to better recall than did pleasantness ratings, but recall was greater when zombies were the threat, as compared to predators or attackers. Recall did not differ for the modern (i.e., city) and ancestral (i.e., grasslands) scenarios. These recall differences persisted when valence and arousal ratings for the scenarios were statistically controlled as well. These data challenge the specificity of ancestral priorities in survival-processing advantages in memory.

  8. Musculature in sipunculan worms: ontogeny and ancestral states.

    PubMed

    Schulze, Anja; Rice, Mary E

    2009-01-01

    Molecular phylogenetics suggests that the Sipuncula fall into the Annelida, although they are morphologically very distinct and lack segmentation. To understand the evolutionary transformations from the annelid to the sipunculan body plan, it is important to reconstruct the ancestral states within the respective clades at all life history stages. Here we reconstruct the ancestral states for the head/introvert retractor muscles and the body wall musculature in the Sipuncula using Bayesian statistics. In addition, we describe the ontogenetic transformations of the two muscle systems in four sipunculan species with different developmental modes, using F-actin staining with fluorescent-labeled phalloidin in conjunction with confocal laser scanning microscopy. All four species, which have smooth body wall musculature and less than the full set of four introvert retractor muscles as adults, go through developmental stages with four retractor muscles that are eventually reduced to a lower number in the adult. The circular and sometimes the longitudinal body wall musculature are split into bands that later transform into a smooth sheath. Our ancestral state reconstructions suggest with nearly 100% probability that the ancestral sipunculan had four introvert retractor muscles, longitudinal body wall musculature in bands and circular body wall musculature arranged as a smooth sheath. Species with crawling larvae have more strongly developed body wall musculature than those with swimming larvae. To interpret our findings in the context of annelid evolution, a more solid phylogenetic framework is needed for the entire group and more data on ontogenetic transformations of annelid musculature are desirable. PMID:19196337

  9. Advanced Intestinal Cancers often Maintain a Multi-Ancestral Architecture

    PubMed Central

    Zahm, Christopher D.; Szulczewski, Joseph M.; Leystra, Alyssa A.; Paul Olson, Terrah J.; Clipson, Linda; Albrecht, Dawn M.; Middlebrooks, Malisa; Thliveris, Andrew T.; Matkowskyj, Kristina A.; Washington, Mary Kay; Newton, Michael A.; Eliceiri, Kevin W.; Halberg, Richard B.

    2016-01-01

    A widely accepted paradigm in the field of cancer biology is that solid tumors are uni-ancestral being derived from a single founder and its descendants. However, data have been steadily accruing that indicate early tumors in mice and humans can have a multi-ancestral origin in which an initiated primogenitor facilitates the transformation of neighboring co-genitors. We developed a new mouse model that permits the determination of clonal architecture of intestinal tumors in vivo and ex vivo, have validated this model, and then used it to assess the clonal architecture of adenomas, intramucosal carcinomas, and invasive adenocarcinomas of the intestine. The percentage of multi-ancestral tumors did not significantly change as tumors progressed from adenomas with low-grade dysplasia [40/65 (62%)], to adenomas with high-grade dysplasia [21/37 (57%)], to intramucosal carcinomas [10/23 (43%]), to invasive adenocarcinomas [13/19 (68%)], indicating that the clone arising from the primogenitor continues to coexist with clones arising from co-genitors. Moreover, neoplastic cells from distinct clones within a multi-ancestral adenocarcinoma have even been observed to simultaneously invade into the underlying musculature [2/15 (13%)]. Thus, intratumoral heterogeneity arising early in tumor formation persists throughout tumorigenesis. PMID:26919712

  10. Are survival processing memory advantages based on ancestral priorities?

    PubMed

    Soderstrom, Nicholas C; McCabe, David P

    2011-06-01

    Recent research has suggested that our memory systems are especially tuned to process information according to its survival relevance, and that inducing problems of "ancestral priorities" faced by our ancestors should lead to optimal recall performance (Nairne & Pandeirada, Cognitive Psychology, 2010). The present study investigated the specificity of this idea by comparing an ancestor-consistent scenario and a modern survival scenario that involved threats that were encountered by human ancestors (e.g., predators) or threats from fictitious creatures (i.e., zombies). Participants read one of four survival scenarios in which the environment and the explicit threat were either consistent or inconsistent with ancestrally based problems (i.e., grasslands-predators, grasslands-zombies, city-attackers, city-zombies), or they rated words for pleasantness. After rating words based on their survival relevance (or pleasantness), the participants performed a free recall task. All survival scenarios led to better recall than did pleasantness ratings, but recall was greater when zombies were the threat, as compared to predators or attackers. Recall did not differ for the modern (i.e., city) and ancestral (i.e., grasslands) scenarios. These recall differences persisted when valence and arousal ratings for the scenarios were statistically controlled as well. These data challenge the specificity of ancestral priorities in survival-processing advantages in memory. PMID:21327372

  11. Reaching Children through Their Ancestral Language and Authentic Literature

    ERIC Educational Resources Information Center

    Bannon, Kay Thorpe

    2004-01-01

    In this article, the author describes a program of Eastern Cherokee ancestral language restoration in Cherokee, North Carolina. One of the primary goals of the program is to enhance the self-concept of the children and motivate the students to experience academic excitement and success. The use of authentic legends and stories is one method…

  12. Inferring ancient metabolism using ancestral core metabolic models of enterobacteria

    PubMed Central

    2013-01-01

    Background Enterobacteriaceae diversified from an ancestral lineage ~300-500 million years ago (mya) into a wide variety of free-living and host-associated lifestyles. Nutrient availability varies across niches, and evolution of metabolic networks likely played a key role in adaptation. Results Here we use a paleo systems biology approach to reconstruct and model metabolic networks of ancestral nodes of the enterobacteria phylogeny to investigate metabolism of ancient microorganisms and evolution of the networks. Specifically, we identified orthologous genes across genomes of 72 free-living enterobacteria (16 genera), and constructed core metabolic networks capturing conserved components for ancestral lineages leading to E. coli/Shigella (~10 mya), E. coli/Shigella/Salmonella (~100 mya), and all enterobacteria (~300-500 mya). Using these models we analyzed the capacity for carbon, nitrogen, phosphorous, sulfur, and iron utilization in aerobic and anaerobic conditions, identified conserved and differentiating catabolic phenotypes, and validated predictions by comparison to experimental data from extant organisms. Conclusions This is a novel approach using quantitative ancestral models to study metabolic network evolution and may be useful for identification of new targets to control infectious diseases caused by enterobacteria. PMID:23758866

  13. Isolation of ancestral sylvatic dengue virus type 1, Malaysia.

    PubMed

    Teoh, Boon-Teong; Sam, Sing-Sin; Abd-Jamil, Juraina; AbuBakar, Sazaly

    2010-11-01

    Ancestral sylvatic dengue virus type 1, which was isolated from a monkey in 1972, was isolated from a patient with dengue fever in Malaysia. The virus is neutralized by serum of patients with endemic DENV-1 infection. Rare isolation of this virus suggests a limited spillover infection from an otherwise restricted sylvatic cycle.

  14. A Multi-Functional Tubulovesicular Network as the Ancestral Eukaryotic Endomembrane System

    PubMed Central

    González-Sánchez, Juan Carlos; Costa, Ricardo; Devos, Damien P.

    2015-01-01

    The origin of the eukaryotic endomembrane system is still the subject of much speculation. We argue that the combination of two recent hypotheses addressing the eukaryotic endomembrane’s early evolution supports the possibility that the ancestral membranes were organised as a multi-functional tubulovesicular network. One of the potential selective advantages provided by this organisation was the capacity to perform endocytosis. This possibility is illustrated by membrane organisations observed in current organisms in the three domains of life. Based on this, we propose a coherent model of autogenous eukaryotic endomembrane system evolution in which mitochondria are involved at a late stage. PMID:25811639

  15. Subcomplexes of Ancestral Respiratory Complex I Subunits Rapidly Turn Over in Vivo as Productive Assembly Intermediates in Arabidopsis*

    PubMed Central

    Li, Lei; Nelson, Clark J.; Carrie, Chris; Gawryluk, Ryan M. R.; Solheim, Cory; Gray, Michael W.; Whelan, James; Millar, A. Harvey

    2013-01-01

    Subcomplexes of mitochondrial respiratory complex I (CI; EC 1.6.5.3) are shown to turn over in vivo, and we propose a role in an ancestral assembly pathway. By progressively labeling Arabidopsis cell cultures with 15N and isolating mitochondria, we have identified CI subcomplexes through differences in 15N incorporation into their protein subunits. The 200-kDa subcomplex, containing the ancestral γ-carbonic anhydrase (γ-CA), γ-carbonic anhydrase-like, and 20.9-kDa subunits, had a significantly higher turnover rate than intact CI or CI+CIII2. In vitro import of precursors for these CI subunits demonstrated rapid generation of subcomplexes and revealed that their specific abundance varied when different ancestral subunits were imported. Time course studies of precursor import showed the further assembly of these subcomplexes into CI and CI+CIII2, indicating that the subcomplexes are productive intermediates of assembly. The strong transient incorporation of new subunits into the 200-kDa subcomplex in a γ-CA mutant is consistent with this subcomplex being a key initiator of CI assembly in plants. This evidence alongside the pattern of coincident occurrence of genes encoding these particular proteins broadly in eukaryotes, except for opisthokonts, provides a framework for the evolutionary conservation of these accessory subunits and evidence of their function in ancestral CI assembly. PMID:23271729

  16. Solar energy conversion by green microalgae: a photosystem for hydrogen peroxide production.

    PubMed

    de la Rosa, F F; Montes, O; Galván, F

    2001-09-20

    A photosystem for solar energy conversion, comprised of a culture of green microalgae supplemented with methyl viologen, is proposed. The capture of solar energy is based on the Mehler reaction. The reduction of methyl viologen by the photosynthetic apparatus and its subsequent reoxidation by oxygen produces hydrogen peroxide. This is a rich-energy compound that can be used as a nonpollutant and efficient fuel. Four different species of green microalgae, Chlamydomonas reinhardtii (21gr) C. reinhardtii (CW15), Chlorella fusca, and Monoraphidium braunii, were tested as a possible biocatalyst. Each species presented a different efficiency level in the transformation of energy. Azide was an efficient inhibitor of the hydrogen peroxide scavenging system while maintaining photosynthetic activity of the microalgae, and thus significantly increasing the production of the photosystem. The strain C. reinhardtii (21gr), among the species studied, was the most efficient with an initial production rate of 185 micromol H(2)O(2)/h x mg Chl and reaching a maximum of 42.5 micromol H(2)O(2)/mg Chl when assayed in the presence of azide inhibitor. PMID:11494222

  17. Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for Xenarthra

    PubMed Central

    2012-01-01

    Background Xenarthra (sloths, armadillos and anteaters) represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. Results Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5, 6, 9, 11, 13, 14, 15, 17, 18, 20, 21 and the X chromosome). B. torquatus, three additional human chromosomes were conserved intact (HSA 1, 3 and 4). The remaining human chromosomes were represented by two or three segments on each sloth. Seven associations between human chromosomes were detected in the karyotypes of both B. torquatus and B. variegatus: HSA 3/21, 4/8, 7/10, 7/16, 12/22, 14/15 and 17/19. The ancestral Eutherian association 16/19 was not detected in the Bradypus species. Conclusions Our results together with previous reports enabled us to propose a hypothetical ancestral Xenarthran karyotype with 48 chromosomes that would differ from the proposed ancestral Eutherian karyotype by the presence of the association HSA 7/10 and by the split of HSA 8 into three blocks, instead of the two found in the Eutherian ancestor. These same chromosome features point to the monophyly of Xenarthra, making this the second supraorder of placental mammals to have a chromosome signature supporting its monophyly. PMID:22429690

  18. Amorphous Manganese-Calcium Oxides as a Possible Evolutionary Origin for the CaMn4 Cluster in Photosystem II

    NASA Astrophysics Data System (ADS)

    Najafpour, Mohammad Mahdi

    2011-06-01

    In this paper a few calcium-manganese oxides and calcium-manganese minerals are studied as catalysts for water oxidation. The natural mineral marokite is also studied as a catalyst for water oxidation for the first time. Marokite is made up of edge-sharing Mn3+ in a distorted octahedral environment and eight-coordinate Ca2+ centered polyhedral layers. The structure is similar to recent models of the oxygen evolving complex in photosystem II. Thus, the oxygen evolving complex in photosystem II does not have an unusual structure and could be synthesized hydrothermally. Also in this paper, oxygen evolution is studied with marokite (CaMn2O4), pyrolusite (MnO2) and compared with hollandite (Ba0.2Ca0.15K0.3Mn6.9Al0.2Si0.3O16), hausmannite (Mn3O4), Mn2O3.H2O, CaMn3O6.H2O, CaMn4O8.H2O, CaMn2O4.H2O and synthetic marokite (CaMn2O4). I propose that the origin of the oxygen evolving complex in photosystem II resulted from absorption of calcium and manganese ions that were precipitated together in the archean oceans by protocyanobacteria because of changing pH from ~5 to ~8-10. As reported in this paper, amorphous calcium-manganese oxides with different ratios of manganese and calcium are effective catalysts for water oxidation. The bond types and lengths of the calcium and manganese ions in the calcium-manganese oxides are directly comparable to those in the OEC. This primitive structure of these amorphous calcium-manganese compounds could be changed and modified by environmental groups (amino acids) to form the oxygen evolving complex in photosystem II.

  19. Functional implications on the mechanism of the function of photosystem II including water oxidation based on the structure of photosystem II.

    PubMed Central

    Fromme, Petra; Kern, Jan; Loll, Bernhard; Biesiadka, Jaceck; Saenger, Wolfram; Witt, Horst T; Krauss, Norbert; Zouni, Athina

    2002-01-01

    The structure of photosystem I at 3.8 A resolution illustrated the main structural elements of the water-oxidizing photosystem II complex, including the constituents of the electron transport chain. The location of the Mn cluster within the complex has been identified for the first time to our knowledge. At this resolution, no individual atoms are visible, however, the electron density of the Mn cluster can be used to discuss both the present models of the Mn cluster as revealed from various spectroscopic methods and the implications for the mechanisms of water oxidation. Twenty-six chlorophylls from the antenna system of photosystem II have been identified. They are arranged in two layers, one close to the stromal side and one close to the lumenal side. Comparing the structure of the antenna system of photosystem II with the chlorophyll arrangement in photosystem I, which was recently determined at 2.5 A resolution shows that photosystem II lacks the central domain of the photosystem I antenna, which is discussed in respect of the repair cycle of photosystem II due to photoinhibition. PMID:12437872

  20. Ancestral developmental potential facilitates parallel evolution in ants.

    PubMed

    Rajakumar, Rajendhran; San Mauro, Diego; Dijkstra, Michiel B; Huang, Ming H; Wheeler, Diana E; Hiou-Tim, Francois; Khila, Abderrahman; Cournoyea, Michael; Abouheif, Ehab

    2012-01-01

    Complex worker caste systems have contributed to the evolutionary success of advanced ant societies; however, little is known about the developmental processes underlying their origin and evolution. We combined hormonal manipulation, gene expression, and phylogenetic analyses with field observations to understand how novel worker subcastes evolve. We uncovered an ancestral developmental potential to produce a "supersoldier" subcaste that has been actualized at least two times independently in the hyperdiverse ant genus Pheidole. This potential has been retained and can be environmentally induced throughout the genus. Therefore, the retention and induction of this potential have facilitated the parallel evolution of supersoldiers through a process known as genetic accommodation. The recurrent induction of ancestral developmental potential may facilitate the adaptive and parallel evolution of phenotypes.

  1. Inferring ancestral sequences in taxon-rich phylogenies.

    PubMed

    Gascuel, Olivier; Steel, Mike

    2010-10-01

    Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, it is also useful to consider a dual type of statistical consistency where we increase the number of species, rather than characters. This raises some basic questions: what can we learn about the evolutionary process as we increase the number of species? In particular, does having more species allow us to infer the ancestral state of characters accurately? This question is particularly important when sequence evolution varies in a complex way from character to character, as methods applicable for i.i.d. models may no longer be valid. In this paper, we assemble a collection of results to analyse various approaches for inferring ancestral information with increasing accuracy as the number of taxa increases.

  2. Bilingualism (Ancestral Language Maintenance) among Native American, Vietnamese American, and Hispanic American College Students.

    ERIC Educational Resources Information Center

    Wharry, Cheryl

    1993-01-01

    A survey of 21 Hispanic, 22 Native American, and 10 Vietnamese American college students found that adoption or maintenance of ancestral language was related to attitudes toward ancestral language, beliefs about parental attitudes, and integrative motivation (toward family and ancestral ethnic group). There were significant differences by gender…

  3. Multiway admixture deconvolution using phased or unphased ancestral panels.

    PubMed

    Churchhouse, Claire; Marchini, Jonathan

    2013-01-01

    We describe a novel method for inferring the local ancestry of admixed individuals from dense genome-wide single nucleotide polymorphism data. The method, called MULTIMIX, allows multiple source populations, models population linkage disequilibrium between markers and is applicable to datasets in which the sample and source populations are either phased or unphased. The model is based upon a hidden Markov model of switches in ancestry between consecutive windows of loci. We model the observed haplotypes within each window using a multivariate normal distribution with parameters estimated from the ancestral panels. We present three methods to fit the model-Markov chain Monte Carlo sampling, the Expectation Maximization algorithm, and a Classification Expectation Maximization algorithm. The performance of our method on individuals simulated to be admixed with European and West African ancestry shows it to be comparable to HAPMIX, the ancestry calls of the two methods agreeing at 99.26% of loci across the three parameter groups. In addition to it being faster than HAPMIX, it is also found to perform well over a range of extent of admixture in a simulation involving three ancestral populations. In an analysis of real data, we estimate the contribution of European, West African and Native American ancestry to each locus in the Mexican samples of HapMap, giving estimates of ancestral proportions that are consistent with those previously reported. PMID:23136122

  4. Ancestral facial morphology of Old World higher primates.

    PubMed Central

    Benefit, B R; McCrossin, M L

    1991-01-01

    Fossil remains of the cercopithecoid Victoria-pithecus recently recovered from middle Miocene deposits of Maboko Island (Kenya) provide evidence of the cranial anatomy of Old World monkeys prior to the evolutionary divergence of the extant subfamilies Colobinae and Cercopithecinae. Victoria-pithecus shares a suite of craniofacial features with the Oligocene catarrhine Aegyptopithecus and early Miocene hominoid Afropithecus. All three genera manifest supraorbital costae, anteriorly convergent temporal lines, the absence of a postglabellar fossa, a moderate to long snout, great facial height below the orbits, a deep cheek region, and anteriorly tapering premaxilla. The shared presence of these features in a catarrhine generally ancestral to apes and Old World monkeys, an early ape, and an early Old World monkey indicates that they are primitive characteristics that typified the last common ancestor of Hominoidea and Cercopithecoidea. These results contradict prevailing cranial morphotype reconstructions for ancestral catarrhines as Colobus- or Hylobates-like, characterized by a globular anterior braincase and orthognathy. By resolving several equivocal craniofacial morphocline polarities, these discoveries lay the foundation for a revised interpretation of the ancestral cranial morphology of Catarrhini more consistent with neontological and existing paleontological evidence. Images PMID:2052606

  5. An ancestral bacterial division system is widespread in eukaryotic mitochondria.

    PubMed

    Leger, Michelle M; Petrů, Markéta; Žárský, Vojtěch; Eme, Laura; Vlček, Čestmír; Harding, Tommy; Lang, B Franz; Eliáš, Marek; Doležal, Pavel; Roger, Andrew J

    2015-08-18

    Bacterial division initiates at the site of a contractile Z-ring composed of polymerized FtsZ. The location of the Z-ring in the cell is controlled by a system of three mutually antagonistic proteins, MinC, MinD, and MinE. Plastid division is also known to be dependent on homologs of these proteins, derived from the ancestral cyanobacterial endosymbiont that gave rise to plastids. In contrast, the mitochondria of model systems such as Saccharomyces cerevisiae, mammals, and Arabidopsis thaliana seem to have replaced the ancestral α-proteobacterial Min-based division machinery with host-derived dynamin-related proteins that form outer contractile rings. Here, we show that the mitochondrial division system of these model organisms is the exception, rather than the rule, for eukaryotes. We describe endosymbiont-derived, bacterial-like division systems comprising FtsZ and Min proteins in diverse less-studied eukaryote protistan lineages, including jakobid and heterolobosean excavates, a malawimonad, stramenopiles, amoebozoans, a breviate, and an apusomonad. For two of these taxa, the amoebozoan Dictyostelium purpureum and the jakobid Andalucia incarcerata, we confirm a mitochondrial localization of these proteins by their heterologous expression in Saccharomyces cerevisiae. The discovery of a proteobacterial-like division system in mitochondria of diverse eukaryotic lineages suggests that it was the ancestral feature of all eukaryotic mitochondria and has been supplanted by a host-derived system multiple times in distinct eukaryote lineages.

  6. The association of the antenna system to photosystem I in higher plants. Cooperative interactions stabilize the supramolecular complex and enhance red-shifted spectral forms.

    PubMed

    Morosinotto, Tomas; Ballottari, Matteo; Klimmek, Frank; Jansson, Stefan; Bassi, Roberto

    2005-09-01

    We report on the association of the antenna system to the reaction center in Photosystem I. Biochemical analysis of mutants depleted in antenna polypeptides showed that the binding of the antenna moiety is strongly cooperative. The minimal building block for the antenna system was shown to be a dimer. Specific protein-protein interactions play an important role in antenna association, and the gap pigments, bound at the interface between core and antenna, are proposed to mediate these interactions Gap pigments have been characterized by comparing the spectra of the Photosystem I to those of the isolated antenna and core components. CD spectroscopy showed that they are involved in pigment-pigment interactions, supporting their relevance in energy transfer from antenna to the reaction center. Moreover, gap pigments contribute to the red-shifted emission forms of Photosystem I antenna. When compared with Photosystem II, the association of peripheral antenna complexes in PSI appears to be more stable, but far less flexible and functional implications are discussed.

  7. Chloramphenicol Mediates Superoxide Production in Photosystem II and Enhances Its Photodamage in Isolated Membrane Particles

    PubMed Central

    Rehman, Ateeq Ur; Kodru, Sandeesha; Vass, Imre

    2016-01-01

    Chloramphenicol (CAP) is an inhibitor of protein synthesis, which is frequently used to decouple photodamage and protein synthesis dependent repair of Photosystem II during the process of photoinhibition. It has been reported earlier that CAP is able to mediate superoxide production by transferring electrons from the acceptor side of Photosystem I to oxygen. Here we investigated the interaction of CAP with Photosystem II electron transport processes by oxygen uptake and variable chlorophyll fluorescence measurements. Our data show that CAP can accept electrons at the acceptor side of Photosystem II, most likely from Pheophytin, and deliver them to molecular oxygen leading to superoxide production. In addition, the presence of CAP enhances photodamage of Photosystem II electron transport in isolated membrane particles, which effect is reversible by superoxide dismutase. It is concluded that CAP acts as electron acceptor in Photosystem II and mediates its superoxide dependent photodamage. This effect has potential implications for the application of CAP in photoinhibitory studies in intact systems. PMID:27092170

  8. Wiring of Photosystem II to Hydrogenase for Photoelectrochemical Water Splitting.

    PubMed

    Mersch, Dirk; Lee, Chong-Yong; Zhang, Jenny Zhenqi; Brinkert, Katharina; Fontecilla-Camps, Juan C; Rutherford, A William; Reisner, Erwin

    2015-07-01

    In natural photosynthesis, light is used for the production of chemical energy carriers to fuel biological activity. The re-engineering of natural photosynthetic pathways can provide inspiration for sustainable fuel production and insights for understanding the process itself. Here, we employ a semiartificial approach to study photobiological water splitting via a pathway unavailable to nature: the direct coupling of the water oxidation enzyme, photosystem II, to the H2 evolving enzyme, hydrogenase. Essential to this approach is the integration of the isolated enzymes into the artificial circuit of a photoelectrochemical cell. We therefore developed a tailor-made hierarchically structured indium-tin oxide electrode that gives rise to the excellent integration of both photosystem II and hydrogenase for performing the anodic and cathodic half-reactions, respectively. When connected together with the aid of an applied bias, the semiartificial cell demonstrated quantitative electron flow from photosystem II to the hydrogenase with the production of H2 and O2 being in the expected two-to-one ratio and a light-to-hydrogen conversion efficiency of 5.4% under low-intensity red-light irradiation. We thereby demonstrate efficient light-driven water splitting using a pathway inaccessible to biology and report on a widely applicable in vitro platform for the controlled coupling of enzymatic redox processes to meaningfully study photocatalytic reactions.

  9. A requirement for EDTA in the separation of Photosystems 1 and 2 from the cyanobacterium Chlorogloea fritschii.

    PubMed

    Evans, E H; Pullin, C A

    1981-05-15

    Fractions enriched in Photosystem 1 or Photosystem 2 activity have been isolated from the cyanobacterium Chlorogloea fritschii after extraction of the membranes with digitonin and Triton X-100. Separation of the extract into the two components was achieved by using a Sepharose 6B column, calibration of which gave Kd values of 0.3 for the Photosystem 1 fraction and 0.53 for Photosystem 2. These values corresponded to molecular weights of approx. 500000 and 90000 respectively. The Photosystem 1 particle was shown to aggregate on storage and EDTA was shown to be necessary to separate the Photosystem 1 and 2 fractions.

  10. Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes

    PubMed Central

    Jung, Sook; Main, Dorrie; Staton, Margaret; Cho, Ilhyung; Zhebentyayeva, Tatyana; Arús, Pere; Abbott, Albert

    2006-01-01

    Background Due to the lack of availability of large genomic sequences for peach or other Prunus species, the degree of synteny conservation between the Prunus species and Arabidopsis has not been systematically assessed. Using the recently available peach EST sequences that are anchored to Prunus genetic maps and to peach physical map, we analyzed the extent of conserved synteny between the Prunus and the Arabidopsis genomes. The reconstructed pseudo-ancestral Arabidopsis genome, existed prior to the proposed recent polyploidy event, was also utilized in our analysis to further elucidate the evolutionary relationship. Results We analyzed the synteny conservation between the Prunus and the Arabidopsis genomes by comparing 475 peach ESTs that are anchored to Prunus genetic maps and their Arabidopsis homologs detected by sequence similarity. Microsyntenic regions were detected between all five Arabidopsis chromosomes and seven of the eight linkage groups of the Prunus reference map. An additional 1097 peach ESTs that are anchored to 431 BAC contigs of the peach physical map and their Arabidopsis homologs were also analyzed. Microsyntenic regions were detected in 77 BAC contigs. The syntenic regions from both data sets were short and contained only a couple of conserved gene pairs. The synteny between peach and Arabidopsis was fragmentary; all the Prunus linkage groups containing syntenic regions matched to more than two different Arabidopsis chromosomes, and most BAC contigs with multiple conserved syntenic regions corresponded to multiple Arabidopsis chromosomes. Using the same peach EST datasets and their Arabidopsis homologs, we also detected conserved syntenic regions in the pseudo-ancestral Arabidopsis genome. In many cases, the gene order and content of peach regions was more conserved in the ancestral genome than in the present Arabidopsis region. Statistical significance of each syntenic group was calculated using simulated Arabidopsis genome. Conclusion We

  11. Simultaneous measurements of photocurrents and H2O2 evolution from solvent exposed photosystem 2 complexes.

    PubMed

    Vöpel, Tobias; Ning Saw, En; Hartmann, Volker; Williams, Rhodri; Müller, Frank; Schuhmann, Wolfgang; Plumeré, Nicolas; Nowaczyk, Marc; Ebbinghaus, Simon; Rögner, Matthias

    2016-03-01

    In plants, algae, and cyanobacteria, photosystem 2 (PS2) catalyzes the light driven oxidation of water. The main products of this reaction are protons and molecular oxygen. In vitro, however, it was demonstrated that reactive oxygen species like hydrogen peroxide are obtained as partially reduced side products. The transition from oxygen to hydrogen peroxide evolution might be induced by light triggered degradation of PS2's active center. Herein, the authors propose an analytical approach to investigate light induced bioelectrocatalytic processes such as PS2 catalyzed water splitting. By combining chronoamperometry and fluorescence microscopy, the authors can simultaneously monitor the photocurrent and the hydrogen peroxide evolution of light activated, solvent exposed PS2 complexes, which have been immobilized on a functionalized gold electrode. The authors show that under limited electron mediation PS2 displays a lower photostability that correlates with an enhanced H2O2 generation as a side product of the light induced water oxidation. PMID:26700470

  12. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

    PubMed Central

    2011-01-01

    Background Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae. PMID:21226921

  13. QTL linkage analysis of connected populations using ancestral marker and pedigree information.

    PubMed

    Bink, Marco C A M; Totir, L Radu; ter Braak, Cajo J F; Winkler, Christopher R; Boer, Martin P; Smith, Oscar S

    2012-04-01

    The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals' genotype probability without significantly increasing computational demand.

  14. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates

    PubMed Central

    Peng, Jiguang; He, Bin Z.; Li, Yumei; Liu, Chu-Jun; Luan, Xuke; Ding, Wanqiu; Li, Shuxian; Chen, Chunyan; Tan, Bertrand Chin-Ming; Zhang, Yong E.; He, Aibin; Li, Chuan-Yun

    2015-01-01

    While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts. PMID:26177073

  15. Ancestral Components of Admixed Genomes in a Mexican Cohort

    PubMed Central

    Johnson, Nicholas A.; Coram, Marc A.; Shriver, Mark D.; Romieu, Isabelle; Barsh, Gregory S.; London, Stephanie J.; Tang, Hua

    2011-01-01

    For most of the world, human genome structure at a population level is shaped by interplay between ancient geographic isolation and more recent demographic shifts, factors that are captured by the concepts of biogeographic ancestry and admixture, respectively. The ancestry of non-admixed individuals can often be traced to a specific population in a precise region, but current approaches for studying admixed individuals generally yield coarse information in which genome ancestry proportions are identified according to continent of origin. Here we introduce a new analytic strategy for this problem that allows fine-grained characterization of admixed individuals with respect to both geographic and genomic coordinates. Ancestry segments from different continents, identified with a probabilistic model, are used to construct and study “virtual genomes” of admixed individuals. We apply this approach to a cohort of 492 parent–offspring trios from Mexico City. The relative contributions from the three continental-level ancestral populations—Africa, Europe, and America—vary substantially between individuals, and the distribution of haplotype block length suggests an admixing time of 10–15 generations. The European and Indigenous American virtual genomes of each Mexican individual can be traced to precise regions within each continent, and they reveal a gradient of Amerindian ancestry between indigenous people of southwestern Mexico and Mayans of the Yucatan Peninsula. This contrasts sharply with the African roots of African Americans, which have been characterized by a uniform mixing of multiple West African populations. We also use the virtual European and Indigenous American genomes to search for the signatures of selection in the ancestral populations, and we identify previously known targets of selection in other populations, as well as new candidate loci. The ability to infer precise ancestral components of admixed genomes will facilitate studies of disease

  16. Ancestral Origins and Genetic History of Tibetan Highlanders.

    PubMed

    Lu, Dongsheng; Lou, Haiyi; Yuan, Kai; Wang, Xiaoji; Wang, Yuchen; Zhang, Chao; Lu, Yan; Yang, Xiong; Deng, Lian; Zhou, Ying; Feng, Qidi; Hu, Ya; Ding, Qiliang; Yang, Yajun; Li, Shilin; Jin, Li; Guan, Yaqun; Su, Bing; Kang, Longli; Xu, Shuhua

    2016-09-01

    The origin of Tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. Analyses of deeply sequenced (30×-60×) genomes of 38 Tibetan highlanders and 39 Han Chinese lowlanders, together with available data on archaic and modern humans, allow us to comprehensively characterize the ancestral makeup of Tibetans and uncover their origins. Non-modern human sequences compose ∼6% of the Tibetan gene pool and form unique haplotypes in some genomic regions, where Denisovan-like, Neanderthal-like, ancient-Siberian-like, and unknown ancestries are entangled and elevated. The shared ancestry of Tibetan-enriched sequences dates back to ∼62,000-38,000 years ago, predating the Last Glacial Maximum (LGM) and representing early colonization of the plateau. Nonetheless, most of the Tibetan gene pool is of modern human origin and diverged from that of Han Chinese ∼15,000 to ∼9,000 years ago, which can be largely attributed to post-LGM arrivals. Analysis of ∼200 contemporary populations showed that Tibetans share ancestry with populations from East Asia (∼82%), Central Asia and Siberia (∼11%), South Asia (∼6%), and western Eurasia and Oceania (∼1%). Our results support that Tibetans arose from a mixture of multiple ancestral gene pools but that their origins are much more complicated and ancient than previously suspected. We provide compelling evidence of the co-existence of Paleolithic and Neolithic ancestries in the Tibetan gene pool, indicating a genetic continuity between pre-historical highland-foragers and present-day Tibetans. In particular, highly differentiated sequences harbored in highlanders' genomes were most likely inherited from pre-LGM settlers of multiple ancestral origins (SUNDer) and maintained in high frequency by natural selection.

  17. Ancestral Origins and Genetic History of Tibetan Highlanders.

    PubMed

    Lu, Dongsheng; Lou, Haiyi; Yuan, Kai; Wang, Xiaoji; Wang, Yuchen; Zhang, Chao; Lu, Yan; Yang, Xiong; Deng, Lian; Zhou, Ying; Feng, Qidi; Hu, Ya; Ding, Qiliang; Yang, Yajun; Li, Shilin; Jin, Li; Guan, Yaqun; Su, Bing; Kang, Longli; Xu, Shuhua

    2016-09-01

    The origin of Tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. Analyses of deeply sequenced (30×-60×) genomes of 38 Tibetan highlanders and 39 Han Chinese lowlanders, together with available data on archaic and modern humans, allow us to comprehensively characterize the ancestral makeup of Tibetans and uncover their origins. Non-modern human sequences compose ∼6% of the Tibetan gene pool and form unique haplotypes in some genomic regions, where Denisovan-like, Neanderthal-like, ancient-Siberian-like, and unknown ancestries are entangled and elevated. The shared ancestry of Tibetan-enriched sequences dates back to ∼62,000-38,000 years ago, predating the Last Glacial Maximum (LGM) and representing early colonization of the plateau. Nonetheless, most of the Tibetan gene pool is of modern human origin and diverged from that of Han Chinese ∼15,000 to ∼9,000 years ago, which can be largely attributed to post-LGM arrivals. Analysis of ∼200 contemporary populations showed that Tibetans share ancestry with populations from East Asia (∼82%), Central Asia and Siberia (∼11%), South Asia (∼6%), and western Eurasia and Oceania (∼1%). Our results support that Tibetans arose from a mixture of multiple ancestral gene pools but that their origins are much more complicated and ancient than previously suspected. We provide compelling evidence of the co-existence of Paleolithic and Neolithic ancestries in the Tibetan gene pool, indicating a genetic continuity between pre-historical highland-foragers and present-day Tibetans. In particular, highly differentiated sequences harbored in highlanders' genomes were most likely inherited from pre-LGM settlers of multiple ancestral origins (SUNDer) and maintained in high frequency by natural selection. PMID:27569548

  18. Ancestral components of admixed genomes in a Mexican cohort.

    PubMed

    Johnson, Nicholas A; Coram, Marc A; Shriver, Mark D; Romieu, Isabelle; Barsh, Gregory S; London, Stephanie J; Tang, Hua

    2011-12-01

    For most of the world, human genome structure at a population level is shaped by interplay between ancient geographic isolation and more recent demographic shifts, factors that are captured by the concepts of biogeographic ancestry and admixture, respectively. The ancestry of non-admixed individuals can often be traced to a specific population in a precise region, but current approaches for studying admixed individuals generally yield coarse information in which genome ancestry proportions are identified according to continent of origin. Here we introduce a new analytic strategy for this problem that allows fine-grained characterization of admixed individuals with respect to both geographic and genomic coordinates. Ancestry segments from different continents, identified with a probabilistic model, are used to construct and study "virtual genomes" of admixed individuals. We apply this approach to a cohort of 492 parent-offspring trios from Mexico City. The relative contributions from the three continental-level ancestral populations-Africa, Europe, and America-vary substantially between individuals, and the distribution of haplotype block length suggests an admixing time of 10-15 generations. The European and Indigenous American virtual genomes of each Mexican individual can be traced to precise regions within each continent, and they reveal a gradient of Amerindian ancestry between indigenous people of southwestern Mexico and Mayans of the Yucatan Peninsula. This contrasts sharply with the African roots of African Americans, which have been characterized by a uniform mixing of multiple West African populations. We also use the virtual European and Indigenous American genomes to search for the signatures of selection in the ancestral populations, and we identify previously known targets of selection in other populations, as well as new candidate loci. The ability to infer precise ancestral components of admixed genomes will facilitate studies of disease

  19. Visual system evolution and the nature of the ancestral snake.

    PubMed

    Simões, B F; Sampaio, F L; Jared, C; Antoniazzi, M M; Loew, E R; Bowmaker, J K; Rodriguez, A; Hart, N S; Hunt, D M; Partridge, J C; Gower, D J

    2015-07-01

    The dominant hypothesis for the evolutionary origin of snakes from 'lizards' (non-snake squamates) is that stem snakes acquired many snake features while passing through a profound burrowing (fossorial) phase. To investigate this, we examined the visual pigments and their encoding opsin genes in a range of squamate reptiles, focusing on fossorial lizards and snakes. We sequenced opsin transcripts isolated from retinal cDNA and used microspectrophotometry to measure directly the spectral absorbance of the photoreceptor visual pigments in a subset of samples. In snakes, but not lizards, dedicated fossoriality (as in Scolecophidia and the alethinophidian Anilius scytale) corresponds with loss of all visual opsins other than RH1 (λmax 490-497 nm); all other snakes (including less dedicated burrowers) also have functional sws1 and lws opsin genes. In contrast, the retinas of all lizards sampled, even highly fossorial amphisbaenians with reduced eyes, express functional lws, sws1, sws2 and rh1 genes, and most also express rh2 (i.e. they express all five of the visual opsin genes present in the ancestral vertebrate). Our evidence of visual pigment complements suggests that the visual system of stem snakes was partly reduced, with two (RH2 and SWS2) of the ancestral vertebrate visual pigments being eliminated, but that this did not extend to the extreme additional loss of SWS1 and LWS that subsequently occurred (probably independently) in highly fossorial extant scolecophidians and A. scytale. We therefore consider it unlikely that the ancestral snake was as fossorial as extant scolecophidians, whether or not the latter are para- or monophyletic.

  20. Carotenoid-induced quenching of the phycobilisome fluorescence in photosystem II-deficient mutant of Synechocystis sp.

    PubMed

    Rakhimberdieva, Marina G; Stadnichuk, Igor N; Elanskaya, Irina V; Karapetyan, Navassard V

    2004-09-10

    Brief--10-second long--irradiation of a photosystem II-deficient mutant of cyanobacterium Synechocystis sp. PCC 6803 with intense blue or UV-B light causes an about 40% decrease of phycobilisome (PBS) fluorescence, slowly reversible in the dark. The registered action spectrum of PBS fluorescence quenching only shows bands at 500, 470 and 430 nm, typical of carotenoids, and an additional UV-B band; no peaks in the region of chlorophyll or PBS absorption have been found. We propose that quenching induced by carotenoids, possibly protein-bound or glycoside, reveals a new regulatory mechanism protecting photosynthetic apparatus of cyanobacteria against photodamage.

  1. Direct assignment of vitamin K sub 1 as the secondary acceptor A sub 1 in photosystem I

    SciTech Connect

    Snyder, S.W.; Thurnauer, M.C. ); Rustandi, R.R.; Norris, J.R. Univ. of Chicago, IL ); Biggins, J. )

    1991-11-01

    The characteristic electron spin polarized electron paramagnetic resonance (ESP EPR) signal observed in photosystem I (PSI) has been previously assigned to a radical pair composed of the oxidized primary donor and a reduced vitamin K{sub 1}. Under conditions in which Bottin, H. and Setif, P. proposed that A{sub 1}, is doubly reduced, the ESP EPR signal was not observed. Therefore, the ESP EPR signal can be directly attributed to A{sub 1}{sup {minus}}, and vitamin K{sub 1} can be assigned as this PSI acceptor. The ESP EPR signal was partially restored by removal of the chemical reductants.

  2. Reflections on ancestral haplotypes: medical genomics, evolution, and human individuality.

    PubMed

    Steele, Edward J

    2014-01-01

    The major histocompatibility complex (MHC), once labelled the "sphinx of immunology" by Jan Klein, provides powerful challenges to evolutionary thinking. This essay highlights the main discoveries that established the block ancestral haplotype structure of the MHC and the wider genome, focusing on the work by the Perth (Australia) group, led by Roger Dawkins, and the Boston group, led by Chester Alper and Edmond Yunis. Their achievements have been overlooked in the rush to sequence the first and subsequent drafts of the human genome. In Caucasoids, where most of the detailed work has been done, about 70% of all known allelic MHC diversity can be accounted for by 30 or so ancestral haplotypes (AHs), or conserved sequences of many mega-bases, and their recombinants. The block haplotype structure of the genome, as shown for the MHC (and other genetic regions), is a story that needs to be understood in its own right, particularly given the promotion of the "HapMap" project and single nucleotide polymorphism (SNP) linkage disequilibrium (LD) analysis, which has been wrongly touted as the only way to pinpoint those genes that are important in genetic disorders or other desired (qualitative) characteristics. PMID:25544323

  3. Evidence from opsin genes rejects nocturnality in ancestral primates

    PubMed Central

    Tan, Ying; Yoder, Anne D.; Yamashita, Nayuta; Li, Wen-Hsiung

    2005-01-01

    It is firmly believed that ancestral primates were nocturnal, with nocturnality having been maintained in most prosimian lineages. Under this traditional view, the opsin genes in all nocturnal prosimians should have undergone similar degrees of functional relaxation and accumulated similar extents of deleterious mutations. This expectation is rejected by the short-wavelength (S) opsin gene sequences from 14 representative prosimians. We found severe defects of the S opsin gene only in lorisiforms, but no defect in five nocturnal and two diurnal lemur species and only minor defects in two tarsiers and two nocturnal lemurs. Further, the nonsynonymous-to-synonymous rate ratio of the S opsin gene is highest in the lorisiforms and varies among the other prosimian branches, indicating different time periods of functional relaxation among lineages. These observations suggest that the ancestral primates were diurnal or cathemeral and that nocturnality has evolved several times in the prosimians, first in the lorisiforms but much later in other lineages. This view is further supported by the distribution pattern of the middle-wavelength (M) and long-wavelength (L) opsin genes among prosimians. PMID:16192351

  4. Functional conservation of an ancestral Pellino protein in helminth species.

    PubMed

    Cluxton, Christopher D; Caffrey, Brian E; Kinsella, Gemma K; Moynagh, Paul N; Fares, Mario A; Fallon, Padraic G

    2015-01-01

    The immune system of H. sapiens has innate signaling pathways that arose in ancestral species. This is exemplified by the discovery of the Toll-like receptor (TLR) pathway using free-living model organisms such as Drosophila melanogaster. The TLR pathway is ubiquitous and controls sensitivity to pathogen-associated molecular patterns (PAMPs) in eukaryotes. There is, however, a marked absence of this pathway from the plathyhelminthes, with the exception of the Pellino protein family, which is present in a number of species from this phylum. Helminth Pellino proteins are conserved having high similarity, both at the sequence and predicted structural protein level, with that of human Pellino proteins. Pellino from a model helminth, Schistosoma mansoni Pellino (SmPellino), was shown to bind and poly-ubiquitinate human IRAK-1, displaying E3 ligase activity consistent with its human counterparts. When transfected into human cells SmPellino is functional, interacting with signaling proteins and modulating mammalian signaling pathways. Strict conservation of a protein family in species lacking its niche signalling pathway is rare and provides a platform to examine the ancestral functions of Pellino proteins that may translate into novel mechanisms of immune regulation in humans. PMID:26120048

  5. Functional conservation of an ancestral Pellino protein in helminth species.

    PubMed

    Cluxton, Christopher D; Caffrey, Brian E; Kinsella, Gemma K; Moynagh, Paul N; Fares, Mario A; Fallon, Padraic G

    2015-01-01

    The immune system of H. sapiens has innate signaling pathways that arose in ancestral species. This is exemplified by the discovery of the Toll-like receptor (TLR) pathway using free-living model organisms such as Drosophila melanogaster. The TLR pathway is ubiquitous and controls sensitivity to pathogen-associated molecular patterns (PAMPs) in eukaryotes. There is, however, a marked absence of this pathway from the plathyhelminthes, with the exception of the Pellino protein family, which is present in a number of species from this phylum. Helminth Pellino proteins are conserved having high similarity, both at the sequence and predicted structural protein level, with that of human Pellino proteins. Pellino from a model helminth, Schistosoma mansoni Pellino (SmPellino), was shown to bind and poly-ubiquitinate human IRAK-1, displaying E3 ligase activity consistent with its human counterparts. When transfected into human cells SmPellino is functional, interacting with signaling proteins and modulating mammalian signaling pathways. Strict conservation of a protein family in species lacking its niche signalling pathway is rare and provides a platform to examine the ancestral functions of Pellino proteins that may translate into novel mechanisms of immune regulation in humans.

  6. Functional conservation of an ancestral Pellino protein in helminth species

    PubMed Central

    Cluxton, Christopher D.; Caffrey, Brian E.; Kinsella, Gemma K.; Moynagh, Paul N.; Fares, Mario A.; Fallon, Padraic G.

    2015-01-01

    The immune system of H. sapiens has innate signaling pathways that arose in ancestral species. This is exemplified by the discovery of the Toll-like receptor (TLR) pathway using free-living model organisms such as Drosophila melanogaster. The TLR pathway is ubiquitous and controls sensitivity to pathogen-associated molecular patterns (PAMPs) in eukaryotes. There is, however, a marked absence of this pathway from the plathyhelminthes, with the exception of the Pellino protein family, which is present in a number of species from this phylum. Helminth Pellino proteins are conserved having high similarity, both at the sequence and predicted structural protein level, with that of human Pellino proteins. Pellino from a model helminth, Schistosoma mansoni Pellino (SmPellino), was shown to bind and poly-ubiquitinate human IRAK-1, displaying E3 ligase activity consistent with its human counterparts. When transfected into human cells SmPellino is functional, interacting with signaling proteins and modulating mammalian signaling pathways. Strict conservation of a protein family in species lacking its niche signalling pathway is rare and provides a platform to examine the ancestral functions of Pellino proteins that may translate into novel mechanisms of immune regulation in humans. PMID:26120048

  7. Evidence from opsin genes rejects nocturnality in ancestral primates.

    PubMed

    Tan, Ying; Yoder, Anne D; Yamashita, Nayuta; Li, Wen-Hsiung

    2005-10-11

    It is firmly believed that ancestral primates were nocturnal, with nocturnality having been maintained in most prosimian lineages. Under this traditional view, the opsin genes in all nocturnal prosimians should have undergone similar degrees of functional relaxation and accumulated similar extents of deleterious mutations. This expectation is rejected by the short-wavelength (S) opsin gene sequences from 14 representative prosimians. We found severe defects of the S opsin gene only in lorisiforms, but no defect in five nocturnal and two diurnal lemur species and only minor defects in two tarsiers and two nocturnal lemurs. Further, the nonsynonymous-to-synonymous rate ratio of the S opsin gene is highest in the lorisiforms and varies among the other prosimian branches, indicating different time periods of functional relaxation among lineages. These observations suggest that the ancestral primates were diurnal or cathemeral and that nocturnality has evolved several times in the prosimians, first in the lorisiforms but much later in other lineages. This view is further supported by the distribution pattern of the middle-wavelength (M) and long-wavelength (L) opsin genes among prosimians.

  8. On-chip functionalization of carbon nanotubes with photosystem I.

    PubMed

    Kaniber, Simone M; Brandstetter, Matthias; Simmel, Friedrich C; Carmeli, Itai; Holleitner, Alexander W

    2010-03-10

    We optoelectronically functionalize carbon nanotubes (CNTs) with the photosynthetic reaction center photosystem I (PSI) according to three different on-chip chemical routes. The PSI is bound to the CNTs via covalent, hydrogen, or electrostatic bonds. Our approach allows the electrical contact of single PSI-CNT hybrid systems where the orientation of the PSI with respect to the CNTs depends on the binding mechanism. Our data are consistent with the interpretation that if the PSI is anchored with its internal electron transport path perpendicular to CNTs, the optical excitation of the PSI leads to an enhanced photoconductance of the hybrid system. PMID:20148524

  9. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

    PubMed Central

    Baldwin, Maude W.; Toda, Yasuka; Nakagita, Tomoya; O'Connell, Mary J.; Klasing, Kirk C.; Misaka, Takumi; Edwards, Scott V.; Liberles, Stephen D.

    2015-01-01

    Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies revealed that the ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in hummingbirds to function as a carbohydrate receptor. Furthermore, the molecular recognition properties of T1R1-T1R3 guided taste behavior in captive and wild hummingbirds. We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar, facilitating the massive radiation of hummingbird species. PMID:25146290

  10. Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor.

    PubMed

    Baldwin, Maude W; Toda, Yasuka; Nakagita, Tomoya; O'Connell, Mary J; Klasing, Kirk C; Misaka, Takumi; Edwards, Scott V; Liberles, Stephen D

    2014-08-22

    Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies revealed that the ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in hummingbirds to function as a carbohydrate receptor. Furthermore, the molecular recognition properties of T1R1-T1R3 guided taste behavior in captive and wild hummingbirds. We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar, facilitating the massive radiation of hummingbird species.

  11. Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor.

    PubMed

    Baldwin, Maude W; Toda, Yasuka; Nakagita, Tomoya; O'Connell, Mary J; Klasing, Kirk C; Misaka, Takumi; Edwards, Scott V; Liberles, Stephen D

    2014-08-22

    Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies revealed that the ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in hummingbirds to function as a carbohydrate receptor. Furthermore, the molecular recognition properties of T1R1-T1R3 guided taste behavior in captive and wild hummingbirds. We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar, facilitating the massive radiation of hummingbird species. PMID:25146290

  12. Identification of presumed ancestral DNA sequences of phaseolin in Phaseolus vulgaris.

    PubMed Central

    Kami, J; Velásquez, V B; Debouck, D G; Gepts, P

    1995-01-01

    Common bean (Phaseolus vulgaris) consists of two major geographic gene pools, one distributed in Mexico, Central America, and Colombia and the other in the southern Andes (southern Peru, Bolivia, and Argentina). Amplification and sequencing of members of the multigene family coding for phaseolin, the major seed storage protein of the common bean, provide evidence for accumulation of tandem direct repeats in both introns and exons during evolution of the multigene family in this species. The presumed ancestral phaseolin sequences, without tandem repeats, were found in recently discovered but nearly extinct wild common bean populations of Ecuador and northern Peru that are intermediate between the two major gene pools of the species based on geographical and molecular arguments. Our results illustrate the usefulness of tandem direct repeats in establishing the polarity of DNA sequence divergence and therefore in proposing phylogenies. Images Fig. 1 Fig. 3 PMID:7862642

  13. Light harvesting in photosystem I: modeling based on the 2.5-A structure of photosystem I from Synechococcus elongatus.

    PubMed

    Byrdin, Martin; Jordan, Patrick; Krauss, Norbert; Fromme, Petra; Stehlik, Dietmar; Schlodder, Eberhard

    2002-07-01

    The structure of photosystem I from the thermophilic cyanobacterium Synechococcus elongatus has been recently resolved by x-ray crystallography to 2.5-A resolution. Besides the reaction center, photosystem I consists also of a core antenna containing 90 chlorophyll and 22 carotenoid molecules. It is their function to harvest solar energy and to transfer this energy to the reaction center (RC) where the excitation energy is converted into a charge separated state. Methods of steady-state optical spectroscopy such as absorption, linear, and circular dichroism have been applied to obtain information on the spectral properties of the complex, whereas transient absorption and fluorescence studies reported in the literature provide information on the dynamics of the excitation energy transfer. On the basis of the structure, the spectral properties and the energy transfer kinetics are simultaneously modeled by application of excitonic coupling theory to reveal relationships between structure and function. A spectral assignment of the 96 chlorophylls is suggested that allows us to reproduce both optical spectra and transfer and emission spectra and lifetimes of the photosystem I complex from S. elongatus. The model calculation allowed to study the influence of the following parameters on the excited state dynamics: the orientation factor, the heterogeneous site energies, the modifications arising from excitonic coupling (redistribution of oscillator strength, energetic splitting, reorientation of transition dipoles), and presence or absence of the linker cluster chlorophylls between antenna and reaction center. For the Förster radius and the intrinsic primary charge separation rate, the following values have been obtained: R(0) = 7.8 nm and k(CS) = 0.9 ps(-1). Variations of these parameters indicate that the excited state dynamics is neither pure trap limited, nor pure transfer (to-the-trap) limited but seems to be rather balanced.

  14. Growth under Red Light Enhances Photosystem II Relative to Photosystem I and Phycobilisomes in the Red Alga Porphyridium cruentum.

    PubMed

    Cunningham, F X; Dennenberg, R J; Jursinic, P A; Gantt, E

    1990-07-01

    Acclimation of the photosynthetic apparatus to light absorbed primarily by photosystem I (PSI) or by photosystem II (PSII) was studied in the unicellular red alga Porphyridium cruentum (ATCC 50161). Cultures grown under green light of 15 microeinsteins per square meter per second (PSII light; absorbed predominantly by the phycobilisomes) exhibited a PSII/PSI ratio of 0.26 +/- 0.05. Under red light (PSI light; absorbed primarily by chlorophyll) of comparable quantum flux, cells contained nearly five times as many PSII per PSI (1.21 +/- 0.10), and three times as many PSII per cell. About 12% of the chlorophyll was attributed to PSII in green light, 22% in white light, and 39% in red light-grown cultures. Chlorophyll antenna sizes appeared to remain constant at about 75 chlorophyll per PSII and 140 per PSI. Spectral quality had little effect on cell content or composition of the phycobilisomes, thus the number of PSII per phycobilisome was substantially greater in red light-grown cultures (4.2 +/- 0.6) than in those grown under green (1.6 +/- 0.3) or white light (2.9 +/- 0.1). Total photosystems (PSI + PSII) per phycobilisome remained at about eight in each case. Carotenoid content and composition was little affected by the spectral composition of the growth light. Zeaxanthin comprised more than 50% (mole/mole), beta-carotene about 40%, and cryptoxanthin about 4% of the carotenoid pigment. Despite marked changes in the light-harvesting apparatus, red and green light-grown cultures have generation times equal to that of cultures grown under white light of only one-third the quantum flux.

  15. Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25

    PubMed Central

    Ventura, Mario; Mudge, Jonathan M.; Palumbo, Valeria; Burn, Sally; Blennow, Elisabeth; Pierluigi, Mauro; Giorda, Roberto; Zuffardi, Orsetta; Archidiacono, Nicoletta; Jackson, Michael S.; Rocchi, Mariano

    2003-01-01

    The existence of latent centromeres has been proposed as a possible explanation for the ectopic emergence of neocentromeres in humans. This hypothesis predicts an association between the position of neocentromeres and the position of ancient centromeres inactivated during karyotypic evolution. Human chromosomal region 15q24-26 is one of several hotspots where multiple cases of neocentromere emergence have been reported, and it harbors a high density of chromosome-specific duplicons, rearrangements of which have been implicated as a susceptibility factor for panic and phobic disorders with joint laxity. We investigated the evolutionary history of this region in primates and found that it contains the site of an ancestral centromere which became inactivated about 25 million years ago, after great apes/Old World monkeys diverged. This inactivation has followed a noncentromeric chromosomal fission of an ancestral chromosome which gave rise to phylogenetic chromosomes XIV and XV in human and great apes. Detailed mapping of the ancient centromere and two neocentromeres in 15q24-26 has established that the neocentromere domains map approximately 8 Mb proximal and 1.5 Mb distal of the ancestral centromeric region, but that all three map within 500 kb of duplicons, copies of which flank the centromere in Old World Monkey species. This suggests that the association between neocentromere and ancestral centromere position on this chromosome may be due to the persistence of recombinogenic duplications accrued within the ancient pericentromere, rather than the retention of “centromere-competent” sequences per se. The high frequency of neocentromere emergence in the 15q24-26 region and the high density of clinically important duplicons are, therefore, understandable in the light of the evolutionary history of this region. PMID:12915487

  16. Fluorescence changes accompanying short-term light adaptations in photosystem I and photosystem II of the cyanobacterium Synechocystis sp. PCC 6803 and phycobiliprotein-impaired mutants: State 1/State 2 transitions and carotenoid-induced quenching of phycobilisomes.

    PubMed

    Stadnichuk, Igor N; Lukashev, Evgeny P; Elanskaya, Irina V

    2009-03-01

    The features of the two types of short-term light-adaptations of photosynthetic apparatus, State 1/State 2 transitions, and non-photochemical fluorescence quenching of phycobilisomes (PBS) by orange carotene-protein (OCP) were compared in the cyanobacterium Synechocystis sp. PCC 6803 wild type, CK pigment mutant lacking phycocyanin, and PAL mutant totally devoid of phycobiliproteins. The permanent presence of PBS-specific peaks in the in situ action spectra of photosystem I (PSI) and photosystem II (PSII), as well as in the 77 K fluorescence excitation spectra for chlorophyll emission at 690 nm (PSII) and 725 nm (PSI) showed that PBS are constitutive antenna complexes of both photosystems. The mutant strains compensated the lack of phycobiliproteins by higher PSII content and by intensification of photosynthetic linear electron transfer. The detectable changes of energy migration from PBS to the PSI and PSII in the Synechocystis wild type and the CK mutant in State 1 and State 2 according to the fluorescence excitation spectra measurements were not registered. The constant level of fluorescence emission of PSI during State 1/State 2 transitions and simultaneous increase of chlorophyll fluorescence emission of PSII in State 1 in Synechocystis PAL mutant allowed to propose that spillover is an unlikely mechanism of state transitions. Blue-green light absorbed by OCP diminished the rout of energy from PBS to PSI while energy migration from PBS to PSII was less influenced. Therefore, the main role of OCP-induced quenching of PBS is the limitation of PSI activity and cyclic electron transport under relatively high light conditions.

  17. Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites

    PubMed Central

    2012-01-01

    Background The computational prediction of Transcription Factor Binding Sites (TFBS) remains a challenge due to their short length and low information content. Comparative genomics approaches that simultaneously consider several related species and favor sites that have been conserved throughout evolution improve the accuracy (specificity) of the predictions but are limited due to a phenomenon called binding site turnover, where sequence evolution causes one TFBS to replace another in the same region. In parallel to this development, an increasing number of mammalian genomes are now sequenced and it is becoming possible to infer, to a surprisingly high degree of accuracy, ancestral mammalian sequences. Results We propose a TFBS prediction approach that makes use of the availability of inferred ancestral mammalian genomes to improve its accuracy. This method aims to identify binding loci, which are regions of a few hundred base pairs that have preserved their potential to bind a given transcription factor over evolutionary time. After proposing a neutral evolutionary model of predicted TFBS counts in a DNA region of a given length, we use it to identify regions that have preserved the number of predicted TFBS they contain to an unexpected degree given their divergence. The approach is applied to human chromosome 1 and shows significant gains in accuracy as compared to both existing single-species and multi-species TFBS prediction approaches, in particular for transcription factors that are subject to high turnover rates. Availability The source code and predictions made by the program are available at http://www.cs.mcgill.ca/~blanchem/bindingLoci. PMID:23281809

  18. FastML: a web server for probabilistic reconstruction of ancestral sequences.

    PubMed

    Ashkenazy, Haim; Penn, Osnat; Doron-Faigenboim, Adi; Cohen, Ofir; Cannarozzi, Gina; Zomer, Oren; Pupko, Tal

    2012-07-01

    Ancestral sequence reconstruction is essential to a variety of evolutionary studies. Here, we present the FastML web server, a user-friendly tool for the reconstruction of ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in which each gap, possibly spanning multiples sites, is coded as binary data. FastML then reconstructs ancestral indel states assuming a continuous time Markov process. FastML provides the most likely ancestral sequences, integrating both indels and characters; (ii) FastML accounts for uncertainty in ancestral states: it provides not only the posterior probabilities for each character and indel at each sequence position, but also a sample of ancestral sequences from this posterior distribution, and a list of the k-most likely ancestral sequences; (iii) FastML implements a large array of evolutionary models, which makes it generic and applicable for nucleotide, protein and codon sequences; and (iv) a graphical representation of the results is provided, including, for example, a graphical logo of the inferred ancestral sequences. The utility of FastML is demonstrated by reconstructing ancestral sequences of the Env protein from various HIV-1 subtypes. FastML is freely available for all academic users and is available online at http://fastml.tau.ac.il/.

  19. Structural analysis of photosystem I polypeptides using chemical crosslinking

    NASA Technical Reports Server (NTRS)

    Armbrust, T. S.; Odom, W. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

    1994-01-01

    Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

  20. Structure and energy transfer in photosystems of oxygenic photosynthesis.

    PubMed

    Nelson, Nathan; Junge, Wolfgang

    2015-01-01

    Oxygenic photosynthesis is the principal converter of sunlight into chemical energy on Earth. Cyanobacteria and plants provide the oxygen, food, fuel, fibers, and platform chemicals for life on Earth. The conversion of solar energy into chemical energy is catalyzed by two multisubunit membrane protein complexes, photosystem I (PSI) and photosystem II (PSII). Light is absorbed by the pigment cofactors, and excitation energy is transferred among the antennae pigments and converted into chemical energy at very high efficiency. Oxygenic photosynthesis has existed for more than three billion years, during which its molecular machinery was perfected to minimize wasteful reactions. Light excitation transfer and singlet trapping won over fluorescence, radiation-less decay, and triplet formation. Photosynthetic reaction centers operate in organisms ranging from bacteria to higher plants. They are all evolutionarily linked. The crystal structure determination of photosynthetic protein complexes sheds light on the various partial reactions and explains how they are protected against wasteful pathways and why their function is robust. This review discusses the efficiency of photosynthetic solar energy conversion.

  1. Diversity of viral photosystem-I psaA genes

    PubMed Central

    Hevroni, Gur; Enav, Hagay; Rohwer, Forest; Béjà, Oded

    2015-01-01

    Marine photosynthesis is one of the major contributors to the global carbon cycle and the world's oxygen supply. This process is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding photosystem-II (PSII) reaction center proteins are found in many cyanophage genomes, and are expressed during the infection of their hosts. On the basis of metagenomics, cyanophage photosystem-I (PSI) gene cassettes were recently discovered with two gene arrangements psaJF→C→A→B→K→E→D and psaD→C→A→B. It was suggested that the horizontal transfer of PSII and PSI genes is increasing phage fitness. To better understand their diversity, we designed degenerate primers to cover a wide diversity of organisms, and using PCR we targeted the psaC→A arrangement, which is unique to cyanophages cassettes. We examined viral concentrates from four islands in the Pacific Ocean and found samples containing the psaC→A arrangement. Analyses of the amplified viral psaA gene revealed six subgroups varying in their level of similarity and %G+C content, suggesting that the diversity of cyanophage PSI genes is greater than originally thought. PMID:25535938

  2. Switchable photosystem-II designer algae for photobiological hydrogen production

    DOEpatents

    Lee, James Weifu

    2010-01-05

    A switchable photosystem-II designer algae for photobiological hydrogen production. The designer transgenic algae includes at least two transgenes for enhanced photobiological H.sub.2 production wherein a first transgene serves as a genetic switch that can controls photosystem II (PSII) oxygen evolution and a second transgene encodes for creation of free proton channels in the algal photosynthetic membrane. In one embodiment, the algae includes a DNA construct having polymerase chain reaction forward primer (302), a inducible promoter (304), a PSII-iRNA sequence (306), a terminator (308), and a PCR reverse primer (310). In other embodiments, the PSII-iRNA sequence (306) is replaced with a CF.sub.1-iRNA sequence (312), a streptomycin-production gene (314), a targeting sequence (316) followed by a proton-channel producing gene (318), or a PSII-producing gene (320). In one embodiment, a photo-bioreactor and gas-product separation and utilization system produce photobiological H.sub.2 from the switchable PSII designer alga.

  3. O2 evolution and cyclic electron flow around photosystem I in long-term ground batch culture of Euglena gracilis

    NASA Astrophysics Data System (ADS)

    An, Yanjun; Wang, Suqin; Hao, Zongjie; Zhou, Yiyong; Liu, Yongding

    2014-12-01

    Based on the purpose of better exploring the function of green producers in the closed aquatic biological life support system, the condition of dynamic O2 evolution and performance of cyclic electron flow around photosystem I (CEF-PSI) in long-term ground batch culture of Euglena gracilis were studied, the relationship between linear electron flow (LEF) and CEF-PSI was revealed, the function of CEF-PSI was investigated. Excellent consistency in O2 evolution pattern was observed in cultures grown in both closed and open containers, O2 evolution was strictly suppressed in phase 1, but the rate of it increased significantly in phase 2. CEF-PSI was proposed to be active during the whole course of cultivation, even in the declining phase 3, it still operated at the extent of 47-55%. It is suggested that the relationship between LEF and CEF-PSI is not only competition but also reciprocity. CEF-PSI was proposed to contribute to the considerable growth in phase 1; it was also suggested to play an important protective role against photosystem II (PSII) photoinhibition at the greatly enhanced level (approximately 80-95%) on the 2nd day. Our results in this research suggest that E. gracilis had very particular photosynthetic characteristics, the strict O2 evolution suppression in the initial culture phase might be a special light acclimation behavior, and CEF-PSI could be an important mechanism involved in this kind of adaptation to the changeable light environment.

  4. The ancestral gene repertoire of animal stem cells

    PubMed Central

    Alié, Alexandre; Hayashi, Tetsutaro; Sugimura, Itsuro; Manuel, Michaël; Sugano, Wakana; Mano, Akira; Satoh, Nori; Agata, Kiyokazu; Funayama, Noriko

    2015-01-01

    Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the “germ-line multipotency program” and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells. PMID:26644562

  5. The ancestral gene repertoire of animal stem cells.

    PubMed

    Alié, Alexandre; Hayashi, Tetsutaro; Sugimura, Itsuro; Manuel, Michaël; Sugano, Wakana; Mano, Akira; Satoh, Nori; Agata, Kiyokazu; Funayama, Noriko

    2015-12-22

    Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the "germ-line multipotency program" and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells.

  6. The evolution of MICOS: Ancestral and derived functions and interactions

    PubMed Central

    Muñoz-Gómez, Sergio A; Slamovits, Claudio H; Dacks, Joel B; Wideman, Jeremy G

    2015-01-01

    The MItochondrial Contact Site and Cristae Organizing System (MICOS) is required for the biogenesis and maintenance of mitochondrial cristae as well as the proper tethering of the mitochondrial inner and outer membranes. We recently demonstrated that the core components of MICOS, Mic10 and Mic60, are near-ubiquitous eukaryotic features inferred to have been present in the last eukaryote common ancestor. We also showed that Mic60 could be traced to α-proteobacteria, which suggests that mitochondrial cristae evolved from α-proteobacterial intracytoplasmic membranes. Here, we extend our evolutionary analysis to MICOS-interacting proteins (e.g., Sam50, Mia40, DNAJC11, DISC-1, QIL1, Aim24, and Cox17) and discuss the implications for both derived and ancestral functions of MICOS. PMID:27065250

  7. The ancestral gene repertoire of animal stem cells.

    PubMed

    Alié, Alexandre; Hayashi, Tetsutaro; Sugimura, Itsuro; Manuel, Michaël; Sugano, Wakana; Mano, Akira; Satoh, Nori; Agata, Kiyokazu; Funayama, Noriko

    2015-12-22

    Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the "germ-line multipotency program" and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells. PMID:26644562

  8. Experimental evidence for the thermophilicity of ancestral life

    PubMed Central

    Akanuma, Satoshi; Nakajima, Yoshiki; Yokobori, Shin-ichi; Kimura, Mitsuo; Nemoto, Naoki; Mase, Tomoko; Miyazono, Ken-ichi; Tanokura, Masaru; Yamagishi, Akihiko

    2013-01-01

    Theoretical studies have focused on the environmental temperature of the universal common ancestor of life with conflicting conclusions. Here we provide experimental support for the existence of a thermophilic universal common ancestor. We present the thermal stabilities and catalytic efficiencies of nucleoside diphosphate kinases (NDK), designed using the information contained in predictive phylogenetic trees, that seem to represent the last common ancestors of Archaea and of Bacteria. These enzymes display extreme thermal stabilities, suggesting thermophilic ancestries for Archaea and Bacteria. The results are robust to the uncertainties associated with the sequence predictions and to the tree topologies used to infer the ancestral sequences. Moreover, mutagenesis experiments suggest that the universal ancestor also possessed a very thermostable NDK. Because, as we show, the stability of an NDK is directly related to the environmental temperature of its host organism, our results indicate that the last common ancestor of extant life was a thermophile that flourished at a very high temperature. PMID:23776221

  9. Catastrophic debris avalanche from ancestral Mount Shasta volcano, California

    NASA Astrophysics Data System (ADS)

    Crandell, D. R.; Miller, C. D.; Glicken, H. X.; Christiansen, R. L.; Newhall, C. G.

    1984-03-01

    A debris-avalanche deposit extends 43 km northwestward from the base of Mount Shasta across the floor of Shasta Valley, California, where it covers an area of at least 450 km2. The surface of the deposit is dotted with hundreds of mounds, hills, and ridges, all formed of blocks of pyroxene andesite and unconsolidated volcaniclastic deposits derived from an ancestral Mount Shasta. Individual hills are separated by flat-topped laharlike deposits that also form the matrix of the debris avalanche and slope northwestward about 5 m/km. Radiometric ages of rocks in the deposit and of a postavalanche basalt flow indicate that the avalanche occurred between about 300,000 and 360,000 yr ago. An inferred average thickness of the deposit, plus a computed volume of about 4 km3 for the hills and ridges, indicate an estimated volume of about 26 km3, making it the largest known Quaternary landslide on Earth.

  10. Ancestral dichlorodiphenyltrichloroethane (DDT) exposure promotes epigenetic transgenerational inheritance of obesity

    PubMed Central

    2013-01-01

    Background Ancestral environmental exposures to a variety of environmental factors and toxicants have been shown to promote the epigenetic transgenerational inheritance of adult onset disease. The present work examined the potential transgenerational actions of the insecticide dichlorodiphenyltrichloroethane (DDT) on obesity and associated disease. Methods Outbred gestating female rats were transiently exposed to a vehicle control or DDT and the F1 generation offspring bred to generate the F2 generation and F2 generation bred to generate the F3 generation. The F1 and F3 generation control and DDT lineage rats were aged and various pathologies investigated. The F3 generation male sperm were collected to investigate methylation between the control and DDT lineage male sperm. Results The F1 generation offspring (directly exposed as a fetus) derived from the F0 generation exposed gestating female rats were not found to develop obesity. The F1 generation DDT lineage animals did develop kidney disease, prostate disease, ovary disease and tumor development as adults. Interestingly, the F3 generation (great grand-offspring) had over 50% of males and females develop obesity. Several transgenerational diseases previously shown to be associated with metabolic syndrome and obesity were observed in the testis, ovary and kidney. The transgenerational transmission of disease was through both female (egg) and male (sperm) germlines. F3 generation sperm epimutations, differential DNA methylation regions (DMR), induced by DDT were identified. A number of the genes associated with the DMR have previously been shown to be associated with obesity. Conclusions Observations indicate ancestral exposure to DDT can promote obesity and associated disease transgenerationally. The etiology of disease such as obesity may be in part due to environmentally induced epigenetic transgenerational inheritance. PMID:24228800

  11. Ancestral genome inference using a genetic algorithm approach.

    PubMed

    Gao, Nan; Yang, Ning; Tang, Jijun

    2013-01-01

    Recent advancement of technologies has now made it routine to obtain and compare gene orders within genomes. Rearrangements of gene orders by operations such as reversal and transposition are rare events that enable researchers to reconstruct deep evolutionary histories. An important application of genome rearrangement analysis is to infer gene orders of ancestral genomes, which is valuable for identifying patterns of evolution and for modeling the evolutionary processes. Among various available methods, parsimony-based methods (including GRAPPA and MGR) are the most widely used. Since the core algorithms of these methods are solvers for the so called median problem, providing efficient and accurate median solver has attracted lots of attention in this field. The "double-cut-and-join" (DCJ) model uses the single DCJ operation to account for all genome rearrangement events. Because mathematically it is much simpler than handling events directly, parsimony methods using DCJ median solvers has better speed and accuracy. However, the DCJ median problem is NP-hard and although several exact algorithms are available, they all have great difficulties when given genomes are distant. In this paper, we present a new algorithm that combines genetic algorithm (GA) with genomic sorting to produce a new method which can solve the DCJ median problem in limited time and space, especially in large and distant datasets. Our experimental results show that this new GA-based method can find optimal or near optimal results for problems ranging from easy to very difficult. Compared to existing parsimony methods which may severely underestimate the true number of evolutionary events, the sorting-based approach can infer ancestral genomes which are much closer to their true ancestors. The code is available at http://phylo.cse.sc.edu. PMID:23658708

  12. Isolation of a highly active photosystem II preparation from Synechocystis 6803 using a histidine-tagged mutant of CP 47.

    PubMed

    Bricker, T M; Morvant, J; Masri, N; Sutton, H M; Frankel, L K

    1998-11-01

    Site-directed mutagenesis was used to produce a Synechocystis mutant containing a histidine tag at the C terminus of the CP 47 protein of Photosystem II. This mutant cell line, designated HT-3, exhibited slightly above normal rates of oxygen evolution and appeared to accumulate somewhat more Photosystem II reaction centers than a control strain. A rapidly isolatable (<7 h) oxygen-evolving Photosystem II preparation was prepared from HT-3 using dodecyl-beta-d-maltoside solubilization and Co2+ metal affinity chromatography. This histidine-tagged Photosystem II preparation stably evolved oxygen at a high rate (2440 micromol O2 (mg chl)-1 h-1), exhibited an alpha-band absorption maximum at 674 nm, and was highly enriched in a number of Photosystem II components including cytochrome c550. Fluorescence yield analysis using water or hydroxylamine as an electron donor to the Photosystem II preparation indicated that virtually all of the Photosystem II reaction centers were capable of evolving oxygen. Proteins associated with Photosystem II were highly enriched in this preparation. 3,3',5, 5'-Tetramethylbenzidine staining indicated that the histidine-tagged preparation was enriched in cytochromes c550 and b559 and depleted of cytochrome f. This result was confirmed by optical difference spectroscopy. This histidine-tagged Photosystem II preparation may be very useful for the isolation of Photosystem II preparations from mutants containing lesions in other Photosystem II proteins. PMID:9804889

  13. Ergodicity, configurational entropy and free energy in pigment solutions and plant photosystems: influence of excited state lifetime.

    PubMed

    Jennings, Robert C; Zucchelli, Giuseppe

    2014-01-01

    We examine ergodicity and configurational entropy for a dilute pigment solution and for a suspension of plant photosystem particles in which both ground and excited state pigments are present. It is concluded that the pigment solution, due to the extreme brevity of the excited state lifetime, is non-ergodic and the configurational entropy approaches zero. Conversely, due to the rapid energy transfer among pigments, each photosystem is ergodic and the configurational entropy is positive. This decreases the free energy of the single photosystem pigment array by a small amount. On the other hand, the suspension of photosystems is non-ergodic and the configurational entropy approaches zero. The overall configurational entropy which, in principle, includes contributions from both the single excited photosystems and the suspension which contains excited photosystems, also approaches zero. Thus the configurational entropy upon photon absorption by either a pigment solution or a suspension of photosystem particles is approximately zero.

  14. Lateral heterogeneity of photosystems in thylakoid membranes studied by Brownian dynamics simulations.

    PubMed

    Borodich, Andrei; Rojdestvenski, Igor; Cottam, Michael

    2003-08-01

    The aggregation and segregation of photosystems in higher plant thylakoid membranes as stromal cation-induced phenomena are studied by the Brownian dynamics method. A theoretical model of photosystems lateral movement within the membrane plane is developed, assuming their pairwise effective potential interaction in aqueous and lipid media and their diffusion. Along with the screened electrostatic repulsive interaction the model accounts for the van der Waals-type, elastic, and lipid-induced attractive forces between photosystems of different sizes and charges. Simulations with a priori estimated parameters demonstrate that all three studied repulsion-attraction alternatives might favor the local segregation of photosystems under physiologically reasonable conditions. However, only the lipid-induced potential combined with the size-corrected screened Coulomb interaction provides the segregated configurations with photosystems II localized in the central part of the grana-size simulation cell and photosystems I occupying its margins, as observed experimentally. Mapping of thermodynamic states reveals that the coexistence curves between isotropic and aggregated phases are the sigmoidlike functions regardless of the effective potential type. It correlates with measurements of the chlorophyll content of thylakoid fragments. Also the universality of the phase curves characterizes the aggregation and segregation of photosystems as order-disorder phase transitions with the Debye radius as a governing parameter.

  15. Photosynthetic Quantum Yield Dynamics: From Photosystems to Leaves[W][OA

    PubMed Central

    Hogewoning, Sander W.; Wientjes, Emilie; Douwstra, Peter; Trouwborst, Govert; van Ieperen, Wim; Croce, Roberta; Harbinson, Jeremy

    2012-01-01

    The mechanisms underlying the wavelength dependence of the quantum yield for CO2 fixation (α) and its acclimation to the growth-light spectrum are quantitatively addressed, combining in vivo physiological and in vitro molecular methods. Cucumber (Cucumis sativus) was grown under an artificial sunlight spectrum, shade light spectrum, and blue light, and the quantum yield for photosystem I (PSI) and photosystem II (PSII) electron transport and α were simultaneously measured in vivo at 20 different wavelengths. The wavelength dependence of the photosystem excitation balance was calculated from both these in vivo data and in vitro from the photosystem composition and spectroscopic properties. Measuring wavelengths overexciting PSI produced a higher α for leaves grown under the shade light spectrum (i.e., PSI light), whereas wavelengths overexciting PSII produced a higher α for the sun and blue leaves. The shade spectrum produced the lowest PSI:PSII ratio. The photosystem excitation balance calculated from both in vivo and in vitro data was substantially similar and was shown to determine α at those wavelengths where absorption by carotenoids and nonphotosynthetic pigments is insignificant (i.e., >580 nm). We show quantitatively that leaves acclimate their photosystem composition to their growth light spectrum and how this changes the wavelength dependence of the photosystem excitation balance and quantum yield for CO2 fixation. This also proves that combining different wavelengths can enhance quantum yields substantially. PMID:22623496

  16. Characterization of ancestral and derived Y-chromosome haplotypes of New World native populations.

    PubMed Central

    Bianchi, N O; Catanesi, C I; Bailliet, G; Martinez-Marignac, V L; Bravi, C M; Vidal-Rioja, L B; Herrera, R J; López-Camelo, J S

    1998-01-01

    We analyze the allelic polymorphisms in seven Y-specific microsatellite loci and a Y-specific alphoid system with 27 variants (alphah I-XXVII), in a total of 89 Y chromosomes carrying the DYS199T allele and belonging to populations representing Amerindian and Na-Dene linguistic groups. Since there are no indications of recurrence for the DYS199C-->T transition, it is assumed that all DYS199T haplotypes derive from a single individual in whom the C-->T mutation occurred for the first time. We identified both the ancestral founder haplotype, 0A, of the DYS199T lineage and seven derived haplogroups diverging from the ancestral one by one to seven mutational steps. The 0A haplotype (5.7% of Native American chromosomes) had the following constitution: DYS199T, alphah II, DYS19/13, DYS389a/10, DYS389b/27, DYS390/24, DYS391/10, DYS392/14, and DYS393/13 (microsatellite alleles are indicated as number of repeats). We analyzed the Y-specific microsatellite mutation rate in 1,743 father-son transmissions, and we pooled our data with data in the literature, to obtain an average mutation rate of.0012. We estimated that the 0A haplotype has an average age of 22,770 years (minimum 13,500 years, maximum 58,700 years). Since the DYS199T allele is found with high frequency in Native American chromosomes, we propose that 0A is one of the most prevalent founder paternal lineages of New World aborigines. PMID:9837838

  17. Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies.

    PubMed

    Steiner, Cynthia C; Mitelberg, Anna; Tursi, Rosanna; Ryder, Oliver A

    2012-11-01

    Short divergence times and processes such as incomplete lineage sorting and species hybridization are known to hinder the inference of species-level phylogenies due to the lack of sufficient informative genetic variation or the presence of shared but incongruent polymorphism among taxa. Extant equids (horses, zebras, and asses) are an example of a recently evolved group of mammals with an unresolved phylogeny, despite a large number of molecular studies. Previous surveys have proposed trees with rather poorly supported nodes, and the bias caused by genetic introgression or ancestral polymorphism has not been assessed. Here we studied the phylogenetic relationships of all extant species of Equidae by analyzing 22 partial mitochondrial and nuclear genes using maximum likelihood and Bayesian inferences that account for heterogeneous gene histories. We also examined genetic signatures of lineage sorting and/or genetic introgression in zebras by evaluating patterns of intraspecific genetic variation. Our study improved the resolution and support of the Equus phylogeny and in particular the controversial positions of the African wild ass (E. asinus) and mountain zebra (E. zebra): the African wild ass is placed as a sister species of the Asiatic asses and the mountain zebra as the sister taxon of Grevy's and Burchell's zebras. A shared polymorphism (indel) detected among zebra species in the Estrogen receptor 1 gene was likely due to incomplete lineage sorting and not genetic introgression as also indicated by other mitochondrial (Cytochrome b) and nuclear (Y chromosome and microsatellites) markers. Ancestral polymorphism in equids might have contributed to the long-standing lack of clarity in the phylogeny of this highly threatened group of mammals.

  18. Immunolocalization of serotonin in Onychophora argues against segmental ganglia being an ancestral feature of arthropods

    PubMed Central

    Mayer, Georg; Harzsch, Steffen

    2007-01-01

    Background Onychophora (velvet worms) represent the most basal arthropod group and play a pivotal role in the current discussion on the evolution of nervous systems and segmentation in arthropods. Although there is a wealth of information on the immunolocalization of serotonin (5-hydroxytryptamine, 5-HT) in various euarthropods, as yet no comparable localization data are available for Onychophora. In order to understand how the onychophoran nervous system compares to that of other arthropods, we studied the distribution of serotonin-like immunoreactive neurons and histological characteristics of ventral nerve cords in Metaperipatus blainvillei (Onychophora, Peripatopsidae) and Epiperipatus biolleyi (Onychophora, Peripatidae). Results We demonstrate that paired leg nerves are the only segmental structures associated with the onychophoran nerve cord. Although the median commissures and peripheral nerves show a repeated pattern, their arrangement is independent from body segments characterized by the position of legs and associated structures. Moreover, the somata of serotonin-like immunoreactive neurons do not show any ordered arrangement in both species studied but are instead scattered throughout the entire length of each nerve cord. We observed neither a serially iterated nor a bilaterally symmetric pattern, which is in contrast to the strictly segmental arrangement of serotonergic neurons in other arthropods. Conclusion Our histological findings and immunolocalization experiments highlight the medullary organization of the onychophoran nerve cord and argue against segmental ganglia of the typical euarthropodan type being an ancestral feature of Onychophora. These results contradict a priori assumptions of segmental ganglia being an ancestral feature of arthropods and, thus, weaken the traditional Articulata hypothesis, which proposes a sistergroup relationship of Annelida and Arthropoda. PMID:17629937

  19. Clinical and biological implications of ancestral and non-ancestral IDH1 and IDH2 mutations in myeloid neoplasms.

    PubMed

    Molenaar, R J; Thota, S; Nagata, Y; Patel, B; Clemente, M; Przychodzen, B; Hirsh, C; Viny, A D; Hosano, N; Bleeker, F E; Meggendorfer, M; Alpermann, T; Shiraishi, Y; Chiba, K; Tanaka, H; van Noorden, C J F; Radivoyevitch, T; Carraway, H E; Makishima, H; Miyano, S; Sekeres, M A; Ogawa, S; Haferlach, T; Maciejewski, J P

    2015-11-01

    Mutations in isocitrate dehydrogenase 1/2 (IDH1/2(MT)) are drivers of a variety of myeloid neoplasms. As they yield the same oncometabolite, D-2-hydroxyglutarate, they are often treated as equivalent, and pooled. We studied the validity of this approach and found IDH1/2 mutations in 179 of 2119 myeloid neoplasms (8%). Cross-sectionally, the frequencies of these mutations increased from lower- to higher risk disease, thus suggesting a role in clinical progression. Variant allelic frequencies indicated that IDH1(MT) and IDH2(MT) are ancestral in up to 14/74 (19%) vs 34/99 (34%; P=0.027) of cases, respectively, illustrating the pathogenic role of these lesions in myeloid neoplasms. IDH1/2(MT) was associated with poor overall survival, particularly in lower risk myelodysplastic syndromes. Ancestral IDH1(MT) cases were associated with a worse prognosis than subclonal IDH1(MT) cases, whereas the position of IDH2(MT) within clonal hierarchy did not impact survival. This may relate to distinct mutational spectra with more DNMT3A and NPM1 mutations associated with IDH1(MT) cases, and more ASXL1, SRSF2, RUNX1, STAG2 mutations associated with IDH2(MT) cases. Our data demonstrate important clinical and biological differences between IDH1(MT) and IDH2(MT) myeloid neoplasms. These mutations should be considered separately as their differences could have implications for diagnosis, prognosis and treatment with IDH1/2(MT) inhibitors of IDH1/2(MT) patients. PMID:25836588

  20. Estimating Ancestral Ranges: Testing Methods with a Clade of Neotropical Lizards (Iguania: Liolaemidae)

    PubMed Central

    Díaz Gómez, Juan Manuel

    2011-01-01

    Establishing the ancestral ranges of distribution of a monophyletic clade, called the ancestral area, is one of the central objectives of historical biogeography. In this study, I used three common methodologies to establish the ancestral area of an important clade of Neotropical lizards, the family Liolaemidae. The methods used were: Fitch optimization, Weighted Ancestral Area Analysis and Dispersal-Vicariance Analysis (DIVA). A main difference from previous studies is that the areas used in the analysis are defined based on actual distributions of the species of Liolaemidae, instead of areas defined arbitrarilyor based on other taxa. The ancestral area of Liolaemidae found by Fitch optimization is Prepuna on Argentina, Central Chile and Coastal Peru. Weighted Ancestral Area Analysis found Central Chile, Coquimbo, Payunia, Austral Patagonia and Coastal Peru. Dispersal-Vicariance analysis found an ancestral area that includes almost all the areas occupied by Liolaemidae, except Atacama, Coquimbo and Austral Patagonia. The results can be resumed on two opposing hypothesis: a restricted ancestral area for the ancestor of Liolaemidae in Central Chile and Patagonia, or a widespread ancestor distributed along the Andes. Some limitations of the methods were identified, for example the excessive importance of plesiomorphic areas in the cladograms. PMID:22028873

  1. Estimation of the ancestral effective population sizes of African great apes under different selection regimes.

    PubMed

    Schrago, Carlos G

    2014-08-01

    Reliable estimates of ancestral effective population sizes are necessary to unveil the population-level phenomena that shaped the phylogeny and molecular evolution of the African great apes. Although several methods have previously been applied to infer ancestral effective population sizes, an analysis of the influence of the selective regime on the estimates of ancestral demography has not been thoroughly conducted. In this study, three independent data sets under different selective regimes were used were composed to tackle this issue. The results showed that selection had a significant impact on the estimates of ancestral effective population sizes of the African great apes. The inference of the ancestral demography of African great apes was affected by the selection regime. The effects, however, were not homogeneous along the ancestral populations of great apes. The effective population size of the ancestor of humans and chimpanzees was more impacted by the selection regime when compared to the same parameter in the ancestor of humans, chimpanzees and gorillas. Because the selection regime influenced the estimates of ancestral effective population size, it is reasonable to assume that a portion of the discrepancy found in previous studies that inferred the ancestral effective population size may be attributable to the differential action of selection on the genes sampled.

  2. Primary charge separation in isolated photosystem II reaction centers

    SciTech Connect

    Seibert, M.; Toon, S. ); Govindjee ); O'Neil, M.P.; Wasielewski, M.R. )

    1992-08-24

    Primary charge-separation in isolated bacterial reaction center (RC) complex occurs in 2.8 ps at room temperature and 0.7--1.2 ps at 10 K. Because of similarities between the bacterial and photosystem II (PSII) RCs, it has been of considerable interest to obtain analogous charge-separation rates in the higher plant system. Our previous femtosecond transient absorption studies used PSII RC material stabilized with PEG or by exchanging dodecyl maltoside (DM) for Triton in the isolation procedure. These materials gave charge-separation 1/e times of 3.0 [plus minus] 0.6 ps at 4[degree]C and 1.4[plus minus] 0.2 ps at 15 K based on the risetime of transient absorption kinetics at 820 nm. These values were thought to represent the time required for formation of the P680[sup +]-Pheo[sup [minus

  3. Isolation of Plant Photosystem II Complexes by Fractional Solubilization

    PubMed Central

    Haniewicz, Patrycja; Floris, Davide; Farci, Domenica; Kirkpatrick, Joanna; Loi, Maria C.; Büchel, Claudia; Bochtler, Matthias; Piano, Dario

    2015-01-01

    Photosystem II (PSII) occurs in different forms and supercomplexes in thylakoid membranes. Using a transplastomic strain of Nicotiana tabacum histidine tagged on the subunit PsbE, we have previously shown that a mild extraction protocol with β-dodecylmaltoside enriches PSII characteristic of lamellae and grana margins. Here, we characterize residual granal PSII that is not extracted by this first solubilization step. Using affinity purification, we demonstrate that this PSII fraction consists of PSII-LHCII mega- and supercomplexes, PSII dimers, and PSII monomers, which were separated by gel filtration and functionally characterized. Our findings represent an alternative demonstration of different PSII populations in thylakoid membranes, and they make it possible to prepare PSII-LHCII supercomplexes in high yield. PMID:26697050

  4. Nano-sized manganese-calcium cluster in photosystem II.

    PubMed

    Najafpour, M M; Ghobadi, M Z; Haghighi, B; Eaton-Rye, J J; Tomo, T; Shen, J-R; Allakhverdiev, S I

    2014-04-01

    Cyanobacteria, algae, and plants are the manufacturers that release O2 via water oxidation during photosynthesis. Since fossil resources are running out, researchers are now actively trying to use the natural catalytic center of water oxidation found in the photosystem II (PS II) reaction center of oxygenic photosynthetic organisms to synthesize a biomimetic supercatalyst for water oxidation. Success in this area of research will transcend the current bottleneck for the development of energy-conversion schemes based on sunlight. In this review, we go over the structure and function of the water-oxidizing complex (WOC) found in Nature by focusing on the recent advances made by the international research community dedicated to achieve the goal of artificial water splitting based on the WOC of PS II. PMID:24910206

  5. Manganese Deficiency in Plants: The Impact on Photosystem II.

    PubMed

    Schmidt, Sidsel Birkelund; Jensen, Poul Erik; Husted, Søren

    2016-07-01

    Manganese (Mn) is an essential plant micronutrient with an indispensable function as a catalyst in the oxygen-evolving complex (OEC) of photosystem II (PSII). Even so, Mn deficiency frequently occurs without visual leaf symptoms, thereby masking the distribution and dimension of the problem restricting crop productivity in many places of the world. Hence, timely alleviation of latent Mn deficiency is a challenge in promoting plant growth and quality. We describe here the key mechanisms of Mn deficiency in plants by focusing on the impact of Mn on PSII stability and functionality. We also address the mechanisms underlying the differential tolerance towards Mn deficiency observed among plant genotypes, which enable Mn-efficient plants to grow on marginal land with poor Mn availability. PMID:27150384

  6. Isolation of Plant Photosystem II Complexes by Fractional Solubilization.

    PubMed

    Haniewicz, Patrycja; Floris, Davide; Farci, Domenica; Kirkpatrick, Joanna; Loi, Maria C; Büchel, Claudia; Bochtler, Matthias; Piano, Dario

    2015-01-01

    Photosystem II (PSII) occurs in different forms and supercomplexes in thylakoid membranes. Using a transplastomic strain of Nicotiana tabacum histidine tagged on the subunit PsbE, we have previously shown that a mild extraction protocol with β-dodecylmaltoside enriches PSII characteristic of lamellae and grana margins. Here, we characterize residual granal PSII that is not extracted by this first solubilization step. Using affinity purification, we demonstrate that this PSII fraction consists of PSII-LHCII mega- and supercomplexes, PSII dimers, and PSII monomers, which were separated by gel filtration and functionally characterized. Our findings represent an alternative demonstration of different PSII populations in thylakoid membranes, and they make it possible to prepare PSII-LHCII supercomplexes in high yield.

  7. Economic photoprotection in photosystem II that retains a complete light-harvesting system with slow energy traps.

    PubMed

    Belgio, Erica; Kapitonova, Ekaterina; Chmeliov, Jevgenij; Duffy, Christopher D P; Ungerer, Petra; Valkunas, Leonas; Ruban, Alexander V

    2014-07-11

    The light-harvesting antenna of higher plant photosystem II has an intrinsic capability for self-defence against intense sunlight. The thermal dissipation of excess energy can be measured as the non-photochemical quenching of chlorophyll fluorescence. It has recently been proposed that the transition between the light-harvesting and self-defensive modes is associated with a reorganization of light-harvesting complexes. Here we show that despite structural changes, the photosystem II cross-section does not decrease. Our study reveals that the efficiency of energy trapping by the non-photochemical quencher(s) is lower than the efficiency of energy capture by the reaction centres. Consequently, the photoprotective mechanism works effectively for closed rather than open centres. This type of defence preserves the exceptional efficiency of electron transport in a broad range of light intensities, simultaneously ensuring high photosynthetic productivity and, under hazardous light conditions, sufficient photoprotection for both the reaction centre and the light-harvesting pigments of the antenna.

  8. Long-range energy transport in photosystem II

    NASA Astrophysics Data System (ADS)

    Roden, Jan J. J.; Bennett, Doran I. G.; Whaley, K. Birgitta

    2016-06-01

    We simulate the long-range inter-complex electronic energy transfer in photosystem II - from the antenna complex, via a core complex, to the reaction center - using a non-Markovian (ZOFE) quantum master equation description that allows the electronic coherence involved in the energy transfer to be explicitly included at all length scales. This allows us to identify all locations where coherence is manifested and to further identify the pathways of the energy transfer in the full network of coupled chromophores using a description based on excitation probability currents. We investigate how the energy transfer depends on the initial excitation - localized, coherent initial excitation versus delocalized, incoherent initial excitation - and find that the overall energy transfer is remarkably robust with respect to such strong variations of the initial condition. To explore the importance of vibrationally enhanced transfer and to address the question of optimization in the system parameters, we systematically vary the strength of the coupling between the electronic and the vibrational degrees of freedom. We find that the natural parameters lie in a (broad) region that enables optimal transfer efficiency and that the overall long-range energy transfer on a ns time scale appears to be very robust with respect to variations in the vibronic coupling of up to an order of magnitude. Nevertheless, vibrationally enhanced transfer appears to be crucial to obtain a high transfer efficiency, with the latter falling sharply for couplings outside the optimal range. Comparison of our full quantum simulations to results obtained with a "classical" rate equation based on a modified-Redfield/generalized-Förster description previously used to simulate energy transfer dynamics in the entire photosystem II complex shows good agreement for the overall time scales of excitation energy transport.

  9. Phytotoxicity of four photosystem II herbicides to tropical seagrasses.

    PubMed

    Flores, Florita; Collier, Catherine J; Mercurio, Philip; Negri, Andrew P

    2013-01-01

    Coastal waters of the Great Barrier Reef (GBR) are contaminated with agricultural pesticides, including the photosystem II (PSII) herbicides which are the most frequently detected at the highest concentrations. Designed to control weeds, these herbicides are equally potent towards non-target marine species, and the close proximity of seagrass meadows to flood plumes has raised concerns that seagrasses may be the species most threatened by herbicides from runoff. While previous work has identified effects of PSII herbicides on the photophysiology, growth and mortality in seagrass, there is little comparative quantitative toxicity data for seagrass. Here we applied standard ecotoxicology protocols to quantify the concentrations of four priority PSII herbicides that inhibit photochemistry by 10, 20 and 50% (IC10, IC20 and IC50) over 72 h in two common seagrass species from the GBR lagoon. The photosystems of seagrasses Zosteramuelleri and Haloduleuninervis were shown to be generally more sensitive to the PSII herbicides Diuron, Atrazine, Hexazinone and Tebuthiuron than corals and tropical microalgae. The herbicides caused rapid inhibition of effective quantum yield (∆F/F m '), indicating reduced photosynthesis and maximum effective yields (Fv/Fm ) corresponding to chronic damage to PSII. The PSII herbicide concentrations which affected photosynthesis have been exceeded in the GBR lagoon and all of the herbicides inhibited photosynthesis at concentrations lower than current marine park guidelines. There is a strong likelihood that the impacts of light limitation from flood plumes and reduced photosynthesis from PSII herbicides exported in the same waters would combine to affect seagrass productivity. Given that PSII herbicides have been demonstrated to affect seagrass at environmental concentrations, we suggest that revision of environmental guidelines and further efforts to reduce PSII herbicide concentrations in floodwaters may both help protect seagrass meadows of

  10. Fluorescence decay kinetics of wild type and D2-H117N mutant photosystem II reaction centers isolated from Chlamydomonas reinhardtii

    SciTech Connect

    Johnston, H.G.; Want, J.; Ruffle, S.V.; Sayre, R.T.; Gustafson, T.L.

    2000-05-18

    The authors compare the chlorophyll fluorescence decay kinetics of the wild type and the D2-H117N mutant photosystem II reaction centers isolated from Chlamydomonas reinhardtii. The histidine residue located at site 117 on the D2 polypeptide of photosystem II is a proposed binding site for one of two peripheral accessory chlorophylls located in the reaction center complex. The peripheral accessory chlorophylls are thought to be coupled with the primary electron donor, P680, and thus involved in energy transfer with P680. The conservative replacement of the histidine residue with an asparagine residue allows the chlorophyll to remain bound to the reaction center. However, slight changes in the structural organization of the reaction center may exist that can affect the energy transfer kinetics. The authors show that the D2-H117N mutation causes a shift in the 20--30 ps lifetime component that has been associated with energy equilibration among coupled chlorophylls in the photosystem II reaction center.

  11. Replacement of tyrosine D with phenylalanine affects the normal proton transfer pathways for the reduction of P680+ in oxygen-evolving photosystem II particles from Chlamydomonas.

    PubMed

    Jeans, C; Schilstra, M J; Ray, N; Husain, S; Minagawa, J; Nugent, J H A; Klug, D R

    2002-12-31

    We have probed the electrostatics of P680(+) reduction in oxygenic photosynthesis using histidine-tagged and histidine-tagged Y(D)-less Photosystem II cores. We make two main observations: (i) that His-tagged Chlamydomonas cores show kinetics which are essentially identical to those of Photosystem II enriched thylakoid membranes from spinach; (ii) that the microsecond kinetics, previously shown to be proton/hydrogen transfer limited [Schilstra et al. (1998) Biochemistry 37, 3974-3981], are significantly different in Y(D)-less Chlamydomonas particles when compared with both the His-tagged Chlamydomonas particles and the spinach membranes. The oscillatory nature of the kinetics in both Chlamydomonas samples is normal, indicating that S-state cycling is unaffected by either the histidine-tagging or the replacement of tyrosine D with phenylalanine. We propose that the effects on the proton-coupled electron transfers of P680(+) reduction in the absence of Y(D) are likely to be due to pK shifts of residues in a hydrogen-bonded network of amino acids in the vicinity of Y(Z). Tyrosine D is 35 A from Y(Z) and yet has a significant influence on proton-coupled electron transfer events in the vicinity of Y(Z). This finding emphasizes the delicacy of the proton balance that Photosystem II has to achieve during the water splitting process. PMID:12501204

  12. The quest for energy traps in the CP43 antenna of photosystem II.

    PubMed

    Müh, Frank; Plöckinger, Melanie; Ortmayer, Helmut; Schmidt Am Busch, Marcel; Lindorfer, Dominik; Adolphs, Julian; Renger, Thomas

    2015-11-01

    To identify energy traps in CP43, a subcomplex of the photosystem II antenna system, site energies and excitonic couplings of the QY transitions of chlorophyll (Chl) a pigments bound to CP43 are computed using electrostatic models of pigment-protein and pigment-pigment interactions. The computations are based on recent crystal structures of the photosystem II core complex with resolutions of 1.9 and 2.1Å and compared to earlier results obtained at 2.9Å resolution. Linear optical spectra (i.e., absorption, linear dichroism, circular dichroism, and fluorescence) are simulated using the computed excitonic couplings, a refinement fit for the site energies, and a dynamical theory of optical lineshapes. A comparison of the obtained root mean square deviation of about 100 cm(-1) between directly calculated and refined site energies with the maximum range of about 350 cm(-1) of directly calculated site energies shows that the combined quantum chemical/electrostatic approach provides a semi-quantitative agreement with experiment. Possible reasons for the deviations are discussed, including limits of the electrostatic models and the lineshape theory as well as structural alterations of CP43 upon detachment from the core complex. Based on the simulations, an assignment of the two low-energy exciton states A and B of CP43, that where observed earlier in hole burning studies, is suggested. State A is assigned to a localized exciton state on Chl 37 in the lumenal layer of pigments. State B is assigned to an exciton state that is delocalized over several pigments in the cytoplasmic layer. The delocalization explains the smaller inhomogeneous width of state B compared to state A observed in hole burning spectra, which is proposed to be due to exchange narrowing. The assignment of states A and B largely confirms our earlier suggestion that was based on a fit of linear optical spectra and electrostatic calculations using the 2.9Å resolution structure. Interestingly, for the

  13. Structure and functional role of supercomplexes of IsiA and Photosystem I in cyanobacterial photosynthesis.

    PubMed

    Kouril, Roman; Arteni, Ana A; Lax, Julia; Yeremenko, Nataliya; D'Haene, Sandrine; Rögner, Matthias; Matthijs, Hans C P; Dekker, Jan P; Boekema, Egbert J

    2005-06-13

    Cyanobacteria express large quantities of the iron stress-inducible protein IsiA under iron deficiency. IsiA can assemble into numerous types of single or double rings surrounding Photosystem I. These supercomplexes are functional in light-harvesting, empty IsiA rings are effective energy dissipaters. Electron microscopy studies of these supercomplexes show that Photosystem I trimers bind 18 IsiA copies in a single ring, whereas monomers may bind up to 35 copies in two rings. Work on mutants indicates that the PsaF/J and PsaL subunits facilitate the formation of closed rings around Photosystem I monomers but are not obligatory components in the formation of Photosystem I-IsiA supercomplexes. PMID:15943969

  14. Antenna entropy in plant photosystems does not reduce the free energy for primary charge separation.

    PubMed

    Jennings, Robert C; Zucchelli, Giuseppe

    2014-12-01

    We have investigated the concept of the so-called "antenna entropy" of higher plant photosystems. Several interesting points emerge: 1. In the case of a photosystemwhich harbours an excited state, the “antenna entropy” is equivalent to the configurational (mixing) entropy of a thermodynamic canonical ensemble. The energy associated with this parameter has been calculated for a hypothetical isoenergetic photosystem, photosystem I and photosystem II, and comes out in the range of 3.5 - 8% of the photon energy considering 680 nm. 2. The “antenna entropy” seems to be a rather unique thermodynamic phenomenon, in as much as it does not modify the free energy available for primary photochemistry, as has been previously suggested. 3. It is underlined that this configurational (mixing) entropy, unlike heat dispersal in a thermal system, does not involve energy dilution. This points out an important difference between thermal and electronic energy dispersal.

  15. Assembly of photo-bioelectrochemical cells using photosystem I-functionalized electrodes

    NASA Astrophysics Data System (ADS)

    Efrati, Ariel; Lu, Chun-Hua; Michaeli, Dorit; Nechushtai, Rachel; Alsaoub, Sabine; Schuhmann, Wolfgang; Willner, Itamar

    2016-02-01

    The design of photo-bioelectrochemical cells based on native photosynthetic reaction centres is attracting substantial recent interest as a means for the conversion of solar light energy into electrical power. In the natural photosynthetic apparatus, the photosynthetic reaction centres are coupled to biocatalytic transformations leading to CO2 fixation and O2 evolution. Although significant progress in the integration of native photosystems with electrodes for light-to-electrical energy conversion has been achieved, the conjugation of the photosystems to enzymes to yield photo-bioelectrocatalytic solar cells remains a challenge. Here we demonstrate the assembly of integrated photosystem I/glucose oxidase or glucose dehydrogenase photo-bioelectrochemical electrodes. We highlight the photonic wiring of the biocatalysts by means of photosystem I using glucose as fuel. Our results provide a general approach to assemble photo-bioelectrochemical solar cells with wide implications for solar energy conversion, bioelectrocatalysis and sensing.

  16. Deep phylogeny, ancestral groups and the four ages of life.

    PubMed

    Cavalier-Smith, Thomas

    2010-01-12

    Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution. PMID:20008390

  17. Allatotropin: An Ancestral Myotropic Neuropeptide Involved in Feeding

    PubMed Central

    Alzugaray, María Eugenia; Adami, Mariana Laura; Diambra, Luis Anibal; Hernandez-Martinez, Salvador; Damborenea, Cristina; Noriega, Fernando Gabriel; Ronderos, Jorge Rafael

    2013-01-01

    Background Cell-cell interactions are a basic principle for the organization of tissues and organs allowing them to perform integrated functions and to organize themselves spatially and temporally. Peptidic molecules secreted by neurons and epithelial cells play fundamental roles in cell-cell interactions, acting as local neuromodulators, neurohormones, as well as endocrine and paracrine messengers. Allatotropin (AT) is a neuropeptide originally described as a regulator of Juvenile Hormone synthesis, which plays multiple neural, endocrine and myoactive roles in insects and other organisms. Methods A combination of immunohistochemistry using AT-antibodies and AT-Qdot nanocrystal conjugates was used to identify immunoreactive nerve cells containing the peptide and epithelial-muscular cells targeted by AT in Hydra plagiodesmica. Physiological assays using AT and AT- antibodies revealed that while AT stimulated the extrusion of the hypostome in a dose-response fashion in starved hydroids, the activity of hypostome in hydroids challenged with food was blocked by treatments with different doses of AT-antibodies. Conclusions AT antibodies immunolabeled nerve cells in the stalk, pedal disc, tentacles and hypostome. AT-Qdot conjugates recognized epithelial-muscular cell in the same tissues, suggesting the existence of anatomical and functional relationships between these two cell populations. Physiological assays indicated that the AT-like peptide is facilitating food ingestion. Significance Immunochemical, physiological and bioinformatics evidence advocates that AT is an ancestral neuropeptide involved in myoregulatory activities associated with meal ingestion and digestion. PMID:24143240

  18. Color vision of ancestral organisms of higher primates.

    PubMed

    Nei, M; Zhang, J; Yokoyama, S

    1997-06-01

    The color vision of mammals is controlled by photosensitive proteins called opsins. Most mammals have dichromatic color vision, but hominoids and Old World (OW) monkeys enjoy trichromatic vision, having the blue-, green-, and red-sensitive opsin genes. Most New World (NW) monkeys are either dichromatic or trichromatic, depending on the sex and genotype. Trichromacy in higher primates is believed to have evolved to facilitate the detection of yellow and red fruits against dappled foliage, but the process of evolutionary change from dichromacy to trichromacy is not well understood. Using the parsimony and the newly developed Bayesian methods, we inferred the amino acid sequences of opsins of ancestral organisms of higher primates. The results suggest that the ancestors of OW and NW monkeys lacked the green gene and that the green gene later evolved from the red gene. The fact that the red/green opsin gene has survived the long nocturnal stage of mammalian evolution and that it is under strong purifying selection in organisms that live in dark environments suggests that this gene has another important function in addition to color vision, probably the control of circadian rhythms. PMID:9190062

  19. The common ancestral core of vertebrate and fungal telomerase RNAs.

    PubMed

    Qi, Xiaodong; Li, Yang; Honda, Shinji; Hoffmann, Steve; Marz, Manja; Mosig, Axel; Podlevsky, Joshua D; Stadler, Peter F; Selker, Eric U; Chen, Julian J-L

    2013-01-01

    Telomerase is a ribonucleoprotein with an intrinsic telomerase RNA (TER) component. Within yeasts, TER is remarkably large and presents little similarity in secondary structure to vertebrate or ciliate TERs. To better understand the evolution of fungal telomerase, we identified 74 TERs from Pezizomycotina and Taphrinomycotina subphyla, sister clades to budding yeasts. We initially identified TER from Neurospora crassa using a novel deep-sequencing-based approach, and homologous TER sequences from available fungal genome databases by computational searches. Remarkably, TERs from these non-yeast fungi have many attributes in common with vertebrate TERs. Comparative phylogenetic analysis of highly conserved regions within Pezizomycotina TERs revealed two core domains nearly identical in secondary structure to the pseudoknot and CR4/5 within vertebrate TERs. We then analyzed N. crassa and Schizosaccharomyces pombe telomerase reconstituted in vitro, and showed that the two RNA core domains in both systems can reconstitute activity in trans as two separate RNA fragments. Furthermore, the primer-extension pulse-chase analysis affirmed that the reconstituted N. crassa telomerase synthesizes TTAGGG repeats with high processivity, a common attribute of vertebrate telomerase. Overall, this study reveals the common ancestral cores of vertebrate and fungal TERs, and provides insights into the molecular evolution of fungal TER structure and function.

  20. Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.

    PubMed

    Yang, Shuo; Carmi, Shai; Pe'er, Itsik

    2016-06-01

    The genomes of remotely related individuals occasionally contain long segments that are identical by descent (IBD). Sharing of IBD segments has many applications in population and medical genetics, and it is thus desirable to study their properties in simulations. However, no current method provides a direct, efficient means to extract IBD segments from simulated genealogies. Here, we introduce computationally efficient approaches to extract ground-truth IBD segments from a sequence of genealogies, or equivalently, an ancestral recombination graph. Specifically, we use a two-step scheme, where we first identify putative shared segments by comparing the common ancestors of all pairs of individuals at some distance apart. This reduces the search space considerably, and we then proceed by determining the true IBD status of the candidate segments. Under some assumptions and when allowing a limited resolution of segment lengths, our run-time complexity is reduced from O(n(3) log n) for the naïve algorithm to O(n log n), where n is the number of individuals in the sample.

  1. Female rule in lemurs is ancestral and hormonally mediated

    PubMed Central

    Petty, Joseph M. A.; Drea, Christine M.

    2015-01-01

    Female social dominance (FSD) over males is unusual in mammals, yet characterizes most Malagasy lemurs, which represent almost 30% of all primates. Despite its prevalence in this suborder, both the evolutionary trajectory and proximate mechanism of FSD remain unclear. Potentially associated with FSD is a suite of behavioural, physiological and morphological traits in females that implicates (as a putative mechanism) ‘masculinization’ via androgen exposure; however, relative to conspecific males, female lemurs curiously show little evidence of raised androgen concentrations. By observing mixed‐sex pairs of related Eulemur species, we identified two key study groups ‐‐ one comprised of species expressing FSD and increased female scent marking, the other comprised of species (from a recently evolved clade) showing equal status between the sexes and the more traditional pattern of sexually dimorphic behaviour. Comparing females from these two groups, we show that FSD is associated with more masculine androgen profiles. Based on the widespread prevalence of male‐like features in female lemurs and a current phylogeny, we suggest that relaxation of hormonally mediated FSD emerged only recently and that female masculinization may be the ancestral lemur condition, an idea that could revolutionize our understanding of the ancient socioecology and evolution of primate social systems. PMID:25950904

  2. Deep phylogeny, ancestral groups and the four ages of life

    PubMed Central

    Cavalier-Smith, Thomas

    2010-01-01

    Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria—the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution. PMID:20008390

  3. Modeling X-Linked Ancestral Origins in Multiparental Populations

    PubMed Central

    Zheng, Chaozhi

    2015-01-01

    The models for the mosaic structure of an individual’s genome from multiparental populations have been developed primarily for autosomes, whereas X chromosomes receive very little attention. In this paper, we extend our previous approach to model ancestral origin processes along two X chromosomes in a mapping population, which is necessary for developing hidden Markov models in the reconstruction of ancestry blocks for X-linked quantitative trait locus mapping. The model accounts for the joint recombination pattern, the asymmetry between maternally and paternally derived X chromosomes, and the finiteness of population size. The model can be applied to various mapping populations such as the advanced intercross lines (AIL), the Collaborative Cross (CC), the heterogeneous stock (HS), the Diversity Outcross (DO), and the Drosophila synthetic population resource (DSPR). We further derive the map expansion, density (per Morgan) of recombination breakpoints, in advanced intercross populations with L inbred founders under the limit of an infinitely large population size. The analytic results show that for X chromosomes the genetic map expands linearly at a rate (per generation) of two-thirds times 1 – 10/(9L) for the AIL, and at a rate of two-thirds times 1 – 1/L for the DO and the HS, whereas for autosomes the map expands at a rate of 1 – 1/L for the AIL, the DO, and the HS. PMID:25740936

  4. Excitation energy transfer between photosystem II and photosystem I in red algae: larger amounts of phycobilisome enhance spillover.

    PubMed

    Yokono, Makio; Murakami, Akio; Akimoto, Seiji

    2011-07-01

    We examined energy transfer dynamics from the photosystem II reaction center (PSII-RC) in intact red algae cells of Porphyridium cruentum, Bangia fuscopurpurea, Porphyra yezoensis, Chondrus giganteus, and Prionitis crispata. Time resolved fluorescence measurements were conducted in the range of 0-80ns at -196°C. The delayed fluorescence spectra were then determined, where the delayed fluorescence was derived from the charge recombination between P680(+) and pheophytin a in PSII-RC. Therefore, the delayed fluorescence spectrum reflected the energy migration processes including PSII-RC. All samples examined showed prominent distribution of delayed fluorescence in PSII and PSI, which suggests that a certain amount of PSII attaches to PSI to share excitation energy in red algae. The energy transfer from PSII to PSI was found to be dominant when the amount of phycoerythrobilin was increased.

  5. Photosynthetic membrane topography: quantitative in situ localization of photosystems I and II.

    PubMed

    Mustardy, L; Cunningham, F X; Gantt, E

    1992-11-01

    An immunolabeling approach was developed for quantitative in situ labeling of photosystems I and II (PSI and PSII). Photosynthetic membranes from the phycobilisome-containing red alga Porphyridium cruentum were isolated from cells in which different photosystem compositions were predetermined by growing cells in green light (GL) or red light (RL). Based on phycobilisome densities per membrane area of 390 per m2 (GL) and 450 per m2 (RL) and the PSI reaction center (P700) and PSII reaction center (QA) content, the photosystem densities per m2 of membrane were calculated to be 2520 PSI in GL and 1580 in RL and 630 PSII in GL and 1890 in RL. PSI was detected in the membranes with 10-nm Au particles conjugated to affinity-purified anti-PSI, and PSII was detected with 15-nm Au particles conjugated to anti-PSII. Distribution of Au particles appeared relatively uniform, and the degree of labeling was consistent with the calculated photosystem densities. However, the absolute numbers of Au-labeled sites were lower than would be obtained if all reaction center monomers were labeled. Specific labeling of PSI was 25% in GL and RL membranes, and PSII labeling was 33% in GL but only 17% in RL membranes. An IgG-Au particle is larger than a monomer of either photosystem and could shield several closely packed photosystems. We suggest that clustering of photosystems exists and that the cluster size of PSI is the same in GL and RL cells, but the PSII cluster size is 2 times greater in RL than in GL cells. Such variations may reflect changes in functional domains whereby increased clustering can maximize the cooperativity between the photosystems, resulting in enhancement of the quantum yield.

  6. Characterization of a purified photosystem II-phycobilisome particle preparation from Porphyridium cruentum

    SciTech Connect

    Chereskin, B.M.; Clement-Metral, J.D.; Gantt, E.

    1985-01-01

    Detergent preparations isolated from thylakoids of the red alga Porphyridium cruentum, in a sucrose, phosphate, citrate, magnesium chloride medium consist of phycobilisomes and possess high rates of photosystem II activity. Characterization of these particles shows that the O/sub 2/-evolving activity is stable for several hours and the pH optimum is about 6.5 to 7.2. Response of the system to light, electron donors and acceptors, and inhibitors verify that the observed activity, measured both as O/sub 2/ evolution and 2,6-dichlorophenol-indophenol reduction, is due to photosystem II. Furthermore, photosystem II is functionally coupled to the phycobilisome in this preparation since green light, absorbed by phycobilisomes of P. cruentum, is effective in promoting both O/sub 2/ evolution and 2,6-dichlorophenol-indophenol reduction. Photosystem II activity declines when light with wavelengths shorter than 665 nm is removed. Both 3-(3,4-dichlorophenyl)-1,1-dimethylurea and atrazine inhibit photosystem II activity in this preparation, indicating that the herbicide binding site is a component of the photosystem II-phycobilisome particle. 24 references, 4 figures, 2 tables.

  7. Initial Taxonomy and Classification Scheme for Artificial Space Objects Based on Ancestral Relation and Clustering

    NASA Astrophysics Data System (ADS)

    Fruh, C.; Jah, M.

    2013-09-01

    As space gets more and more populated a classification scheme based upon scientific taxonomy is needed to properly identify and discriminate space objects. An artificial space object taxonomy also allows for scientific understanding of the nature of the space object population and the processes, natural or not, that drive changes of an artificial space object class from one to another. In general, parametric and non-parametric classification schemes based upon the developed taxonomy have to be distinguished. In both cases a priori information is needed either as training data or to outline error distributions as direct input values. In this paper a classification scheme based on the ancestral-dynamic state of space objects is proposed and linked to a cluster analysis of orbital element space without a priori clustering information is provided. The cluster analysis is based on a two step approach, a first using a cluster-feature tree and secondly, a minimal euclidian tree approach. Test cases are used to show the efficiency and potential of the proposed classification scheme.

  8. The photochemistry in Photosystem II at 5 K is different in visible and far-red light.

    PubMed

    Mokvist, Fredrik; Sjöholm, Johannes; Mamedov, Fikret; Styring, Stenbjörn

    2014-07-01

    We have earlier shown that all electron transfer reactions in Photosystem II are operational up to 800 nm at room temperature [Thapper, A., et al. (2009) Plant Cell 21, 2391-2401]. This led us to suggest an alternative charge separation pathway for far-red excitation. Here we extend these studies to a very low temperature (5 K). Illumination of Photosystem II (PS II) with visible light at 5 K is known to result in oxidation of almost similar amounts of YZ and the Cyt b559/ChlZ/CarD2 pathway. This is reproduced here using laser flashes at 532 nm, and we find the partition ratio between the two pathways to be 1:0.8 at 5 K [the partition ratio is here defined as (yield of YZ/CaMn4 oxidation):(yield of Cyt b559/ChlZ/CarD2 oxidation)]. The result using far-red laser flashes is very different. We find partition ratios of 1.8 at 730 nm, 2.7 at 740 nm, and >2.7 at 750 nm. No photochemistry involving these pathways is observed above 750 nm at this temperature. Thus, far-red illumination preferentially oxidizes YZ, while the Cyt b559/ChlZ/CarD2 pathway is hardly touched. We propose that the difference in the partition ratio between visible and far-red light at 5 K reflects the formation of a different first stable charge pair. In visible light, the first stable charge pair is considered to be PD1+QA-. In contrast, we propose that the electron hole is residing on the ChlD1 molecule after illumination by far-red light at 5 K, resulting in the first stable charge pair being ChlD1+QA-. ChlD1 is much closer to YZ (11.3 Å) than to any component in the Cyt b559/ChlZ/CarD2 pathway (shortest ChlD1-CarD2 distance of 28.8 Å). This would then explain that far-red illumination preferentially drives efficient electron transfer from YZ. We also discuss mechanisms for accounting for the absorption of the far-red light and the existence of hitherto unobserved charge transfer states. The involvement of two or more of the porphyrin molecules in the core of the Photosystem II reaction center

  9. Genome-wide inference of ancestral recombination graphs.

    PubMed

    Rasmussen, Matthew D; Hubisz, Melissa J; Gronau, Ilan; Siepel, Adam

    2014-01-01

    The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of [Formula: see text] chromosomes conditional on an ARG of [Formula: see text] chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective sweeps. PMID:24831947

  10. Hominoid seminal protein evolution and ancestral mating behavior.

    PubMed

    Carnahan, Sarah J; Jensen-Seaman, Michael I

    2008-10-01

    Hominoid mating systems show extensive variation among species. The degree of sexual dimorphism in body size and canine size varies among primates in accordance with their mating system, as does the testes size and the consistency of ejaculated semen, in response to differing levels of sperm competition. To investigate patterns of evolution at hominoid seminal proteins and to make inferences regarding the mating systems of extinct taxa, we sequenced the entire coding region of the prostate-specific transglutaminase (TGM4) gene in human, chimpanzee, bonobo, western lowland gorilla, eastern lowland gorilla, orangutan, and siamang, including multiple humans, chimps, and gorillas. Partial DNA sequence of the coding regions was also obtained for one eastern lowland gorilla at the semenogelin genes (SEMG1 and SEMG2), which code for the predominant proteins in semen. Patterns of nucleotide variation and inferred protein sequence change were evaluated within and between species. Combining the present data with previous studies demonstrates a high rate of amino acid substitutions, and low intraspecific variation, at seminal proteins in Pan, presumably driven by strong sperm competition. Both gorilla species apparently possess nonfunctional TGM4, SEMG1, and SEMG2 genes, suggesting that gorillas have had low sperm competition, and therefore their current polygynous mating system, for a long time before their divergence. Similarly, orangutans show longstanding stasis at TGM4, which may be interpreted as evidence for an unchanging mating system for most of their evolution after their divergence from African apes. In contrast to the great apes, the data from humans could be interpreted as evidence of fluctuations between different mating systems or alternatively as a relaxed functional constraint in these proteins. It is our hope that this study is a first step toward developing a model to predict ancestral mating systems from extant molecular data to complement interpretations

  11. The Korarchaeota: Archaeal orphans representing an ancestral lineage of life

    SciTech Connect

    Elkins, James G.; Kunin, Victor; Anderson, Iain; Barry, Kerrie; Goltsman, Eugene; Lapidus, Alla; Hedlund, Brian; Hugenholtz, Phil; Kyrpides, Nikos; Graham, David; Keller, Martin; Wanner, Gerhard; Richardson, Paul; Stetter, Karl O.

    2007-05-01

    Based on conserved cellular properties, all life on Earth can be grouped into different phyla which belong to the primary domains Bacteria, Archaea, and Eukarya. However, tracing back their evolutionary relationships has been impeded by horizontal gene transfer and gene loss. Within the Archaea, the kingdoms Crenarchaeota and Euryarchaeota exhibit a profound divergence. In order to elucidate the evolution of these two major kingdoms, representatives of more deeply diverged lineages would be required. Based on their environmental small subunit ribosomal (ss RNA) sequences, the Korarchaeota had been originally suggested to have an ancestral relationship to all known Archaea although this assessment has been refuted. Here we describe the cultivation and initial characterization of the first member of the Korarchaeota, highly unusual, ultrathin filamentous cells about 0.16 {micro}m in diameter. A complete genome sequence obtained from enrichment cultures revealed an unprecedented combination of signature genes which were thought to be characteristic of either the Crenarchaeota, Euryarchaeota, or Eukarya. Cell division appears to be mediated through a FtsZ-dependent mechanism which is highly conserved throughout the Bacteria and Euryarchaeota. An rpb8 subunit of the DNA-dependent RNA polymerase was identified which is absent from other Archaea and has been described as a eukaryotic signature gene. In addition, the representative organism possesses a ribosome structure typical for members of the Crenarchaeota. Based on its gene complement, this lineage likely diverged near the separation of the two major kingdoms of Archaea. Further investigations of these unique organisms may shed additional light onto the evolution of extant life.

  12. Genome-Wide Inference of Ancestral Recombination Graphs

    PubMed Central

    Rasmussen, Matthew D.; Hubisz, Melissa J.; Gronau, Ilan; Siepel, Adam

    2014-01-01

    The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the “ancestral recombination graph” (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of chromosomes conditional on an ARG of chromosomes, an operation we call “threading.” Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective sweeps. PMID:24831947

  13. Ancestral Heterogeneity in a Bi-ethnic Stroke Population

    PubMed Central

    Lisabeth, Lynda D; Morgenstern, Lewis B; Burke, David T; Sun, Yan V; Long, Jeffrey C

    2011-01-01

    SUMMARY To test for and characterize heterogeneity in ancestral contributions to individuals among a population of Mexican American (MA) and non-Hispanic white (NHW) stroke/TIA cases, data from a community-based stroke surveillance study in south Texas were used. Strokes/TIA cases were identified (2004–2006) with a random sample asked to provide blood. Race-ethnicity was self-reported. Thirty-three ancestry informative markers (AIMs) were genotyped and individual genetic admixture estimated using maximum likelihood methods. Three hypotheses were tested for each MA using likelihood ratio tests: 1) H0: μi=0 (100% Native American), 2) H0: μi=1.00 (100% European), 3) H0: μi=0.59 (average European). Among 154 self-identified MAs, estimated European ancestry varied from 0.26–0.98, with an average of 0.59(se=0.014). We rejected hypothesis 1 for every MA and rejected hypothesis 2 for all but two MAs. We rejected hypothesis 3 for 40 MAs (20<59%, 20>59%). Among 84 self-identified NHWs, the estimated fraction of European ancestry ranged from 0.83–1.0, with an average of 0.97 (se=0.014). Self-identified MAs, and to a lesser extent NHWs, from an established bi-ethnic community were heterogeneous with respect to genetic admixture. Researchers should not use simple race-ethnic categories as proxies for homogeneous genetic populations when conducting gene mapping and disease association studies in multi-ethnic populations. PMID:21668907

  14. On the tomato trail: in search of ancestral roots.

    PubMed

    Estabrook, Barry

    2010-01-01

    A profile of Roger Chetelat, the director of the C.M. Rick Tomato Genetics Resource Center at the University of California, Davis. Chetelat maintains one of the largest collections of tomato seeds in the world. Many of those seeds come from wild tomato species that Chetelat and his associates collect on field research trips to the dry coastal areas of Chile, Peru, and Ecuador. Wild tomatoes are tough, versatile organisms that have evolved resistance to virtually all common tomato diseases and pests and stubbornly tolerate extreme environmental conditions. Some boast extraordinarily high levels of sugars, beta carotene, vitamin C, lycopene, and antioxidants. Chetelat has dedicated his career to finding and preserving these genetic riches. Modern cultivated tomatoes are a frail, inbred lot. They all trace their origins to a single, wild tomato plant that underwent a random mutation sometime in prehistory. Because of this genetic fluke, that plant's fruits were plump, juicy, and many, many times larger than the output of its progenitors. Offspring from that tomato were taken away from the Andes and domesticated in what is present-day Mexico, becoming severed from their wild ancestors and the vast pool of genetic diversity that tomatoes had evolved over the millennia. Botanists call this a “bottleneck.” It leaves subsequent generations susceptible to disease and unable to adjust to rapid climate changes. The stored wild seeds at the Rick Center enable plant breeders to re-incorporate desirable wild traits into new tomato varieties, literally reconnecting them to their ancestral roots, ensuring that this vast reservoir of genetic diversity will be available when it is needed.

  15. Double Mutation in Photosystem II Reaction Centers and Elevated CO2 Grant Thermotolerance to Mesophilic Cyanobacterium

    PubMed Central

    Dinamarca, Jorge; Shlyk-Kerner, Oksana; Kaftan, David; Goldberg, Eran; Dulebo, Alexander; Gidekel, Manuel; Gutierrez, Ana; Scherz, Avigdor

    2011-01-01

    Photosynthetic biomass production rapidly declines in mesophilic cyanobacteria grown above their physiological temperatures largely due to the imbalance between degradation and repair of the D1 protein subunit of the heat susceptible Photosystem II reaction centers (PSIIRC). Here we show that simultaneous replacement of two conserved residues in the D1 protein of the mesophilic Synechocystis sp. PCC 6803, by the analogue residues present in the thermophilic Thermosynechococcus elongatus, enables photosynthetic growth, extensive biomass production and markedly enhanced stability and repair rate of PSIIRC for seven days even at 43°C but only at elevated CO2 (1%). Under the same conditions, the Synechocystis control strain initially presented very slow growth followed by a decline after 3 days. Change in the thylakoid membrane lipids, namely the saturation of the fatty acids is observed upon incubation for the different strains, but only the double mutant shows a concomitant major change of the enthalpy and entropy for the light activated QA−→QB electron transfer, rendering them similar to those of the thermophilic strain. Following these findings, computational chemistry and protein dynamics simulations we propose that the D1 double mutation increases the folding stability of the PSIIRC at elevated temperatures. This, together with the decreased impairment of D1 protein repair under increased CO2 concentrations result in the observed photothermal tolerance of the photosynthetic machinery in the double mutant PMID:22216094

  16. Cation Effects on the Electron-Acceptor Side of Photosystem II.

    PubMed

    Khan, Sahr; Sun, Jennifer S; Brudvig, Gary W

    2015-06-18

    The normal pathway of electron transfer on the electron-acceptor side of photosystem II (PSII) involves electron transfer from quinone A, QA, to quinone B, QB. It is possible to redirect electrons from QA(-) to water-soluble Co(III) complexes, which opens a new avenue for harvesting electrons from water oxidation by immobilization of PSII on electrode surfaces. Herein, the kinetics of electron transfer from QA(-) to [Co(III)(terpy)2](3+) (terpy = 2,2';6',2″-terpyridine) are investigated with a spectrophotometric assay revealing that the reaction follows Michaelis-Menten saturation kinetics, is inhibited by cations, and is not affected by variation of the QA reduction potential. A negatively charged site on the stromal surface of the PSII protein complex, composed of glutamic acid residues near QA, is hypothesized to bind cations, especially divalent cations. The cations are proposed to tune the redox properties of QA through electrostatic interactions. These observations may thus explain the molecular basis of the effect of divalent cations like Ca(2+), Sr(2+), Mg(2+), and Zn(2+) on the redox properties of the quinones in PSII, which has previously been attributed to long-range conformational changes propagated from divalent cations binding to the Ca(II)-binding site in the oxygen-evolving complex on the lumenal side of the PSII complex.

  17. Characterization and evolution of tetrameric photosystem I from the thermophilic cyanobacterium Chroococcidiopsis sp TS-821.

    PubMed

    Li, Meng; Semchonok, Dmitry A; Boekema, Egbert J; Bruce, Barry D

    2014-03-01

    Photosystem I (PSI) is a reaction center associated with oxygenic photosynthesis. Unlike the monomeric reaction centers in green and purple bacteria, PSI forms trimeric complexes in most cyanobacteria with a 3-fold rotational symmetry that is primarily stabilized via adjacent PsaL subunits; however, in plants/algae, PSI is monomeric. In this study, we discovered a tetrameric form of PSI in the thermophilic cyanobacterium Chroococcidiopsis sp TS-821 (TS-821). In TS-821, PSI forms tetrameric and dimeric species. We investigated these species by Blue Native PAGE, Suc density gradient centrifugation, 77K fluorescence, circular dichroism, and single-particle analysis. Transmission electron microscopy analysis of native membranes confirms the presence of the tetrameric PSI structure prior to detergent solubilization. To investigate why TS-821 forms tetramers instead of trimers, we cloned and analyzed its psaL gene. Interestingly, this gene product contains a short insert between the second and third predicted transmembrane helices. Phylogenetic analysis based on PsaL protein sequences shows that TS-821 is closely related to heterocyst-forming cyanobacteria, some of which also have a tetrameric form of PSI. These results are discussed in light of chloroplast evolution, and we propose that PSI evolved stepwise from a trimeric form to tetrameric oligomer en route to becoming monomeric in plants/algae. PMID:24681621

  18. Ammonia Binding in the Second Coordination Sphere of the Oxygen-Evolving Complex of Photosystem II.

    PubMed

    Vinyard, David J; Askerka, Mikhail; Debus, Richard J; Batista, Victor S; Brudvig, Gary W

    2016-08-01

    Ammonia binds to two sites in the oxygen-evolving complex (OEC) of Photosystem II (PSII). The first is as a terminal ligand to Mn in the S2 state, and the second is at a site outside the OEC that is competitive with chloride. Binding of ammonia in this latter secondary site results in the S2 state S = (5)/2 spin isomer being favored over the S = (1)/2 spin isomer. Using electron paramagnetic resonance spectroscopy, we find that ammonia binds to the secondary site in wild-type Synechocystis sp. PCC 6803 PSII, but not in D2-K317A mutated PSII that does not bind chloride. By combining these results with quantum mechanics/molecular mechanics calculations, we propose that ammonia binds in the secondary site in competition with D1-D61 as a hydrogen bond acceptor to the OEC terminal water ligand, W1. Implications for the mechanism of ammonia binding via its primary site directly to Mn4 in the OEC are discussed. PMID:27433995

  19. WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States1

    PubMed Central

    Gruenstaeudl, Michael

    2016-01-01

    Premise of the study: Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. Methods and Results: A set of command line–based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results. Conclusions: WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion. PMID:26949580

  20. A red-shifted antenna protein associated with photosystem II in Physcomitrella patens.

    PubMed

    Alboresi, Alessandro; Gerotto, Caterina; Cazzaniga, Stefano; Bassi, Roberto; Morosinotto, Tomas

    2011-08-19

    Antenna systems of plants and green algae are made up of pigment-protein complexes belonging to the light-harvesting complex (LHC) multigene family. LHCs increase the light-harvesting cross-section of photosystems I and II and catalyze photoprotective reactions that prevent light-induced damage in an oxygenic environment. The genome of the moss Physcomitrella patens contains two genes encoding LHCb9, a new antenna protein that bears an overall sequence similarity to photosystem II antenna proteins but carries a specific motif typical of photosystem I antenna proteins. This consists of the presence of an asparagine residue as a ligand for Chl 603 (A5) chromophore rather than a histidine, the common ligand in all other LHCbs. Asparagine as a Chl 603 (A5) ligand generates red-shifted spectral forms associated with photosystem I rather than with photosystem II, suggesting that in P. patens, the energy landscape of photosystem II might be different with respect to that of most green algae and plants. In this work, we show that the in vitro refolded LHCb9-pigment complexes carry a red-shifted fluorescence emission peak, different from all other known photosystem II antenna proteins. By using a specific antibody, we localized LHCb9 within PSII supercomplexes in the thylakoid membranes. This is the first report of red-shifted spectral forms in a PSII antenna system, suggesting that this biophysical feature might have a special role either in optimization of light use efficiency or in photoprotection in the specific environmental conditions experienced by this moss.

  1. Triton X-100 as an effective surfactant for the isolation and purification of photosystem I from Arthrospira platensis.

    PubMed

    Yu, Daoyong; Huang, Guihong; Xu, Fengxi; Wang, Mengfei; Liu, Shuang; Huang, Fang

    2014-06-01

    Surfactants play important roles in the preparation, structural, and functional research of membrane proteins, and solubilizing and isolating membrane protein, while keeping their structural integrity and activity intact is complicated. The commercial n-Dodecyl-β-D-maltoside (DDM) and Triton X-100 (TX) were used as solubilizers to extract and purify trimeric photosystem I (PSI) complex, an important photosynthetic membrane protein complex attracting broad interests. With an optimized procedure, TX can be used as an effective surfactant to isolate and purify PSI, as a replace of the much more expensive DDM. A mechanism was proposed to interpret the solubilization process at surfactant concentrations lower than the critical solubilization concentration. PSI-TX and PSI-DDM had identical polypeptide bands, pigment compositions, oxygen consumption, and photocurrent activities. This provides an alternative procedure and paves a way for economical and large-scale trimeric PSI preparation.

  2. Oxygen-evolving complex of photosystem II: correlating structure with spectroscopy.

    PubMed

    Pokhrel, Ravi; Brudvig, Gary W

    2014-06-28

    Water oxidation at the oxygen-evolving complex (OEC) of photosystem II (PSII) involves multiple redox states called Sn states (n = 0-4). The S1 → S2 redox transition of the OEC has been studied extensively using various forms of spectroscopy, including electron paramagnetic resonance (EPR) and Fourier transform infrared (FTIR) spectroscopy. In the S2 state, two isomers of the OEC are observed by EPR: a ST = 1/2 form and a ST = 5/2 form. DFT-based structural models of the OEC have been proposed for the two spin isomers in the S2 state, but the factors that determine the stability of one form or the other are not known. Using structural information on the OEC and its surroundings, in conjunction with spectroscopic information available on the S1 → S2 transition for a variety of site-directed mutations, Ca(2+) and Cl(-) substitutions, and small molecule inhibitors, we propose that the hydrogen-bonding network encompassing D1-D61 and the OEC-bound waters plays an important role in stabilizing one spin isomer over the other. In the presence of ammonia, PSII centers can be trapped in either the ST = 5/2 form after a 200 K illumination procedure or an ammonia-altered ST = 1/2 form upon annealing at 273 K. We propose a mechanism for ammonia binding to the OEC in the S2 state that takes into account the hydrogen-binding requirements for ammonia binding and the specificity for binding of ammonia but not methylamine. A discussion regarding the possibility of spin isomers of the OEC in the S1 state, analogous to the spin isomers of the S2 state, is also presented. PMID:24700294

  3. Photosystem II repair in marine diatoms with contrasting photophysiologies.

    PubMed

    Lavaud, Johann; Six, Christophe; Campbell, Douglas A

    2016-02-01

    Skeletonema costatum and Phaeodactylum tricornutum are model marine diatoms with differing strategies for non-photochemical dissipation of excess excitation energy within photosystem II (PSII). We showed that S. costatum, with connectivity across the pigment bed serving PSII, and limited capacity for induction of sustained non-photochemical quenching (NPQ), maintained a large ratio of [PSII(Total)]/[PSII(Active)] to buffer against fluctuations in light intensity. In contrast, P. tricornutum, with a larger capacity to induce sustained NPQ, could maintain a lower [PSII(Total)]/[PSII(Active)]. Induction of NPQ was correlated with an active PSII repair cycle in both species, and inhibition of chloroplastic protein synthesis with lincomycin leads to run away over-excitation of remaining PSII(Active), particularly in S. costatum. We discuss these distinctions in relation to the differing capacities, induction and relaxation rates for NPQ, and as strain adaptations to the differential light regimes of their originating habitats. The present work further confirms the important role for the light-dependent fast regulation of photochemistry by NPQ interacting with PSII repair cycle capacity in the ecophysiology of both pennate and centric diatoms. PMID:26156125

  4. Multiscale model of light harvesting by photosystem II in plants.

    PubMed

    Amarnath, Kapil; Bennett, Doran I G; Schneider, Anna R; Fleming, Graham R

    2016-02-01

    The first step of photosynthesis in plants is the absorption of sunlight by pigments in the antenna complexes of photosystem II (PSII), followed by transfer of the nascent excitation energy to the reaction centers, where long-term storage as chemical energy is initiated. Quantum mechanical mechanisms must be invoked to explain the transport of excitation within individual antenna. However, it is unclear how these mechanisms influence transfer across assemblies of antenna and thus the photochemical yield at reaction centers in the functional thylakoid membrane. Here, we model light harvesting at the several-hundred-nanometer scale of the PSII membrane, while preserving the dominant quantum effects previously observed in individual complexes. We show that excitation moves diffusively through the antenna with a diffusion length of 50 nm until it reaches a reaction center, where charge separation serves as an energetic trap. The diffusion length is a single parameter that incorporates the enhancing effect of excited state delocalization on individual rates of energy transfer as well as the complex kinetics that arise due to energy transfer and loss by decay to the ground state. The diffusion length determines PSII's high quantum efficiency in ideal conditions, as well as how it is altered by the membrane morphology and the closure of reaction centers. We anticipate that the model will be useful in resolving the nonphotochemical quenching mechanisms that PSII employs in conditions of high light stress.

  5. Electron transfer around photosystem I in cyanobacterial heterocyst membranes

    SciTech Connect

    Hawkesford, M.J.; Houchins, J.P.; Hind, G.

    1983-01-01

    Cyanobacteria are unique among the prokaryotes in possessing a higher plant-type of photosynthesis, with two photosystems linked in series. The heterocyst is a specialized cell type occurring in some filamentous strains at a frequency of 5 to 10%, and is the site of N/sub 2/-fixation under aerobic conditions. During differentiation of the heterocyst, the O/sub 2/-evolving PSII is lost and cyclic electron transfer around PSI predominates. The absence of PSII reaction centres and the diminished levels of accessory pigments give membranes isolated from heterocysts excellent properties for spectroscopic studies. Soluble components such as plastocyanin, cytochrome c-553 and PSI acceptors, washed from the membranes during isolation, may be selectively reconstituted. Additionally, the presence of an endogenous uptake hydrogenase which can be utilized experimentally to reduce the plastoquinone pool and the electron transfer chain, make heterocyst membranes a useful system in which to study cyclic electron flow. This paper reports an initial flash spectroscopic characterization of the electron transfer chain and speculates on the potential of the system.

  6. Multiscale model of light harvesting by photosystem II in plants

    PubMed Central

    Amarnath, Kapil; Bennett, Doran I. G.; Schneider, Anna R.; Fleming, Graham R.

    2016-01-01

    The first step of photosynthesis in plants is the absorption of sunlight by pigments in the antenna complexes of photosystem II (PSII), followed by transfer of the nascent excitation energy to the reaction centers, where long-term storage as chemical energy is initiated. Quantum mechanical mechanisms must be invoked to explain the transport of excitation within individual antenna. However, it is unclear how these mechanisms influence transfer across assemblies of antenna and thus the photochemical yield at reaction centers in the functional thylakoid membrane. Here, we model light harvesting at the several-hundred-nanometer scale of the PSII membrane, while preserving the dominant quantum effects previously observed in individual complexes. We show that excitation moves diffusively through the antenna with a diffusion length of 50 nm until it reaches a reaction center, where charge separation serves as an energetic trap. The diffusion length is a single parameter that incorporates the enhancing effect of excited state delocalization on individual rates of energy transfer as well as the complex kinetics that arise due to energy transfer and loss by decay to the ground state. The diffusion length determines PSII’s high quantum efficiency in ideal conditions, as well as how it is altered by the membrane morphology and the closure of reaction centers. We anticipate that the model will be useful in resolving the nonphotochemical quenching mechanisms that PSII employs in conditions of high light stress. PMID:26787911

  7. Primary charge separation in isolated photosystem II reaction centers

    SciTech Connect

    Seibert, M.; Toon, S.; Govindjee; O`Neil, M.P.; Wasielewski, M.R.

    1992-08-24

    Primary charge-separation in isolated bacterial reaction center (RC) complex occurs in 2.8 ps at room temperature and 0.7--1.2 ps at 10 K. Because of similarities between the bacterial and photosystem II (PSII) RCs, it has been of considerable interest to obtain analogous charge-separation rates in the higher plant system. Our previous femtosecond transient absorption studies used PSII RC material stabilized with PEG or by exchanging dodecyl maltoside (DM) for Triton in the isolation procedure. These materials gave charge-separation 1/e times of 3.0 {plus_minus} 0.6 ps at 4{degree}C and 1.4{plus_minus} 0.2 ps at 15 K based on the risetime of transient absorption kinetics at 820 nm. These values were thought to represent the time required for formation of the P680{sup +}-Pheo{sup {minus}} state. Recent results of Hastings et al. obtained at high data acquisition rates and low flash intensities, suggest that the Pheo{sup {minus}} state may form more slowly. In light of this work, we have carried out additional time domain studies of both electron transport and energy transfer phenomena in stabilized DM PSII RCs at room temperature. We used a 1-kHz repetition rate femtosecond transient absorption spectrometer with a 200 fs instrumental time resolution and compared the results with those obtained by others using frequency domain hole-burning techniques.

  8. Protein film photoelectrochemistry of the water oxidation enzyme photosystem II.

    PubMed

    Kato, Masaru; Zhang, Jenny Z; Paul, Nicholas; Reisner, Erwin

    2014-09-21

    Photosynthesis is responsible for the sunlight-powered conversion of carbon dioxide and water into chemical energy in the form of carbohydrates and the release of O2 as a by-product. Although many proteins are involved in photosynthesis, the fascinating machinery of Photosystem II (PSII) is at the heart of this process. This tutorial review describes an emerging technique named protein film photoelectrochemistry (PF-PEC), which allows for the light-dependent activity of PSII adsorbed onto an electrode surface to be studied. The technique is straightforward to use, does not require highly specialised and/or expensive equipment, is highly selective for the active fractions of the adsorbed enzyme, and requires a small amount of enzyme sample. The use of PF-PEC to study PSII can yield insights into its activity, stability, quantum yields, redox behaviour, and interfacial electron transfer pathways. It can also be used in PSII inhibition studies and chemical screening, which may prove useful in the development of biosensors. PSII PF-PEC cells also serve as proof-of-principle solar water oxidation systems; here, a comparison is made against PSII-inspired synthetic photocatalysts and materials for artificial photosynthesis.

  9. (Unraveling photosystems): Progress report, July 1, 1982-June 30, 1983

    SciTech Connect

    Bogorad, L.

    1983-01-01

    The overall objective of this program is to identify and characterize genes for components of the photosynthetic apparatus - especially genes for components of photosystem II (PS II). During the past year two atrazine resistant mutants of the blue-green alga Anacystis nidulans R-2 have been isolated and partially characterized. Thylakoid membranes have been prepared from these cells as well as from wild type cells and their rates of oxygen evolution measured in the presence and absence of atrazine. The I/sub 50/ for the two mutants was approximately 2 x 10/sup -8/M whereas for wild type cells it was 7.5 x 10/sup -10/M. Visible absorption and fluorescence emission spectra of the mutant and wild type cells have been compared. One of the mutants possesses spectra similar to the wild type while the second mutant does not. The latter mutant appears to have increased absorption peaks due to phycocyanin and allophycocyanin. DNA has been purified from both atrazine resistant mutants and used to transform wild type cells to atrazine resistance. Transformation of cells to the resistant phenotype is reproducible although the frequency of transformation varies. ''Mutant DNA'' subjected to restriction enzyme cleavage prior to use for transformation yields transformants but the frequency is generally about one order of magnitude lower than with uncut DNA. 54 refs., 3 figs.

  10. Fluorescence spectroscopy of excitation transfer in Photosystem 1

    SciTech Connect

    Mukerji, I.

    1990-12-01

    This thesis centers on the study of excitation transfer in a photosynthetic antenna array. The spectroscopic properties of two pigment-protein complexes were investigated. These complexes, isolated from higher plants, display an unusual temperature dependent fluorescence behavior. The author have chosen to study this fluorescence behavior with respect to energy transfer to the reaction center and in an isolated intact antenna preparation. A Photosystem 1 complex, PSI-200, was isolated from spinach. We have characterized this system by both steady state and time-resolved fluorescence spectroscopy. Fluorescence polarization measurements indicate that this emission arises from pigments which absorb in the long wavelength region of the spectrum and comprise a relatively small portion of the antenna population. Comparison of spectral characteristics were made with a PSI complex isolated from the thermophilic cyanobacterium, Synechococcus, sp. To address the role of Chl b in stimulating long wavelength fluorescence and the temperature dependence of the system, we have studied the energy transfer dynamics in an antenna complex, LHC-I isolated from PSI-200. Kinetic measurements indicate that initially absorbed excitation is rapidly redistributed to longer wavelength emitting pigments within 40 ps. The temperature dependence of F685 results from increased back transfer from long wavelength emitters to F685. We suggest that changes in excitation transfer between the various emitting species and a non-radiative fluorescence quenching mechanism account for the temperature dependence of the system. 144 refs., 50 figs., 3 tabs.

  11. Functional Implications of Photosystem II Crystal Formation in Photosynthetic Membranes.

    PubMed

    Tietz, Stefanie; Puthiyaveetil, Sujith; Enlow, Heather M; Yarbrough, Robert; Wood, Magnus; Semchonok, Dmitry A; Lowry, Troy; Li, Zhirong; Jahns, Peter; Boekema, Egbert J; Lenhert, Steven; Niyogi, Krishna K; Kirchhoff, Helmut

    2015-05-29

    The structural organization of proteins in biological membranes can affect their function. Photosynthetic thylakoid membranes in chloroplasts have the remarkable ability to change their supramolecular organization between disordered and semicrystalline states. Although the change to the semicrystalline state is known to be triggered by abiotic factors, the functional significance of this protein organization has not yet been understood. Taking advantage of an Arabidopsis thaliana fatty acid desaturase mutant (fad5) that constitutively forms semicrystalline arrays, we systematically test the functional implications of protein crystals in photosynthetic membranes. Here, we show that the change into an ordered state facilitates molecular diffusion of photosynthetic components in crowded thylakoid membranes. The increased mobility of small lipophilic molecules like plastoquinone and xanthophylls has implications for diffusion-dependent electron transport and photoprotective energy-dependent quenching. The mobility of the large photosystem II supercomplexes, however, is impaired, leading to retarded repair of damaged proteins. Our results demonstrate that supramolecular changes into more ordered states have differing impacts on photosynthesis that favor either diffusion-dependent electron transport and photoprotection or protein repair processes, thus fine-tuning the photosynthetic energy conversion.

  12. Functional Implications of Photosystem II Crystal Formation in Photosynthetic Membranes*

    PubMed Central

    Tietz, Stefanie; Puthiyaveetil, Sujith; Enlow, Heather M.; Yarbrough, Robert; Wood, Magnus; Semchonok, Dmitry A.; Lowry, Troy; Li, Zhirong; Jahns, Peter; Boekema, Egbert J.; Lenhert, Steven; Niyogi, Krishna K.; Kirchhoff, Helmut

    2015-01-01

    The structural organization of proteins in biological membranes can affect their function. Photosynthetic thylakoid membranes in chloroplasts have the remarkable ability to change their supramolecular organization between disordered and semicrystalline states. Although the change to the semicrystalline state is known to be triggered by abiotic factors, the functional significance of this protein organization has not yet been understood. Taking advantage of an Arabidopsis thaliana fatty acid desaturase mutant (fad5) that constitutively forms semicrystalline arrays, we systematically test the functional implications of protein crystals in photosynthetic membranes. Here, we show that the change into an ordered state facilitates molecular diffusion of photosynthetic components in crowded thylakoid membranes. The increased mobility of small lipophilic molecules like plastoquinone and xanthophylls has implications for diffusion-dependent electron transport and photoprotective energy-dependent quenching. The mobility of the large photosystem II supercomplexes, however, is impaired, leading to retarded repair of damaged proteins. Our results demonstrate that supramolecular changes into more ordered states have differing impacts on photosynthesis that favor either diffusion-dependent electron transport and photoprotection or protein repair processes, thus fine-tuning the photosynthetic energy conversion. PMID:25897076

  13. Functional architecture of higher plant photosystem II supercomplexes

    PubMed Central

    Caffarri, Stefano; Kouřil, Roman; Kereïche, Sami; Boekema, Egbert J; Croce, Roberta

    2009-01-01

    Photosystem II (PSII) is a large multiprotein complex, which catalyses water splitting and plastoquinone reduction necessary to transform sunlight into chemical energy. Detailed functional and structural studies of the complex from higher plants have been hampered by the impossibility to purify it to homogeneity. In this work, homogeneous preparations ranging from a newly identified particle composed by a monomeric core and antenna proteins to the largest C2S2M2 supercomplex were isolated. Characterization by biochemical methods and single particle electron microscopy allowed to relate for the first time the supramolecular organization to the protein content. A projection map of C2S2M2 at 12 Å resolution was obtained, which allowed determining the location and the orientation of the antenna proteins. Comparison of the supercomplexes obtained from WT and Lhcb-deficient plants reveals the importance of the individual subunits for the supramolecular organization. The functional implications of these findings are discussed and allow redefining previous suggestions on PSII energy transfer, assembly, photoinhibition, state transition and non-photochemical quenching. PMID:19696744

  14. Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral "Salicoid" Genome Duplication.

    PubMed

    Hou, Jing; Ye, Ning; Dong, Zhongyuan; Lu, Mengzhu; Li, Laigeng; Yin, Tongming

    2016-01-01

    Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the "salicoid" duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants. PMID:27352946

  15. Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral “Salicoid” Genome Duplication

    PubMed Central

    Hou, Jing; Ye, Ning; Dong, Zhongyuan; Lu, Mengzhu; Li, Laigeng; Yin, Tongming

    2016-01-01

    Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the “salicoid” duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants. PMID:27352946

  16. The Survival Effect in Memory: Does It Hold into Old Age and Non-Ancestral Scenarios?

    PubMed Central

    Yang, Lixia; Lau, Karen P. L.; Truong, Linda

    2014-01-01

    The survival effect in memory refers to the memory enhancement for materials encoded in reference to a survival scenario compared to those encoded in reference to a control scenario or with other encoding strategies [1]. The current study examined whether this effect is well maintained in old age by testing young (ages 18–29) and older adults (ages 65–87) on the survival effect in memory for words encoded in ancestral and/or non-ancestral modern survival scenarios relative to a non-survival control scenario. A pilot study was conducted to select the best matched comparison scenarios based on potential confounding variables, such as valence and arousal. Experiment 1 assessed the survival effect with a well-matched negative control scenario in both young and older adults. The results showed an age-equivalent survival effect across an ancestral and a non-ancestral modern survival scenario. Experiment 2 replicated the survival effect in both age groups with a positive control scenario. Taken together, the data suggest a robust survival effect that is well preserved in old age across ancestral and non-ancestral survival scenarios. PMID:24788755

  17. Crystal structure of photosystem II from Synechococcus elongatus at 3.8 A resolution.

    PubMed

    Zouni, A; Witt, H T; Kern, J; Fromme, P; Krauss, N; Saenger, W; Orth, P

    2001-02-01

    Oxygenic photosynthesis is the principal energy converter on earth. It is driven by photosystems I and II, two large protein-cofactor complexes located in the thylakoid membrane and acting in series. In photosystem II, water is oxidized; this event provides the overall process with the necessary electrons and protons, and the atmosphere with oxygen. To date, structural information on the architecture of the complex has been provided by electron microscopy of intact, active photosystem II at 15-30 A resolution, and by electron crystallography on two-dimensional crystals of D1-D2-CP47 photosystem II fragments without water oxidizing activity at 8 A resolution. Here we describe the X-ray structure of photosystem II on the basis of crystals fully active in water oxidation. The structure shows how protein subunits and cofactors are spatially organized. The larger subunits are assigned and the locations and orientations of the cofactors are defined. We also provide new information on the position, size and shape of the manganese cluster, which catalyzes water oxidation.

  18. Effective Absorption Cross-Sections in Porphyridium cruentum: Implications for Energy Transfer between Phycobilisomes and Photosystem II Reaction Centers.

    PubMed

    Ley, A C

    1984-02-01

    Effective absorption cross-sections for O(2) production by Porphyridium cruentum were measured at 546 and 596 nanometers. Although all photosystem II reaction centers are energetically coupled to phycobilisomes, any single phycobilisome acts as antenna for several photosystem II reaction centers. The cross-section measured in state I was 50% larger than that measured in state II.

  19. Characterization of the Expression of the Photosystem II-Oxygen Evolving Complex in C4 Species of Flaveria 1

    PubMed Central

    Ketchner, Susan L.; Sayre, Richard T.

    1992-01-01

    We have determined the levels of photosystem II activity and polypeptide abundance in whole leaves and isolated bundle sheath and mesophyll cells of C4, “C4-like,” and C3 species of the genus Flaveria (Asteraceae). On a chlorophyll basis, the whole leaf levels of the D1, D2, and 34-kilodalton photosystem II polypeptides were similar for each Flaveria species. Photosystem II activity varied twofold, but was not correlated with photosynthetic type (C3 or C4). The bundle sheath cell levels of photosystem II activity and associated polypeptides in C4-like and C4 Flaveria species were approximately one-half those observed in mesophyll cells but equivalent to those in bundle sheath cells of the C3 species, Flaveria cronquistii. Analyses of the steady-state levels of transcripts encoding photosystem II polypeptides indicated that there were no differences in transcript abundance between mesophyll and bundle sheath cells of the C4 Flaveria species. This pattern was in contrast to the three- to tenfold higher levels of transcripts encoding photosystem II polypeptides in mesophyll versus bundle sheath cells of maize. It is apparent that the higher mesophyll cell to bundle sheath ratio of photosystem II polypeptides in C4- and C4-like species of Flaveria is the result of higher levels of photosystem II expression in mesophyll cells rather than lower levels of expression in bundle sheath cells. ImagesFigure 1Figure 3Figure 4Figure 5 PMID:16668740

  20. Three-dimensional structure of photosystem II from Thermosynechococcus elongates in complex with terbutryn

    SciTech Connect

    Gabdulkhakov, A. G. Dontsova, M. V.; Saenger, W.

    2011-11-15

    Photosystem II is a key component of the photosynthetic pathway producing oxygen at the thylakoid membrane of cyanobacteria, green algae, and plants. The three-dimensional structure of photosystem II from the cyanobacterium Thermosynechococcus elongates in a complex with herbicide terbutryn (a photosynthesis inhibitor) was determined for the first time by X-ray diffraction and refined at 3.2 Angstrom-Sign resolution (R{sub factor} = 26.9%, R{sub free} = 29.9%, rmsd for bond lengths is 0.013 Angstrom-Sign , and rmsd for bond angles is 2.2 Degree-Sign ). The terbutryn molecule was located in the binding pocket of the mobile plastoquinone. The atomic coordinates of the refined structure of photosystem II in a complex with terbutryn were deposited in the Protein Data Bank.

  1. State transitions redistribute rather than dissipate energy between the two photosystems in Chlamydomonas.

    PubMed

    Nawrocki, Wojciech J; Santabarbara, Stefano; Mosebach, Laura; Wollman, Francis-André; Rappaport, Fabrice

    2016-01-01

    Photosynthesis converts sunlight into biologically useful compounds, thus fuelling practically the entire biosphere. This process involves two photosystems acting in series powered by light harvesting complexes (LHCs) that dramatically increase the energy flux to the reaction centres. These complexes are the main targets of the regulatory processes that allow photosynthetic organisms to thrive across a broad range of light intensities. In microalgae, one mechanism for adjusting the flow of energy to the photosystems, state transitions, has a much larger amplitude than in terrestrial plants, whereas thermal dissipation of energy, the dominant regulatory mechanism in plants, only takes place after acclimation to high light. Here we show that, at variance with recent reports, microalgal state transitions do not dissipate light energy but redistribute it between the two photosystems, thereby allowing a well-balanced influx of excitation energy. PMID:27249564

  2. Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution.

    PubMed

    Jordan, P; Fromme, P; Witt, H T; Klukas, O; Saenger, W; Krauss, N

    2001-06-21

    Life on Earth depends on photosynthesis, the conversion of light energy from the Sun to chemical energy. In plants, green algae and cyanobacteria, this process is driven by the cooperation of two large protein-cofactor complexes, photosystems I and II, which are located in the thylakoid photosynthetic membranes. The crystal structure of photosystem I from the thermophilic cyanobacterium Synechococcus elongatus described here provides a picture at atomic detail of 12 protein subunits and 127 cofactors comprising 96 chlorophylls, 2 phylloquinones, 3 Fe4S4 clusters, 22 carotenoids, 4 lipids, a putative Ca2+ ion and 201 water molecules. The structural information on the proteins and cofactors and their interactions provides a basis for understanding how the high efficiency of photosystem I in light capturing and electron transfer is achieved.

  3. Kinetics of phyllosemiquinone oxidation in the Photosystem I reaction centre of Acaryochloris marina.

    PubMed

    Santabarbara, Stefano; Bailleul, Benjamin; Redding, Kevin; Barber, James; Rappaport, Fabrice; Telfer, Alison

    2012-02-01

    Light-induced electron transfer reactions in the chlorophyll a/d-binding Photosystem I reaction centre of Acaryochloris marina were investigated in whole cells by pump-probe optical spectroscopy with a temporal resolution of ~5ns at room temperature. It is shown that phyllosemiquinone, the secondary electron transfer acceptor anion, is oxidised with bi-phasic kinetics characterised by lifetimes of 88±6ns and 345±10ns. These lifetimes, particularly the former, are significantly slower than those reported for chlorophyll a-binding Photosystem I, which typically range in the 5-30ns and 200-300ns intervals. The possible mechanism of electron transfer reactions in the chlorophyll a/d-binding Photosystem I and the slower oxidation kinetics of the secondary acceptors are discussed. PMID:22037394

  4. Acetate in mixotrophic growth medium affects photosystem II in Chlamydomonas reinhardtii and protects against photoinhibition.

    PubMed

    Roach, Thomas; Sedoud, Arezki; Krieger-Liszkay, Anja

    2013-10-01

    Chlamydomonas reinhardtii is a photoautotrophic green alga, which can be grown mixotrophically in acetate-supplemented media (Tris-acetate-phosphate). We show that acetate has a direct effect on photosystem II (PSII). As a consequence, Tris-acetate-phosphate-grown mixotrophic C. reinhardtii cultures are less susceptible to photoinhibition than photoautotrophic cultures when subjected to high light. Spin-trapping electron paramagnetic resonance spectroscopy showed that thylakoids from mixotrophic C. reinhardtii produced less (1)O2 than those from photoautotrophic cultures. The same was observed in vivo by measuring DanePy oxalate fluorescence quenching. Photoinhibition can be induced by the production of (1)O2 originating from charge recombination events in photosystem II, which are governed by the midpoint potentials (Em) of the quinone electron acceptors. Thermoluminescence indicated that the Em of the primary quinone acceptor (QA/QA(-)) of mixotrophic cells was stabilised while the Em of the secondary quinone acceptor (QB/QB(-)) was destabilised, therefore favouring direct non-radiative charge recombination events that do not lead to (1)O2 production. Acetate treatment of photosystem II-enriched membrane fragments from spinach led to the same thermoluminescence shifts as observed in C. reinhardtii, showing that acetate exhibits a direct effect on photosystem II independent from the metabolic state of a cell. A change in the environment of the non-heme iron of acetate-treated photosystem II particles was detected by low temperature electron paramagnetic resonance spectroscopy. We hypothesise that acetate replaces the bicarbonate associated to the non-heme iron and changes the environment of QA and QB affecting photosystem II charge recombination events and photoinhibition.

  5. Relevance of the photosynthetic reaction center from purple bacteria to the structure of photosystem II

    SciTech Connect

    Michel, H.; Deisenhofer, J.

    1988-01-12

    Photosynthetic organisms are able to oxidize organic or inorganic compounds upon the absorption of light, and they use the extracted electron for the fixation of carbon dioxide. The most important oxidation product is oxygen due to the splitting of water. In eukaryotes these processes occur in photosystem II of chloroplasts. Among prokaryotes photosynthetic oxygen evolution is restricted to cyanobacteria and prochloron-type organisms. How water is split in the oxygen-evolving complex of photosystem II belongs to the most important question to be answered. The primary charge separation occurs in the reaction center of photosystem II. This reaction center is a complex consisting of peripheral and integral membrane proteins, several chlorophyll A molecules, two pheophytin A molecules, two and three plastoquinone molecules, and one non-heme iron atom. The location of the photosystem II reaction center is still a matter of debate. Nakatani et al. (l984) concluded from fluorescence measurements that a protein of apparent molecular weight 47,000 (CP47) is the apoprotein of the photosystem II reaction center. A different view emerged from work with the photosynthetic reaction centers from the purple bacteria. The amino acid sequence of the M subunit of the reaction center from Phodopseudomonas (Rps.) sphaeroides has sequence homologies with the D1 protein from spinach. A substantial amount of structural information can be obtained with the reaction center from Rhodopseudomonas viridis, which can be crystallized. Here the authors discuss the structure of the photosynthetic reaction center from the purple bacterium Rps. viridis and describe the role of those amino acids that are conserved between the bacterial and photosystem II reaction center.

  6. Both chlorophylls a and d are essential for the photochemistry in photosystem II of the cyanobacteria, Acaryochloris marina.

    PubMed

    Schlodder, Eberhard; Cetin, Marianne; Eckert, Hann-Jörg; Schmitt, Franz-Josef; Barber, James; Telfer, Alison

    2007-06-01

    We have measured the flash-induced absorbance difference spectrum attributed to the formation of the secondary radical pair, P(+)Q(-), between 270 nm and 1000 nm at 77 K in photosystem II of the chlorophyll d containing cyanobacterium, Acaryochloris marina. Despite the high level of chlorophyll d present, the flash-induced absorption difference spectrum of an approximately 2 ms decay component shows a number of features which are typical of the difference spectrum seen in oxygenic photosynthetic organisms containing no chlorophyll d. The spectral shape in the near-UV indicates that a plastoquinone is the secondary acceptor molecule (Q(A)). The strong C-550 change at 543 nm confirms previous reports that pheophytin a is the primary electron acceptor. The bleach at 435 nm and increase in absorption at 820 nm indicates that the positive charge is stabilized on a chlorophyll a molecule. In addition a strong electrochromic band shift, centred at 723 nm, has been observed. It is assigned to a shift of the Qy band of the neighbouring accessory chlorophyll d, Chl(D1). It seems highly likely that it accepts excitation energy from the chlorophyll d containing antenna. We therefore propose that primary charge separation is initiated from this chlorophyll d molecule and functions as the primary electron donor. Despite its lower excited state energy (0.1 V less), as compared to chlorophyll a, this chlorophyll d molecule is capable of driving the plastoquinone oxidoreductase activity of photosystem II. However, chlorophyll a is used to stabilize the positive charge and ultimately to drive water oxidation.

  7. Petrologic, tectonic, and metallogenic evolution of the Ancestral Cascades magmatic arc, Washington, Oregon, and northern California

    USGS Publications Warehouse

    du Bray, Edward A.; John, David A.

    2011-01-01

    Present-day High Cascades arc magmatism was preceded by ~40 m.y. of nearly cospatial magmatism represented by the ancestral Cascades arc in Washington, Oregon, and northernmost California (United States). Time-space-composition relations for the ancestral Cascades arc have been synthesized from a recent compilation of more than 4000 geochemical analyses and associated age data. Neither the composition nor distribution of ancestral Cascades magmatism was uniform along the length of the ancestral arc through time. Initial (>40 to 36 Ma) ancestral Cascades magmatism (mostly basalt and basaltic andesite) was focused at the north end of the arc between the present-day locations of Mount Rainier and the Columbia River. From 35 to 18 Ma, initial basaltic andesite and andesite magmatism evolved to include dacite and rhyolite; magmatic activity became more voluminous and extended along most of the arc. Between 17 and 8 Ma, magmatism was focused along the part of the arc coincident with the northern two-thirds of Oregon and returned to more mafic compositions. Subsequent ancestral Cascades magmatism was dominated by basaltic andesite to basalt prior to the post–4 Ma onset of High Cascades magmatism. Transitional tholeiitic to calc-alkaline compositions dominated early (before 40 to ca. 25 Ma) ancestral Cascades eruptive products, whereas the majority of the younger arc rocks have a calc-alkaline affinity. Tholeiitic compositions characteristic of the oldest ancestral arc magmas suggest development associated with thin, immature crust and slab window processes, whereas the younger, calc-alkaline magmas suggest interaction with thicker, more evolved crust and more conventional subduction-related magmatic processes. Presumed changes in subducted slab dip through time also correlate with fundamental magma composition variation. The predominance of mafic compositions during latest ancestral arc magmatism and throughout the history of modern High Cascades magmatism probably

  8. Stoichiometry of photosystem I, photosystem II, and phycobilisomes in the red alga Porphyridium cruentum as a function of growth irradiance

    SciTech Connect

    Cunningham, F.X. Jr.; Mustardy, L.; Gantt, E. ); Dennenberg, R.J.; Jursinic, P.A. )

    1989-11-01

    Cells of the red alga Porphyridium cruentum (ATCC 50161) exposed to increasing growth irradiance exhibited up to a three-fold reduction in photosystems I and II (PSI and PSII) and phycobilisomes but little change in the relative numbers of these components. Batch cultures of P. cruentum were grown under four photon flux densities of continuous white light; 6 (low light LL), 35 (medium light, ML), 180 (high light, HL), and 280 (very high light, VHL) microeinsteins per square meter per second and sampled in the exponential phase of growth. Ratios of PSII to PSI ranged between 0.43 and 0.54. About three PSII centers per phycobilisome were found, regardless of growth irradiance. The phycoerythrin content of phycobilisomes decreased by about 25% for HL and VHL compared to LL and ML cultures. The unit sizes of PSI (chlorophyll/P{sub 700}) and PSII (chlorophyll/Q{sub A}) decreased by about 20% with increase in photon flux density from 6 to 280 microeinsteins per square meter per second. A threefold reduction in cell content of chlorophyll at the higher photon flux densities was accompanied by a twofold reduction in {beta}-carotene, and a drastic reduction in thylakoid membrane area. Cell content of zeaxanthin, the major carotenoid in P. cruentum, did not vary with growth irradiance, suggesting a role other than light-harvesting. HL cultures had a growth rate twice that of ML, eight times that of LL, and slightly greater than that of VHL cultures. Cell volume increased threefold from LL to VHL, but volume of the single chloroplast did not change. From this study it is evident that a relatively fixed stoichiometry of PSI, PSII, and phycobilisomes is maintained in the photosynthetic apparatus of this red alga over a wide range of growth irradiance.

  9. Thermal bleaching induced changes in photosystem II function not reflected by changes in photosystem II protein content of Stylophora pistillata

    NASA Astrophysics Data System (ADS)

    Jeans, J.; Szabó, M.; Campbell, D. A.; Larkum, A. W. D.; Ralph, P. J.; Hill, R.

    2014-03-01

    Scleractinian corals exist in a symbiosis with marine dinoflagellates of the genus Symbiodinium that is easily disrupted by changes in the external environment. Increasing seawater temperatures cause loss of pigments and expulsion of the symbionts from the host in a process known as coral bleaching; though, the exact mechanism and trigger of this process has yet to be elucidated. We exposed nubbins of the coral Stylophora pistillata to bleaching temperatures over a period of 14 daylight hours. Fifty-nine percent of the symbiont population was expelled over the course of this short-term treatment. Maximum quantum yield ( F V/ F M) of photosystem (PS) II for the in hospite symbiont population did not change significantly over the treatment period, but there was a significant decline in the quantity of PSII core proteins (PsbA and PsbD) at the onset of the experimental increase in temperature. F V/ F M from populations of expelled symbionts dropped sharply over the first 6 h of temperature treatment, and then toward the end of the experiment, it increased to an F V/ F M value similar to that of the in hospite population. This suggests that the symbionts were likely damaged prior to expulsion from the host, and the most damaged symbionts were expelled earlier in the bleaching. The quantity of PSII core proteins, PsbA and PsbD, per cell was significantly higher in the expelled symbionts than in the remaining in hospite population over 6-10 h of temperature treatment. We attribute this to a buildup of inactive PSII reaction centers, likely caused by a breakdown in the PSII repair cycle. Thus, thermal bleaching of the coral S. pistillata induces changes in PSII content that do not follow the pattern that would be expected based on the results of PSII function.

  10. Genetic Manipulation of the Cyanobacterium Synechocystis sp. PCC 6803 (Development of Strains Lacking Photosystem I for the Analysis of Mutations in Photosystem II).

    PubMed Central

    Smart, L. B.; Bowlby, N. R.; Anderson, S. L.; Sithole, I.; McIntosh, L.

    1994-01-01

    We have taken a genetic approach to eliminating the presence of photosystem I (PSI) in site-directed mutants of photosystem II (PSII) in the cyanobacterium Synechocystis sp. PCC 6803. By selecting under light-activated heterotrophic conditions, we have inactivated the psaA-psaB operon encoding the PSI reaction center proteins in cells containing deletions of the three psbA genes. We have also introduced deletions into both copies of psbD in a strain containing a mutation that inactivates psaA (ADK9). These strains, designated D1-/PSI- and D2-/PSI-, may serve as recipient strains for the incorporation of site-directed mutations in either psbA2 or psbD1. The characterization of these cells, which lack both PSI and PSII, is described. PMID:12232086

  11. Spring Ephemerals Adapt to Extremely High Light Conditions via an Unusual Stabilization of Photosystem II

    PubMed Central

    Tu, Wenfeng; Li, Yang; Liu, Wu; Wu, Lishuan; Xie, Xiaoyan; Zhang, Yuanming; Wilhelm, Christian; Yang, Chunhong

    2016-01-01

    Ephemerals, widely distributed in the Gobi desert, have developed significant characteristics to sustain high photosynthetic efficiency under high light (HL) conditions. Since the light reaction is the basis for photosynthetic conversion of solar energy to chemical energy, the photosynthetic performances in thylakoid membrane of the spring ephemerals in response to HL were studied. Three plant species, namely two C3 spring ephemeral species of Cruciferae: Arabidopsis pumila (A. pumila) and Sisymbrium altissimum (S. altissimum), and the model plant Arabidopsis thaliana (A. thaliana) were chosen for the study. The ephemeral A. pumila, which is genetically close to A. thaliana and ecologically in the same habitat as S. altissimum, was used to avoid complications arising from the superficial differences resulted from comparing plants from two extremely contrasting ecological groups. The findings manifested that the ephemerals showed significantly enhanced activities of photosystem (PS) II under HL conditions, while the activities of PSII in A. thaliana were markedly decreased under the same conditions. Detailed analyses of the electron transport processes revealed that the increased plastoquinone pool oxidization, together with the enhanced PSI activities, ensured a lowered excitation pressure to PSII of both ephemerals, and thus facilitated the photosynthetic control to avoid photodamage to PSII. The analysis of the reaction centers of the PSs, both in terms of D1 protein turnover kinetics and the long-term adaptation, revealed that the unusually stable PSs structure provided the basis for the ephemerals to carry out high photosynthetic performances. It is proposed that the characteristic photosynthetic performances of ephemerals were resulted from effects of the long-term adaptation to the harsh environments. PMID:26779223

  12. Energy transfer and trapping in red-chlorophyll-free photosystem I from Synechococcus WH 7803.

    PubMed

    van Stokkum, Ivo H M; Desquilbet, Thibaut E; van der Weij-de Wit, Chantal D; Snellenburg, Joris J; van Grondelle, Rienk; Thomas, Jean-Claude; Dekker, Jan P; Robert, Bruno

    2013-09-26

    We report for the first time steady-state and time-resolved emission properties of photosystem I (PSI) complexes isolated from the cyanobacterial strain Synechococcus WH 7803. The PSI complexes from this strain display an extremely small fluorescence emission yield at 77 K, which we attribute to the absence of so-called red antenna chlorophylls, chlorophylls with absorption maxima at wavelengths longer than those of the primary electron donor P700. Emission measurements at room temperature with picosecond time resolution resulted in two main decay components with lifetimes of about 7.5 and 18 ps and spectra peaking at about 685 nm. Especially in the red flanks, these spectra show consistent differences, which means that earlier proposed models for the primary charge separation reactions based on ultrafast (∼1 ps) excitation equilibration processes cannot describe the data. We show target analyses of a number of alternative models and conclude that a simple model (Ant2)* ↔ (Ant1/RC)* → RP2 can explain the time-resolved emission data very well. In this model, (Ant2)* represents chlorophylls that spectrally equilibrate in about 7.5 ps and in which RP2 represents the "final" radical pair P700(+)A0(-). Adding an equilibrium (Ant1/RC)* ↔ RP1, in which RP1 represents an "intermediate" radical pair A(+)A0(-), resulted in the same fit quality. We show that the simple model without RP1 can easily be extended to PSI complexes from cyanobacteria with one or more pools of red antenna chlorophylls and also that the model provides a straightforward explanation of steady-state emission properties observed at cryogenic temperatures.

  13. Attachment of phycobilisomes in an antenna-photosystem I supercomplex of cyanobacteria.

    PubMed

    Watanabe, Mai; Semchonok, Dmitry A; Webber-Birungi, Mariam T; Ehira, Shigeki; Kondo, Kumiko; Narikawa, Rei; Ohmori, Masayuki; Boekema, Egbert J; Ikeuchi, Masahiko

    2014-02-18

    Oxygenic photosynthesis is driven by photosystems I and II (PSI and PSII, respectively). Both have specific antenna complexes and the phycobilisome (PBS) is the major antenna protein complex in cyanobacteria, typically consisting of a core from which several rod-like subcomplexes protrude. PBS preferentially transfers light energy to PSII, whereas a PSI-specific antenna has not been identified. The cyanobacterium Anabaena sp. PCC 7120 has rod-core linker genes (cpcG1-cpcG2-cpcG3-cpcG4). Their products, except CpcG3, have been detected in the conventional PBS. Here we report the isolation of a supercomplex that comprises a PSI tetramer and a second, unique type of a PBS, specific to PSI. This rod-shaped PBS includes phycocyanin (PC) and CpcG3 (hereafter renamed "CpcL"), but no allophycocyanin or CpcGs. Fluorescence excitation showed efficient energy transfer from PBS to PSI. The supercomplex was analyzed by electron microscopy and single-particle averaging. In the supercomplex, one to three rod-shaped CpcL-PBSs associate to a tetrameric PSI complex. They are mostly composed of two hexameric PC units and bind at the periphery of PSI, at the interfaces of two monomers. Structural modeling indicates, based on 2D projection maps, how the PsaI, PsaL, and PsaM subunits link PSI monomers into dimers and into a rhombically shaped tetramer or "pseudotetramer." The 3D model further shows where PBSs associate with the large subunits PsaA and PsaB of PSI. It is proposed that the alternative form of CpcL-PBS is functional in harvesting energy in a wide number of cyanobacteria, partially to facilitate the involvement of PSI in nitrogen fixation.

  14. Light-dependent degradation of the D1 protein in photosystem II is accelerated after inhibition of the water splitting reaction

    SciTech Connect

    Jegerschoeld, C.V.; Virgin, I.; Styring, S. )

    1990-07-03

    Strong illumination of oxygen-evolving organisms inhibits the electron transport through photosystem II (photoinhibition). In addition the illumination leads to a rapid turnover of the D1 protein in the reaction center of photosystem II. In this study the light-dependent degradation of the D1 reaction center protein and the light-dependent inhibition of electron-transport reactions have been studied in thylakoid membranes in which the oxygen evolution has been reversibly inhibited by Cl- depletion. The results show that Cl(-)-depleted thylakoid membranes are very vulnerable to damage induced by illumination. Both the D1 protein and the inhibition of the oxygen evolution are 15-20 times more sensitive to illumination than in control thylakoid membranes. The presence, during the illumination, of the herbicide 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) prevented both the light-dependent degradation of the D1 protein and the inhibition of the electron transport. The protection exerted by DCMU is seen only in Cl(-)-depleted thylakoid membranes. These observations lead to the proposal that continuous illumination of Cl(-)-depleted thylakoid membranes generates anomalously long-lived, highly oxidizing radicals on the oxidizing side of photosystem II, which are responsible for the light-induced protein damage and inhibition. The presence of DCMU during the illumination prevents the formation of these radicals, which explains the protective effects of the herbicide. It is also observed that in Cl(-)-depleted thylakoid membranes, oxygen evolution (measured after the readdition of Cl-) is inhibited before electron transfer from diphenylcarbazide to dichlorophenolindophenol.

  15. Identical inferences about correlated evolution arise from ancestral state reconstruction and independent contrasts.

    PubMed

    Elliot, Michael G

    2015-01-01

    Inferences about the evolution of continuous traits based on reconstruction of ancestral states have often been considered more error-prone than analysis of independent contrasts. Here we show that both methods in fact yield identical estimators for the correlation coefficient and regression gradient of correlated traits, indicating that reconstructed ancestral states are a valid source of information about correlated evolution. We show that the independent contrast associated with a pair of sibling nodes on a phylogenetic tree can be expressed in terms of the maximum likelihood ancestral state function at those nodes and their common parent. This expression gives rise to novel formulae for independent contrasts for any model of evolution admitting of a local likelihood function. We thus derive new formulae for independent contrasts applicable to traits evolving under directional drift, and use simulated data to show that these directional contrasts provide better estimates of evolutionary model parameters than standard independent contrasts, when traits in fact evolve with a directional tendency.

  16. Functions of Two Distinct “Prolactin-Releasing Peptides” Evolved from a Common Ancestral Gene

    PubMed Central

    Tachibana, Tetsuya; Sakamoto, Tatsuya

    2014-01-01

    Prolactin-releasing peptide (PrRP) is one of the RF-amide peptides and was originally identified in the bovine hypothalamus as a stimulator of prolactin (PRL) release. Independently, another RF-amide peptide was found in Japanese crucian carp and named Carassius-RFa (C-RFa), which shows high homology to PrRP and stimulates PRL secretion in teleost fish. Therefore, C-RFa has been recognized as fish PrRP. However, recent work has revealed that PrRP and C-RFa in non-mammalian vertebrates are encoded by separate genes originated through duplication of an ancestral gene. Indeed, both PrRP and C-RFa are suggested to exist in teleost, amphibian, reptile, and avian species. Therefore, we propose that non-mammalian PrRP (C-RFa) be renamed PrRP2. Despite a common evolutionary origin, PrRP2 appears to be a physiological regulator of PRL, whereas this is not a consistent role for PrRP itself. Further work revealed that the biological functions of PrRP and PrRP2 are not limited solely to PRL release, because they are also neuromodulators of several hypothalamus–pituitary axes and are involved in some brain circuits related to the regulation of food intake, stress, and cardiovascular functions. However, these actions appear to be different among vertebrates. For example, central injection of PrRP inhibits feeding behavior in rodents and teleosts, while it stimulates it in chicks. Therefore, both PrRP and PrRP2 have acquired diverse actions through evolution. In this review, we integrate the burgeoning information of structures, expression profiles, and multiple biological actions of PrRP in higher vertebrates, as well as those of PrRP2 in non-mammals. PMID:25426099

  17. Toxic and nontoxic components of botulinum neurotoxin complex are evolved from a common ancestral zinc protein

    SciTech Connect

    Inui, Ken; Sagane, Yoshimasa; Miyata, Keita; Miyashita, Shin-Ichiro; Suzuki, Tomonori; Shikamori, Yasuyuki; Ohyama, Tohru; Niwa, Koichi; Watanabe, Toshihiro

    2012-03-16

    Highlights: Black-Right-Pointing-Pointer BoNT and NTNHA proteins share a similar protein architecture. Black-Right-Pointing-Pointer NTNHA and BoNT were both identified as zinc-binding proteins. Black-Right-Pointing-Pointer NTNHA does not have a classical HEXXH zinc-coordinating motif similar to that found in all serotypes of BoNT. Black-Right-Pointing-Pointer Homology modeling implied probable key residues involved in zinc coordination. -- Abstract: Zinc atoms play an essential role in a number of enzymes. Botulinum neurotoxin (BoNT), the most potent toxin known in nature, is a zinc-dependent endopeptidase. Here we identify the nontoxic nonhemagglutinin (NTNHA), one of the BoNT-complex constituents, as a zinc-binding protein, along with BoNT. A protein structure classification database search indicated that BoNT and NTNHA share a similar domain architecture, comprising a zinc-dependent metalloproteinase-like, BoNT coiled-coil motif and concanavalin A-like domains. Inductively coupled plasma-mass spectrometry analysis demonstrated that every single NTNHA molecule contains a single zinc atom. This is the first demonstration of a zinc atom in this protein, as far as we know. However, the NTNHA molecule does not possess any known zinc-coordinating motif, whereas all BoNT serotypes possess the classical HEXXH motif. Homology modeling of the NTNHA structure implied that a consensus K-C-L-I-K-X{sub 35}-D sequence common among all NTNHA serotype molecules appears to coordinate a single zinc atom. These findings lead us to propose that NTNHA and BoNT may have evolved distinct functional specializations following their branching out from a common ancestral zinc protein.

  18. Functions of two distinct "prolactin-releasing peptides" evolved from a common ancestral gene.

    PubMed

    Tachibana, Tetsuya; Sakamoto, Tatsuya

    2014-01-01

    Prolactin-releasing peptide (PrRP) is one of the RF-amide peptides and was originally identified in the bovine hypothalamus as a stimulator of prolactin (PRL) release. Independently, another RF-amide peptide was found in Japanese crucian carp and named Carassius-RFa (C-RFa), which shows high homology to PrRP and stimulates PRL secretion in teleost fish. Therefore, C-RFa has been recognized as fish PrRP. However, recent work has revealed that PrRP and C-RFa in non-mammalian vertebrates are encoded by separate genes originated through duplication of an ancestral gene. Indeed, both PrRP and C-RFa are suggested to exist in teleost, amphibian, reptile, and avian species. Therefore, we propose that non-mammalian PrRP (C-RFa) be renamed PrRP2. Despite a common evolutionary origin, PrRP2 appears to be a physiological regulator of PRL, whereas this is not a consistent role for PrRP itself. Further work revealed that the biological functions of PrRP and PrRP2 are not limited solely to PRL release, because they are also neuromodulators of several hypothalamus-pituitary axes and are involved in some brain circuits related to the regulation of food intake, stress, and cardiovascular functions. However, these actions appear to be different among vertebrates. For example, central injection of PrRP inhibits feeding behavior in rodents and teleosts, while it stimulates it in chicks. Therefore, both PrRP and PrRP2 have acquired diverse actions through evolution. In this review, we integrate the burgeoning information of structures, expression profiles, and multiple biological actions of PrRP in higher vertebrates, as well as those of PrRP2 in non-mammals.

  19. Inheritance of the 8.1 ancestral haplotype in recurrent pregnancy loss

    PubMed Central

    Kolte, Astrid M.; Nielsen, Henriette S.; Steffensen, Rudi; Crespi, Bernard; Christiansen, Ole B.

    2015-01-01

    Background and objectives: The 8.1 ancestral haplotype (AH) (HLA-A1, C7, B8, C4AQ0, C4B1, DR3, DQ2) is a remarkably long and conserved haplotype in the human major histocompatibility complex. It has been associated with both beneficial and detrimental effects, consistent with antagonistic pleiotropy. It has also been proposed that the survival of long, conserved haplotypes may be due to gestational drive, i.e. selective miscarriage of fetuses who have not inherited the haplotype from a heterozygous mother. Recurrent pregnancy loss (RPL) is defined as three or more consecutive pregnancy losses. The objective was to test the gestational drive theory for the 8.1AH in women with RPL and their live born children. Methodology: We investigated the inheritance of the 8.1AH from 82 heterozygous RPL women to 110 live born children. All participants were genotyped for HLA-A, -B and -DRB1 in DNA from EDTA-treated blood or buccal swaps. Inheritance was compared with a Mendelian inheritance of 50% using a two-sided exact binomial test. Results: We found that 55% of the live born children had inherited the 8.1AH, which was not significantly higher than the expected 50% (P = 0.29). Interestingly, we found a non-significant trend toward a higher inheritance of the 8.1AH in girls, 63%, P = 0.11 as opposed to boys, 50%, P = 1.00. Conclusions and implications: We did not find that the 8.1AH was significantly more often inherited by live born children of 8.1AH heterozygous RPL women. However our data suggest that there may be a sex-specific effect which would be interesting to explore further, both in RPL and in a background population. PMID:26675299

  20. Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties.

    PubMed

    Hobbs, Joanne K; Prentice, Erica J; Groussin, Mathieu; Arcus, Vickery L

    2015-10-01

    Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported--high thermostability and high catalytic activity--compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network. PMID:26349578

  1. Asymptotic Distributions of Coalescence Times and Ancestral Lineage Numbers for Populations with Temporally Varying Size

    PubMed Central

    Chen, Hua; Chen, Kun

    2013-01-01

    The distributions of coalescence times and ancestral lineage numbers play an essential role in coalescent modeling and ancestral inference. Both exact distributions of coalescence times and ancestral lineage numbers are expressed as the sum of alternating series, and the terms in the series become numerically intractable for large samples. More computationally attractive are their asymptotic distributions, which were derived in Griffiths (1984) for populations with constant size. In this article, we derive the asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. For a sample of size n, denote by Tm the mth coalescent time, when m + 1 lineages coalesce into m lineages, and An(t) the number of ancestral lineages at time t back from the current generation. Similar to the results in Griffiths (1984), the number of ancestral lineages, An(t), and the coalescence times, Tm, are asymptotically normal, with the mean and variance of these distributions depending on the population size function, N(t). At the very early stage of the coalescent, when t → 0, the number of coalesced lineages n − An(t) follows a Poisson distribution, and as m → n, n(n−1)Tm/2N(0) follows a gamma distribution. We demonstrate the accuracy of the asymptotic approximations by comparing to both exact distributions and coalescent simulations. Several applications of the theoretical results are also shown: deriving statistics related to the properties of gene genealogies, such as the time to the most recent common ancestor (TMRCA) and the total branch length (TBL) of the genealogy, and deriving the allele frequency spectrum for large genealogies. With the advent of genomic-level sequencing data for large samples, the asymptotic distributions are expected to have wide applications in theoretical and methodological development for population genetic inference. PMID:23666939

  2. Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.

    PubMed

    Tuller, Tamir; Birin, Hadas; Kupiec, Martin; Ruppin, Eytan

    2010-09-01

    The inference of ancestral genomes is a fundamental problem in molecular evolution. Due to the statistical nature of this problem, the most likely or the most parsimonious ancestral genomes usually include considerable error rates. In general, these errors cannot be abolished by utilizing more exhaustive computational approaches, by using longer genomic sequences, or by analyzing more taxa. In recent studies, we showed that co-evolution is an important force that can be used for significantly improving the inference of ancestral genome content. In this work we formally define a computational problem for the inference of ancestral genome content by co-evolution. We show that this problem is NP-hard and hard to approximate and present both a Fixed Parameter Tractable (FPT) algorithm, and heuristic approximation algorithms for solving it. The running time of these algorithms on simulated inputs with hundreds of protein families and hundreds of co-evolutionary relations was fast (up to four minutes) and it achieved an approximation ratio of <1.3. We use our approach to study the ancestral genome content of the Fungi. To this end, we implement our approach on a dataset of 33, 931 protein families and 20, 317 co-evolutionary relations. Our algorithm added and removed hundreds of proteins from the ancestral genomes inferred by maximum likelihood (ML) or maximum parsimony (MP) while slightly affecting the likelihood/parsimony score of the results. A biological analysis revealed various pieces of evidence that support the biological plausibility of the new solutions. In addition, we showed that our approach reconstructs missing values at the leaves of the Fungi evolutionary tree better than ML or MP.

  3. Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states.

    PubMed

    Wright, April M; Lyons, Kathleen M; Brandley, Matthew C; Hillis, David M

    2015-09-01

    Changes in parity mode between egg-laying (oviparity) and live-bearing (viviparity) have occurred repeatedly throughout vertebrate evolution. Oviparity is the ancestral amniote state, and viviparity has evolved many times independently within amniotes (especially in lizards and snakes), with possibly a few reversions to oviparity. In amniotes, the shelled egg is considered a complex structure that is unlikely to re-evolve if lost (i.e., it is an example of Dollo's Principle). However, a recent ancestral state reconstruction analysis concluded that viviparity was the ancestral state of squamate reptiles (lizards and snakes), and that oviparity re-evolved from viviparity many times throughout the evolutionary history of squamates. Here, we re-evaluate support for this provocative conclusion by testing the sensitivity of the analysis to model assumptions and estimates of squamate phylogeny. We found that the models and methods used for parity mode reconstruction are highly sensitive to the specific estimate of phylogeny used, and that the point estimate of phylogeny used to suggest that viviparity is the root state of the squamate tree is far from an optimal phylogenetic solution. The ancestral state reconstructions are also highly sensitive to model choice and specific values of model parameters. A method that is designed to account for biases in taxon sampling actually accentuates, rather than lessens, those biases with respect to ancestral state reconstructions. In contrast to recent conclusions from the same data set, we find that ancestral state reconstruction analyses provide highly equivocal support for the number and direction of transitions between oviparity and viviparity in squamates. Moreover, the reconstructions of ancestral parity state are highly dependent on the assumptions of each model. We conclude that the common ancestor of squamates was oviparous, and subsequent evolutionary transitions to viviparity were common, but reversals to oviparity were

  4. Biogenesis of water splitting by photosystem II during de-etiolation of barley (Hordeum vulgare L.).

    PubMed

    Shevela, Dmitriy; Arnold, Janine; Reisinger, Veronika; Berends, Hans-Martin; Kmiec, Karol; Koroidov, Sergey; Bue, Ann Kristin; Messinger, Johannes; Eichacker, Lutz A

    2016-07-01

    Etioplasts lack thylakoid membranes and photosystem complexes. Light triggers differentiation of etioplasts into mature chloroplasts, and photosystem complexes assemble in parallel with thylakoid membrane development. Plastids isolated at various time points of de-etiolation are ideal to study the kinetic biogenesis of photosystem complexes during chloroplast development. Here, we investigated the chronology of photosystem II (PSII) biogenesis by monitoring assembly status of chlorophyll-binding protein complexes and development of water splitting via O2 production in plastids (etiochloroplasts) isolated during de-etiolation of barley (Hordeum vulgare L.). Assembly of PSII monomers, dimers and complexes binding outer light-harvesting antenna [PSII-light-harvesting complex II (LHCII) supercomplexes] was identified after 1, 2 and 4 h of de-etiolation, respectively. Water splitting was detected in parallel with assembly of PSII monomers, and its development correlated with an increase of bound Mn in the samples. After 4 h of de-etiolation, etiochloroplasts revealed the same water-splitting efficiency as mature chloroplasts. We conclude that the capability of PSII to split water during de-etiolation precedes assembly of the PSII-LHCII supercomplexes. Taken together, data show a rapid establishment of water-splitting activity during etioplast-to-chloroplast transition and emphasize that assembly of the functional water-splitting site of PSII is not the rate-limiting step in the formation of photoactive thylakoid membranes.

  5. Photosystem II inhibitor resistance in the Columbia Basin of Washington state

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potato and mint (peppermint and spearmint) are commonly produced in the irrigated regions of the Pacific Northwest and both crops rely heavily on photosystem II (PSII) inhibitor herbicides metribuzin (potato) and terbacil (mint) for weed management. Seed was collected in 2010 from Powell amaranth, r...

  6. Transcriptional response of two core photosystem genes in Symbiodinium spp. exposed to thermal stress.

    PubMed

    McGinley, Michael P; Aschaffenburg, Matthew D; Pettay, Daniel T; Smith, Robin T; LaJeunesse, Todd C; Warner, Mark E

    2012-01-01

    Mutualistic symbioses between scleractinian corals and endosymbiotic dinoflagellates (Symbiodinium spp.) are the foundation of coral reef ecosystems. For many coral-algal symbioses, prolonged episodes of thermal stress damage the symbiont's photosynthetic capability, resulting in its expulsion from the host. Despite the link between photosynthetic competency and symbiont expulsion, little is known about the effect of thermal stress on the expression of photosystem genes in Symbiodinium. This study used real-time PCR to monitor the transcript abundance of two important photosynthetic reaction center genes, psbA (encoding the D1 protein of photosystem II) and psaA (encoding the P(700) protein of photosystem I), in four cultured isolates (representing ITS2-types A13, A20, B1, and F2) and two in hospite Symbiodinium spp. within the coral Pocillopora spp. (ITS2-types C1b-c and D1). Both cultured and in hospite Symbiodinium samples were exposed to elevated temperatures (32°C) over a 7-day period and examined for changes in photochemistry and transcript abundance. Symbiodinium A13 and C1b-c (both thermally sensitive) demonstrated significant declines in both psbA and psaA during the thermal stress treatment, whereas the transcript levels of the other Symbiodinium types remained stable. The downregulation of both core photosystem genes could be the result of several different physiological mechanisms, but may ultimately limit repair rates of photosynthetic proteins, rendering some Symbiodinium spp. especially susceptible to thermal stress.

  7. Studying the Effect of Light Quality on the Size of the Photosystem II Light Harvesting Complex

    ERIC Educational Resources Information Center

    Muhoz, Romualdo; Quiles, Maria J.

    2003-01-01

    In this article the effect of light quality on the size of the photosystem II (PSII) light harvesting complex (LHCII) is studied by measuring the chlorophyll fluorescence emitted by leaf sections of oat ("Avena sativa," var. Prevision) plants previously treated with either white light or with light filtered through blue, green, red or farred…

  8. Catalytic Oxygen Evolution by a Bioinorganic Model of the Photosystem II Oxygen-Evolving Complex

    ERIC Educational Resources Information Center

    Howard, Derrick L.; Tinoco, Arthur D.; Brudvig, Gary W.; Vrettos, John S.; Allen, Bertha Connie

    2005-01-01

    Bioinorganic models of the manganese Mn4 cluster are important not only as aids in understanding the structure and function of the oxygen-evolving complex (OEC), but also in developing artificial water-oxidation catalysts. The mechanism of water oxidation by photosystem II (PSII) is thought to involve the formation of a high-valent terminal Mn-oxo…

  9. Redox regulation of the antimycin A sensitive pathway of cyclic electron flow around photosystem I in higher plant thylakoids.

    PubMed

    Strand, Deserah D; Fisher, Nicholas; Davis, Geoffry A; Kramer, David M

    2016-01-01

    The chloroplast must regulate supply of reducing equivalents and ATP to meet rapid changes in downstream metabolic demands. Cyclic electron flow around photosystem I (CEF) is proposed to balance the ATP/NADPH budget by using reducing equivalents to drive plastoquinone reduction, leading to the generation of proton motive force and subsequent ATP synthesis. While high rates of CEF have been observed in vivo, isolated thylakoids show only very slow rates, suggesting that the activity of a key complex is lost or down-regulated upon isolation. We show that isolation of thylakoids while in the continuous presence of reduced thiol reductant dithiothreitol (DTT), but not oxidized DTT, maintains high CEF activity through an antimycin A sensitive ferredoxin:quinone reductase (FQR). Maintaining low concentrations (~2 mM) of reduced DTT while modulating the concentration of oxidized DTT leads to reversible activation/inactivation of CEF with an apparent midpoint potential of -306 mV (±10 mV) and n=2, consistent with redox modulation of a thiol/disulfide couple and thioredoxin-mediated regulation of the plastoquinone reductase involved in the antimycin A-sensitive pathway, possibly at the level of the PGRL1 protein. Based on proposed differences in regulatory modes, we propose that the FQR and NADPH:plastoquinone oxidoreductase (NDH) pathways for CEF are activated under different conditions and fulfill different roles in chloroplast energy balance. PMID:26235611

  10. Dynamics of higher plant photosystem cross-section associated with state transitions.

    PubMed

    Ruban, Alexander V; Johnson, Matthew P

    2009-03-01

    Photosynthetic state transitions are a well-known phenomenon of short-term adaptation of the photosynthetic membrane to changes in spectral quality of light in low light environments. The principles of the monitoring and quantification of the process in higher plants are revised here. The use of the low-temperature excitation fluorescence spectroscopy for analysis of the photosystem I antenna cross-section dynamics is described. This cross section was found to increase by 20-25% exclusively due to the migration and attachment of LHCIIb complex in State 2. Analysis of the fine structure of the additional PSI cross-section spectrum revealed the 510 nm band, characteristic of Lutein 2 of LHCIIb and present only when the complex is in a trimeric state. The excitation fluorescence spectrum of the phospho-LHCII resembles the spectrum of aggregated and hence quenched LHCII. This novel observation could explain the fact that at no point in the course of the state transition high fluorescence and long lifetime components of detached trimeric LHCII have ever been observed. In the plants lacking Lhcb1 and 2 proteins and unable to perform state transitions, compensatory sustained adjustments of the photosystem I and II antennae have been revealed. Whilst the major part of the photosystem II antenna is built largely of CP26 trimers, possessing less chlorophyll b and more of the red-shifted chlorophyll a, photosystem I in these plants contains more than 20% of extra LHCI antenna enriched in chlorophyll b. Hence, both photosystems in the plants lacking state transitions have less spectrally distinct antennae, which enable to avoid energy imbalance due to the changes in the light quality. These alterations reveal remarkable plasticity of the higher plant photosynthetic antenna design providing the basis for a flexible adaptation to the light environment.

  11. Chromosome painting between human and lorisiform prosimians: evidence for the HSA 7/16 synteny in the primate ancestral karyotype.

    PubMed

    Nie, Wenhui; O'Brien, Patricia C M; Fu, Beiyuan; Wang, Jinhuan; Su, Weiting; Ferguson-Smith, Malcolm A; Robinson, Terence J; Yang, Fengtang

    2006-02-01

    Multidirectional chromosome painting with probes derived from flow-sorted chromosomes of humans (Homo sapiens, HSA, 2n = 46) and galagos (Galago moholi, GMO, 2n = 38) allowed us to map evolutionarily conserved chromosomal segments among humans, galagos, and slow lorises (Nycticebus coucang, NCO, 2n = 50). In total, the 22 human autosomal painting probes detected 40 homologous chromosomal segments in the slow loris genome. The genome of the slow loris contains 16 sytenic associations of human homologues. The ancient syntenic associations of human chromosomes such as HSA 3/21, 7/16, 12/22 (twice), and 14/15, reported in most mammalian species, were also present in the slow loris genome. Six associations (HSA 1a/19a, 2a/12a, 6a/14b, 7a/12c, 9/15b, and 10a/19b) were shared by the slow loris and galago. Five associations (HSA 1b/6b, 4a/5a, 11b/15a, 12b/19b, and 15b/16b) were unique to the slow loris. In contrast, 30 homologous chromosome segments were identified in the slow loris genome when using galago chromosome painting probes. The data showed that the karyotypic differences between these two species were mainly due to Robertsonian translocations. Reverse painting, using galago painting probes onto human chromosomes, confirmed most of the chromosome homologies between humans and galagos established previously, and documented the HSA 7/16 association in galagos, which was not reported previously. The presence of the HSA 7/16 association in the slow loris and galago suggests that the 7/16 association is an ancestral synteny for primates. Based on our results and the published homology maps between humans and other primate species, we propose an ancestral karyotype (2n = 60) for lorisiform primates.

  12. Mining the semantics of genome super-blocks to infer ancestral architectures.

    PubMed

    Jean, Géraldine; Sherman, David James; Nikolski, Macha

    2009-09-01

    The study of evolutionary mechanisms is made more and more accurate by the increase in the number of fully sequenced genomes. One of the main problems is to reconstruct plausible ancestral genome architectures based on the comparison of contemporary genomes. Current methods have largely focused on finding complete architectures for ancestral genomes, and, due to the computational difficulty of the problem, stop after a small number of equivalent minimal solutions have been found. Recent results suggest, however, that the set of minimum complete architectures is very large and heterogeneous. In fact these solutions are collections of conserved blocks, freely rearranged. In this paper, we identify these conserved super-blocks, using a new method of analysis of ancestral architectures that reconciles both breakpoint and rearrangement analyses, as well as respects biological constraints. The resulting algorithms permit the first reliable reconstruction of plausible ancestral architectures for several non-WGD yeasts simultaneously, a problem hitherto intractable due to the extensive map reshuffling of these species. See online Supplementary Material at www.liebertonline.com. PMID:19772437

  13. Assessing the prediction fidelity of ancestral reconstruction by a library approach.

    PubMed

    Bar-Rogovsky, Hagit; Stern, Adi; Penn, Osnat; Kobl, Iris; Pupko, Tal; Tawfik, Dan S

    2015-11-01

    Ancestral reconstruction is a powerful tool for studying protein evolution as well as for protein design and engineering. However, in many positions alternative predictions with relatively high marginal probabilities exist, and thus the prediction comprises an ensemble of near-ancestor sequences that relate to the historical ancestor. The ancestral phenotype should therefore be explored for the entire ensemble, rather than for the sequence comprising the most probable amino acid at all positions [the most probable ancestor (mpa)]. To this end, we constructed libraries that sample ensembles of near-ancestor sequences. Specifically, we identified positions where alternatively predicted amino acids are likely to affect the ancestor's structure and/or function. Using the serum paraoxonases (PONs) enzyme family as a test case, we constructed libraries that combinatorially sample these alternatives. We next characterized these libraries, reflecting the vertebrate and mammalian PON ancestors. We found that the mpa of vertebrate PONs represented only one out of many different enzymatic phenotypes displayed by its ensemble. The mammalian ancestral library, however, exhibited a homogeneous phenotype that was well represented by the mpa. Our library design strategy that samples near-ancestor ensembles at potentially critical positions therefore provides a systematic way of examining the robustness of inferred ancestral phenotypes.

  14. Ancestral differences in femoral neck axis length: possible implications for forensic anthropological analyses.

    PubMed

    Christensen, Angi M; Leslie, William D; Baim, Sanford

    2014-03-01

    In forensic anthropological contexts, very few methods of estimating ancestry from the postcranial skeleton are available. The cranium is widely recognized to show the greatest ancestral variation, and is often regarded by forensic anthropologists as the only reliable bone for estimating ancestry from unidentified skeletal remains. Several studies have demonstrated ancestral variation in aspects of the femur, but none have shown significant predictive power for discriminating multiple groups, and have therefore not gained wide acceptance by forensic anthropologists. Skeletal health experts (particularly bone densitometrists), however, have long recognized a relationship between proximal femur geometry (especially hip axis length) and osteoporosis-related fracture risk. Moreover, fracture risk has been noted to vary between ancestral groups. Here, we investigate whether measurements that are related to fracture risk might also be used to estimate ancestry from unidentified skeletal remains. Specifically, we investigate ancestral differences in femoral neck axis length (FNAL) and find significant differences between European, Asian and African groups in both women and men. FNAL was largest in European groups followed by African and then Asian groups. The greatest discriminating power was found between European and Asian groups, but was also significant between European and African groups. These differences may have utility in estimating ancestry in forensic anthropological contexts.

  15. Indigenous ancestral sayings contribute to modern conservation partnerships: examples using Phormium tenax.

    PubMed

    Wehi, Priscilla M

    2009-01-01

    Traditional ecological knowledge (TEK) is central to indigenous worldviews and practices and is one of the most important contributions that indigenous people can bring to conservation management partnerships. However, researchers and managers may have difficulty accessing such knowledge, particularly where knowledge transmission has been damaged. A new methodological approach analyzes ancestral sayings from Maori oral traditions for ecological information about Phormium tenax, a plant with high cultural value that is a dominant component in many threatened wetland systems, and frequently used in restoration plantings in New Zealand. Maori ancestral sayings record an association with nectar-feeding native parrots that has only rarely been reported, as well as indications of important environmental parameters (rainfall and drought) for this species. These sayings provide evidence of indigenous management that has not been reported from interviews with elders, including evidence of fire use to create Phormium cultivations. TEK in Maori ancestral sayings imply landscape-scale processes in comparison to intensive, small-scale management methods often reported in interviews. TEK in ancestral sayings can be used to generate new scientific hypotheses, negotiate collaborative pathways, and identify ecological management strategies that support biodiversity retention. TEK can inform restoration ecology, historical ecology, and conservation management of species and ecosystems, especially where data from pollen records and archaeological artifacts are incomplete.

  16. Modeling the NMR signatures associated with the functional conformational switch in the major light-harvesting antenna of photosystem II in higher plants.

    PubMed

    Duffy, Christopher D P; Pandit, Anjali; Ruban, Alexander V

    2014-03-28

    The major photosystem II antenna complex, LHCII, possesses an intrinsic conformational switch linked to the formation of a photoprotective, excitation-quenching state. Recent solid state NMR experiments revealed that aggregation-induced quenching in (13)C-enriched LHCII from C. reinhardtii is associated with changes to the chemical shifts of three specific (13)C atoms in the Chla conjugated macrocycle. We performed DFT-based NMR calculations on the strongly-quenched crystal structure of LHCII (taken from spinach). We demonstrate that specific Chla-xanthophyll interactions in the quenched structure lead to changes in the Chla(13)C chemical shifts that are qualitatively similar to those observed by solid state NMR. We propose that these NMR changes are due to modulations in Chla-xanthophyll associations that occur due to a quenching-associated functional conformation change in the lutein and neoxanthin domains of LHCII. The combination of solid-state NMR and theoretical modeling is therefore a powerful tool for assessing functional conformational switching in the photosystem II antenna.

  17. Function of tyrosine Z in water oxidation by photosystem II: electrostatical promotor instead of hydrogen abstractor.

    PubMed

    Ahlbrink, R; Haumann, M; Cherepanov, D; Bögershausen, O; Mulkidjanian, A; Junge, W

    1998-01-27

    Photosynthetic water oxidation by photosystem II is mediated by a Mn4 cluster, a cofactor X still chemically ill-defined, and a tyrosine, YZ (D1-Tyr161). Before the final reaction with water proceeds to yield O2 (transition S4-->S0), two oxidizing equivalents are stored on Mn4 (S0-->S1-->S2), a third on X (S2-->S3), and a forth on YZ(S3-->S4). It has been proposed that YZ functions as a pure electron transmitter between Mn4X and P680, or, more recently, that it acts as an abstractor of hydrogen from bound water. We scrutinized the coupling of electron and proton transfer during the oxidation of YZ in PSII core particles with intact or impaired oxygen-evolving capacity. The rates of electron transfer to P680+, of electrochromism, and of pH transients were determined as a function of the pH, the temperature, and the H/D ratio. In oxygen-evolving material, we found only evidence for electrostatically induced proton release from peripheral amino acid residues but not from YZox itself. The positive charge stayed near YZox, and the rate of electron transfer was nearly independent of the pH. In core particles with an impaired Mn4 cluster, on the other hand, the rate of the electron transfer became strictly dependent on the protonation state of a single base (pK approximately 7). At pH < 7, the rate of electron transfer revealed the same slow rate (t1/2 approximately 35 microseconds) as that of proton release into the bulk. The deposition of a positive charge around YZox was no longer detected. A large H/D isotope effect (approximately 2.5) on these rates was also indicative of a steering of electron abstraction by proton transfer. That YZox was deprotonated into the bulk in inactive but not in oxygen-evolving material argues against the proposed role of YZox as an acceptor of hydrogen from water. Instead, the positive charge in its vicinity may shift the equilibrium from bound water to bound peroxide upon S3-->S4 as a prerequisite for the formation of oxygen upon S4-->S0.

  18. Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss.

    PubMed

    Avdeyev, Pavel; Jiang, Shuai; Aganezov, Sergey; Hu, Fei; Alekseyev, Max A

    2016-03-01

    Since most dramatic genomic changes are caused by genome rearrangements as well as gene duplications and gain/loss events, it becomes crucial to understand their mechanisms and reconstruct ancestral genomes of the given genomes. This problem was shown to be NP-complete even in the "simplest" case of three genomes, thus calling for heuristic rather than exact algorithmic solutions. At the same time, a larger number of input genomes may actually simplify the problem in practice as it was earlier illustrated with MGRA, a state-of-the-art software tool for reconstruction of ancestral genomes of multiple genomes. One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution. Furthermore, such tools are often limited to genomes composed of the same genes with each gene present in a single copy in every genome. This limitation makes these tools inapplicable for many biological datasets and degrades the resolution of ancestral reconstructions in diverse datasets. We address these deficiencies by extending the MGRA algorithm to genomes with unequal gene contents. The developed next-generation tool MGRA2 can handle gene gain/loss events and shares the ability of MGRA to reconstruct ancestral genomes uniquely in the case of limited breakpoint reuse. Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. In practical experiments, MGRA2 shows superior performance for simulated and real genomes as compared to other ancestral genome reconstruction tools. PMID:26885568

  19. Carbon dioxide fixation and photoevolution of hydrogen and oxygen in a mutant of Chlamydomonas lacking Photosystem I

    SciTech Connect

    Greenbaum, E.; Lee, J.W.; Tevault, C.V.

    1995-09-01

    Sustained photoassimilation of atmospheric CO{sub 2} and simultaneous photoevolution of molecular hydrogen and oxygen has been observed in a Photosystem I deficient mutant B4 of Chlamydomonas reinhardtii that contains only Photosystem II. The data indicate that Photosystem II alone is capable of spanning the potential difference between water oxidation/oxygen evolution and ferredoxin reduction. The rates of both CO{sub 2} fixation and hydrogen and oxygen evolution are similar in the mutant to that of the wild-type C. reinhardtii 137c containing both photosystems. The wild-type had stable photosynthetic activity, measured as CO{sub 2} fixation, under both air and anaerobic conditions, while the mutant was stable only under anaerobic conditions. The results are discussed in terms of the fundamental mechanisms and energetics of photosynthesis and possible implications for the evolution of oxygenic photosynthesis.

  20. Structural response of Photosystem 2 to iron deficiency: characterization of a new photosystem 2-IdiA complex from the cyanobacterium Thermosynechococcus elongatus BP-1.

    PubMed

    Lax, Julia E-M; Arteni, Ana A; Boekema, Egbert J; Pistorius, Elfriede K; Michel, Klaus-Peter; Rögner, Matthias

    2007-06-01

    Iron deficiency triggers various processes in cyanobacterial cells of which the synthesis of an additional antenna system (IsiA) around photosystem (PS) 1 is well documented [T.S. Bibby, J. Nield, J. Barber, Iron deficiency induces the formation of an antenna ring around trimeric photosystem I in cyanobacteria, Nature 412 (2001) 743-745, E.J. Boekema, A. Hifney, A.E. Yakushevska, M. Piotrowski, W. Keegstra, S. Berry, K.P. Michel, E.K. Pistorius, J. Kruip, A giant chlorophyll-protein complex induced by iron deficiency in cyanobacteria, Nature 412 (2001) 745-748]. Here we show that PS2 also undergoes prominent structural changes upon iron deficiency: Prerequisite is the isolation and purification of a PS2-IdiA complex which is exclusively synthesized under these conditions. Immunoblotting in combination with size exclusion chromatography shows that IdiA is only bound to dimeric PS2. Using single particle analysis of negatively stained specimens, IdiA can be localized in averaged electron micrographs on top of the CP43 subunit facing the cytoplasmic side in a model derived from the known 3D structure of PS2 [B. Loll, J. Kern, W. Saenger, A. Zouni, J. Biesiadka, Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II, Nature 438 (2005) 1040-4]. The presence of IdiA as integral part of PS2 is the first example of a new PS2 protein being expressed under stress conditions, which is missing in highly purified PS2 complexes isolated from iron-sufficient cells.

  1. Number of ancestral human species: a molecular perspective.

    PubMed

    Curnoe, D; Thorne, A

    2003-01-01

    Despite the remarkable developments in molecular biology over the past three decades, anthropological genetics has had only limited impact on systematics in human evolution. Genetics offers the opportunity to objectively test taxonomies based on morphology and may be used to supplement conventional approaches to hominid systematics. Our analyses, examining chromosomes and 46 estimates of genetic distance, indicate there may have been only around 4 species on the direct line to modern humans and 5 species in total. This contrasts with current taxonomies recognising up to 23 species. The genetic proximity of humans and chimpanzees has been used to suggest these species are congeneric. Our analysis of genetic distances between them is consistent with this proposal. It is time that chimpanzees, living humans and all fossil humans be classified in Homo. The creation of new genera can no longer be a solution to the complexities of fossil morphologies. Published genetic distances between common chimpanzees and bonobos, along with evidence for interbreeding, suggest they should be assigned to a single species. The short distance between humans and chimpanzees also places a strict limit on the number of possible evolutionary 'side branches' that might be recognised on the human lineage. All fossil taxa were genetically very close to each other and likely to have been below congeneric genetic distances seen for many mammals. Our estimates of genetic divergence suggest that periods of around 2 million years are required to produce sufficient genetic distance to represent speciation. Therefore, Neanderthals and so-called H. erectus were genetically so close to contemporary H. sapiens they were unlikely to have been separate species. Thus, it is likely there was only one species of human (H. sapiens) for most of the last 2 million years. We estimate the divergence time of H. sapiens from 16 genetic distances to be around 1.7 Ma which is consistent with evidence for the earliest

  2. Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins

    PubMed Central

    Koumandou, V Lila; Dacks, Joel B; Coulson, Richard MR; Field, Mark C

    2007-01-01

    Background In membrane trafficking, the mechanisms ensuring vesicle fusion specificity remain to be fully elucidated. Early models proposed that specificity was encoded entirely by SNARE proteins; more recent models include contributions from Rab proteins, Syntaxin-binding (SM) proteins and tethering factors. Most information on membrane trafficking derives from an evolutionarily narrow sampling of model organisms. However, considering factors from a wider diversity of eukaryotes can provide both functional information on core systems and insight into the evolutionary history of the trafficking machinery. For example, the major Qa/syntaxin SNARE families are present in most eukaryotic genomes and likely each evolved via gene duplication from a single ancestral syntaxin before the existing eukaryotic groups diversified. This pattern is also likely for Rabs and various other components of the membrane trafficking machinery. Results We performed comparative genomic and phylogenetic analyses, when relevant, on the SM proteins and components of the tethering complexes, both thought to contribute to vesicle fusion specificity. Despite evidence suggestive of secondary losses amongst many lineages, the tethering complexes are well represented across the eukaryotes, suggesting an origin predating the radiation of eukaryotic lineages. Further, whilst we detect distant sequence relations between GARP, COG, exocyst and DSL1 components, these similarities most likely reflect convergent evolution of similar secondary structural elements. No similarity is found between the TRAPP and HOPS complexes and the other tethering factors. Overall, our data favour independent origins for the various tethering complexes. The taxa examined possess at least one homologue of each of the four SM protein families; since the four monophyletic families each encompass a wide diversity of eukaryotes, the SM protein families very likely evolved before the last common eukaryotic ancestor (LCEA

  3. The involvement of H sub 2 O sub 2 in photoinhibition of photosystem II

    SciTech Connect

    Bradley, R.; Gebregiorgis, A.; Long, K; Roskelley, A.; Williams, S.; Frasch, W.D. )

    1991-05-01

    The involvement of H{sub 2}O{sub 2} in the inactivation of photosystem II and degradation of the D1 protein induced by high light intensities was investigated. Depletion of C1{sup {minus}} from the oxygen-evolving complex (OEC), which accelerates the rate of photoinhibition, allows the OEC to oxidize water to H{sub 2}O{sub 2} rather than to O{sub 2}. The rate of photoinhibition in thylakoids was accelerated more than 2 fold when the endogenous F-catalase is inhibited by 1 mM KCN. The acceleration of photoinhibition by KCN was observed for both C1{sup {minus}}-depleted and C1{sup {minus}}-sufficient thylakoids, which suggests a second site for the formation of H{sub 2}O{sub 2} in PSII. The ability of the reducing side of PSII to reduce O{sub 2} to H{sub 2}O{sub 2} during photoinhibition was eliminated by the addition of the coupled enzyme systems: glucose oxidase with glucose and horseradish peroxidase with catechol. The slow rate of photoinhibition in the presence of these coupled enzyme systems suggests that a second site of photoinhibitory H{sub 2}O{sub 2} production is from O{sub 2} on the reducing side of PSII. Addition of H{sub 2}O{sub 2} was found to induce a low temperature EPR signal centered at g = 2 which is similar to the EPR signal attributed to the induction of photoinhibition in C1{sup {minus}}-depleted samples. A comparison of the degradation products of the D1 protein induced by a 60 min exposure to either photoinhibitory illumination or to exogenous H{sub 2}O{sub 2} was also made using a polyclonal antibody to D1. From these results the authors propose that photoinhibition and D1 degradation is induced by H{sub 2}O{sub 2} produced by PSII at high light intensities. H{sub 2}O{sub 2} may inactivated D1 by crosslinking two tyrosines on the protein and/or by cleavage of the D1 at the three positions where glycine follows asparagine in the sequence.

  4. Biogenesis of a photosystem I light-harvesting complex. Evidence for a membrane intermediate.

    PubMed Central

    Adam, Z; Hoffman, N E

    1993-01-01

    CAB-7p is a chlorophyll a/b binding protein of photosystem I (PSI). It is found in light-harvesting complex I 680 (LHCI-680), one of the chlorophyll complexes produced by detergent solubilization of PSI. Two types of evidence are presented to indicate that assembly of CAB-7p into PSI proceeds through a membrane intermediate. First, when CAB-7p is briefly imported into chloroplasts or isolated thylakoids, we initially observe a fast-migrating membrane form of CAB-7p that is subsequently converted into PSI. The conversion of the fast-migrating form into PSI does not require stroma or ATP. Second, trypsin treatment of thylakoids containing radiolabeled CAB-7p indicates that there are at least two membrane forms of the mature 23-kD protein. The predominant form is completely resistant to proteolysis; a second form of the protein is cleaved by trypsin into 12- and 7-kD polypeptides. We interpret this to mean that the intermediate is a cleavable form that becomes protease resistant during assembly. This notion is supported by the observation that CAB-7p in LHCI-680 is largely cleaved by trypsin into 12- and 7-kD polypeptides, whereas CAB-7p in isolated PSI particles is trypsin resistant. In vitro, we generated a mutant form of CAB-7p, CAB-7/BgI2p, that was able to integrate into thylakoid membranes but was unable to assemble into PSI. The membrane form of CAB-7/BgI2p, like LHCI-680, was predominantly cleaved by trypsin into 12- and 7-kD fragments. We suggest that the mutant protein is arrested at an intermediate stage in the assembly pathway of PSI. Based on its mobility in nondenaturing gels and its susceptibility to protease cleavage, we suggest that the intermediate form is LHCI-680. We propose the following distinct stages in the biogenesis of LHCI: (a) apoprotein is integrated into the thylakoid, (b) chlorophyll is rapidly bound to apoprotein forming LHCI-680, and (c) LHCI-680 assembles into the native PSI complex. PMID:8108505

  5. Optical and Electrical Measurement of Energy Transfer between Nanocrystalline Quantum Dots and Photosystem I

    SciTech Connect

    Jung, Hyeson; Gulis, G.; Gupta, S.; Redding, K.; Gosztola, D. J.; Wiederrecht, Gary P; Stroscio, M. A.; Dutta, M.

    2010-08-31

    In the natural photosynthesis process, light harvesting complexes (LHCs) absorb light and pass excitation energy to photosystem I (PSI) and photosystem II (PSII). In this study, we have used nanocrystalline quantum dots (NQDs) as an artificial LHC by integrating them with PSI to extend their spectral range. We have performed photoluminescence (PL) and ultrafast time-resolved absorption measurements to investigate this process. Our PL experiments showed that emission from the NQDs is quenched, and the fluorescence from PSI is enhanced. Transient absorption and bleaching results can be explained by fluorescence resonance energy transfer (FRET) from the NQDs to the PSI. This nonradiative energy transfer occurs in ~6 ps. Current-voltage (I-V) measurements on the composite NQD-PSI samples demonstrate a clear photoresponse.

  6. Variation in sulfide tolerance of photosystem II in phylogenetically diverse cyanobacteria from sulfidic habitats

    NASA Technical Reports Server (NTRS)

    Miller, Scott R.; Bebout, Brad M.

    2004-01-01

    Physiological and molecular phylogenetic approaches were used to investigate variation among 12 cyanobacterial strains in their tolerance of sulfide, an inhibitor of oxygenic photosynthesis. Cyanobacteria from sulfidic habitats were found to be phylogenetically diverse and exhibited an approximately 50-fold variation in photosystem II performance in the presence of sulfide. Whereas the degree of tolerance was positively correlated with sulfide levels in the environment, a strain's phenotype could not be predicted from the tolerance of its closest relatives. These observations suggest that sulfide tolerance is a dynamic trait primarily shaped by environmental variation. Despite differences in absolute tolerance, similarities among strains in the effects of sulfide on chlorophyll fluorescence induction indicated a common mode of toxicity. Based on similarities with treatments known to disrupt the oxygen-evolving complex, it was concluded that sulfide toxicity resulted from inhibition of the donor side of photosystem II.

  7. Evidence for cyclic electron flow around photosystem II in Chlorella pyrenoidosa

    SciTech Connect

    Falkowski, P.G.; Fujita, Y.; Ley, A.; Mauzerall, D.

    1986-05-01

    Electron flow around photosystem II was investigated in Chlorella pyrenoidosa. Using a bare platinum O/sub 2/ electrode, simultaneous measurements were made of steady-state photosynthesis in continuous light, the yield of oxygen (Yo/sub 2/) produced by a superimposed saturating xenon flash, and the change in fluorescence yield of a weak flash triggered before and 70 microseconds after the saturating flash. Throughout most of the continuous photosynthesis-irradiance curve, normalized O/sub 2/ flash yields (Yo/sub 2//Yo/sub 2//sub max/) and normalized variable fluorescence yields ..delta..omega/..delta..omega' were linearly correlated with a slope of 1.0. As photosynthetic rates reached light saturation, however, the variable fluorescence yields remained relatively constant while O/sub 2/ flash yields decreased. These results strongly suggest that there is a cyclic electron flow around photosystem II in unpoisoned intact cells at light saturation and supraoptimal light intensities.

  8. Optical and electrical measurement of energy transfer between nanocrystalline quantum dots and photosystem I.

    PubMed

    Jung, Hyeson; Gulis, Galina; Gupta, Subhadra; Redding, Kevin; Gosztola, David J; Wiederrecht, Gary P; Stroscio, Michael A; Dutta, Mitra

    2010-11-18

    In the natural photosynthesis process, light harvesting complexes (LHCs) absorb light and pass excitation energy to photosystem I (PSI) and photosystem II (PSII). In this study, we have used nanocrystalline quantum dots (NQDs) as an artificial LHC by integrating them with PSI to extend their spectral range. We have performed photoluminescence (PL) and ultrafast time-resolved absorption measurements to investigate this process. Our PL experiments showed that emission from the NQDs is quenched, and the fluorescence from PSI is enhanced. Transient absorption and bleaching results can be explained by fluorescence resonance energy transfer (FRET) from the NQDs to the PSI. This nonradiative energy transfer occurs in ∼6 ps. Current-voltage (I-V) measurements on the composite NQD-PSI samples demonstrate a clear photoresponse.

  9. Brassinosteroids regulate the thylakoid membrane architecture and the photosystem II function.

    PubMed

    Krumova, S; Zhiponova, M; Dankov, K; Velikova, V; Balashev, K; Andreeva, T; Russinova, E; Taneva, S

    2013-09-01

    Brassinosteroids (BRs) are plant steroid hormones known to positively affect photosynthesis. In this work we investigated the architecture and function of photosynthetic membranes in mature Arabidopsis rosettes of BR gain-of-function (overexpressing the BR receptor BR INSENSITIVE 1 (BRI1), BRI1OE) and loss-of-function (bri1-116 with inactive BRI1 receptor, and constitutive photomorphogenesis and dwarfism (cpd) deficient in BR biosynthesis) mutants. Data from atomic force microscopy, circular dichroism, fluorescence spectroscopy and polarographic determination of oxygen yields revealed major structural (enlarged thylakoids, smaller photosystem II supercomplexes) and functional (strongly inhibited oxygen evolution, reduced photosystem II quantum yield) changes in all the mutants with altered BR response compared to the wild type plants. The recorded thermal dependences showed severe thermal instability of the oxygen yields in the BR mutant plants. Our results suggest that an optimal BR level is required for the normal thylakoid structure and function.

  10. The ancestral cascades arc: Cenozoic evolution of the central Sierra Nevada (California) and the birth of the new plate boundary

    USGS Publications Warehouse

    Busby, C.J.; Hagan, J.C.; Putirka, K.; Pluhar, C.J.; Gans, P.B.; Wagner, D.L.; Rood, D.; DeOreo, S.B.; Skilling, I.

    2008-01-01

    We integrate new stratigraphic, structural, geochemical, geochronological, and magnetostratigraphic data on Cenozoic volcanic rocks in the central Sierra Nevada to arrive at closely inter-related new models for: (1) the paleogeography of the ancestral Cascades arc, (2) the stratigraphic record of uplift events in the Sierra Nevada, (3) the tectonic controls on volcanic styles and compositions in the arc, and (4) the birth of a new plate margin. Previous workers have assumed that the ancestral Cascades arc consisted of stratovolcanoes, similar to the modern Cascades arc, but we suggest that the arc was composed largely of numerous, very small centers, where magmas frequently leaked up strands of the Sierran frontal fault zone. These small centers erupted to produce andesite lava domes that collapsed to produce block-and-ash flows, which were reworked into paleocanyons as volcanic debris flows and streamflow deposits. Where intrusions rose up through water-saturated paleocanyon fill, they formed peperite complexes that were commonly destabilized to form debris flows. Paleocanyons that were cut into Cretaceous bedrock and filled with Oligocene to late Miocene strata not only provide a stratigraphic record of the ancestral Cascades arc volcanism, but also deep unconformities within them record tectonic events. Preliminary correlation of newly mapped unconformities and new geochronological, magnetostratigraphic, and structural data allow us to propose three episodes of Cenozoic uplift that may correspond to (1) early Miocene onset of arc magmatism (ca. 15 Ma), (2) middle Miocene onset of Basin and Range faulting (ca. 10 Ma), and (3) late Miocene arrival of the triple junction (ca. 6 Ma), perhaps coinciding with a second episode of rapid extension on the range front. Oligocene ignimbrites, which erupted from calderas in central Nevada and filled Sierran paleocanyons, were deeply eroded during the early Miocene uplift event. The middle Miocene event is recorded by growth

  11. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II.

    PubMed

    Sierra, Raymond G; Gati, Cornelius; Laksmono, Hartawan; Dao, E Han; Gul, Sheraz; Fuller, Franklin; Kern, Jan; Chatterjee, Ruchira; Ibrahim, Mohamed; Brewster, Aaron S; Young, Iris D; Michels-Clark, Tara; Aquila, Andrew; Liang, Mengning; Hunter, Mark S; Koglin, Jason E; Boutet, Sébastien; Junco, Elia A; Hayes, Brandon; Bogan, Michael J; Hampton, Christina Y; Puglisi, Elisabetta V; Sauter, Nicholas K; Stan, Claudiu A; Zouni, Athina; Yano, Junko; Yachandra, Vittal K; Soltis, S Michael; Puglisi, Joseph D; DeMirci, Hasan

    2016-01-01

    We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure). PMID:26619013

  12. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II.

    PubMed

    Sierra, Raymond G; Gati, Cornelius; Laksmono, Hartawan; Dao, E Han; Gul, Sheraz; Fuller, Franklin; Kern, Jan; Chatterjee, Ruchira; Ibrahim, Mohamed; Brewster, Aaron S; Young, Iris D; Michels-Clark, Tara; Aquila, Andrew; Liang, Mengning; Hunter, Mark S; Koglin, Jason E; Boutet, Sébastien; Junco, Elia A; Hayes, Brandon; Bogan, Michael J; Hampton, Christina Y; Puglisi, Elisabetta V; Sauter, Nicholas K; Stan, Claudiu A; Zouni, Athina; Yano, Junko; Yachandra, Vittal K; Soltis, S Michael; Puglisi, Joseph D; DeMirci, Hasan

    2016-01-01

    We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).

  13. Purification and properties of the intact P-700 and Fx-containing Photosystem I core protein.

    PubMed

    Parrett, K G; Mehari, T; Warren, P G; Golbeck, J H

    1989-02-28

    The intact Photosystem I core protein, containing the psaA and psaB polypeptides, and electron transfer components P-700 through FX, was isolated from cyanobacterial and higher plant Photosystem I complexes with chaotropic agents followed by sucrose density ultracentrifugation. The concentrations of NaClO4, NaSCN, NaI, NaBr or urea required for the functional removal of the 8.9 kDa, FA/FB polypeptide was shown to be inversely related to the strength of the chaotrope. The Photosystem I core protein, which was purified to homogeniety, contains 4 mol of acid-labile sulfide and has the following properties: (i) the FX-containing core consists of the 82 and 83 kDa reaction center polypeptides but is totally devoid of the low-molecular-mass polypeptides; (ii) methyl viologen and other bipyridilium dyes have the ability to accept electrons directly from FX; (iii) the difference spectrum of FX from 400 to 900 nm is characteristic of an iron-sulfur cluster; (iv) the midpoint potential of FX, determined optically at room temperature, is 60 mV more positive than in the control; (v) there is indication by ESR spectroscopy of low-temperature heterogeneity within FX; and (vi) the heterogeneity is seen by optical spectroscopy as inefficiency in low-temperature electron flow to FX. The constraints imposed by the amount of non-heme iron and labile sulfide in the Photosystem I core protein, the cysteine content of the psaA and psaB polypeptides, and the stoichiometry of high-molecular-mass polypeptides, cause us to re-examine the possibility that FX is a [4Fe-4S] rather than a [2Fe-2S] cluster ligated by homologous cysteine residues on the psaA and psaB heterodimer.

  14. What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy.

    PubMed

    Chavan, Arun Rajendra; Bhullar, Bhart-Anjan S; Wagner, Günter P

    2016-04-01

    In human and mouse, decidual stromal cells (DSC) are necessary for the establishment (implantation) and the maintenance of pregnancy by preventing inflammation and the immune rejection of the semi-allograft conceptus. DSC originated along the stem lineage of eutherian mammals, coincidental with the origin of invasive placentation. Surprisingly, in many eutherian lineages decidual cells are lost after the implantation phase of pregnancy, making it unlikely that DSC are necessary for the maintenance of pregnancy in these animals. In order to understand this variation, we review the literature on the fetal-maternal interface in all major eutherian clades Euarchontoglires, Laurasiatheria, Xenarthra and Afrotheria, as well as the literature about the ancestral eutherian species. We conclude that maintaining pregnancy may not be a shared derived function of DSC among all eutherian mammals. Rather, we propose that DSC originated to manage the inflammatory reaction associated with invasive implantation. We envision that this happened in a stem eutherian that had invasive placenta but still a short gestation. We further propose that extended gestation evolved independently in the major eutherian clades explaining why the major lineages of eutherian mammals differ with respect to the mechanisms maintaining pregnancy. PMID:27016782

  15. Topography of thylakoid membranes: In situ localization of photosystems I and II. [Porphyridium cruentum

    SciTech Connect

    Gantt, E.; Mustardy, L.; Cunningham, F.X. Jr. )

    1991-05-01

    The organization of the photosynthetic membrane structure is being studied in the red alga Porphyridium cruentum. Excitation energy transfer between the photosystems, which occurs readily in red algae and cyanobacteria, requires a close spatial relationship between the photosystems. The authors initial efforts have focused on the in situ labelling of PSI and PSII, two of four major protein complexes in thylakoids. Stoichiometries of PSI and PSII in P. cruentum are readily affected by light spectral quality. Cultures grown under continuous red light contain nearly five times as many A{sub A}'s per P{sub 700} as cells grown under green light. Thylakoids were isolated from cells grown under red or green light, and rinsed exhaustively to remove stromal proteins and phycobilisomes. These membranes were spread on electron microscope grids and immunolabelled with affinity-purified IgG antibodies to PSI and PSII. Gold particles were directly coupled to the antibodies of PSI (10 nm Au) and PSII (15nm Au). The labelling results are consistent with the Q{sub A} and P{sub 700} determinations. The density of PSII is greater in membranes from red light cells relative to green light cells, while the PSI density is greater in green light cells. The photosystems appear to be uniformly distributed over the thylakoid membranes. Double labelling experiments indicate that PSI and PSII can occur in close proximity with a distance of less than 20 nm. Such proximity increases the possibility of excitation energy transfer between PSI and PSII.

  16. Cryo-imaging of photosystems and phycobilisomes in Anabaena sp. PCC 7120 cells.

    PubMed

    Steinbach, Gábor; Schubert, Félix; Kaňa, Radek

    2015-11-01

    Primary photosynthetic reactions take place inside thylakoid membrane where light-to-chemical energy conversion is catalyzed by two pigment-protein complexes, photosystem I (PSI) and photosystem II (PSII). Light absorption in cyanobacteria is increased by pigment-protein supercomplexes--phycobilisomes (PBSs) situated on thylakoid membrane surfaces that transfer excitation energy into both photosystems. We have explored the localization of PSI, PSII and PBSs in thylakoid membrane of native cyanobacteria cell Anabaena sp. 7120 by means of cryogenic confocal microscopy. We have adapted a conventional temperature controlling stage to an Olympus FV1000 confocal microscope. The presence of red shifted emission of chlorophylls from PSI has been confirmed by spectral measurements. Confocal fluorescence images of PSI (in a spectral range 710-750 nm), PSII (in a spectral range 690-705 nm) and PBSs (in a spectral range 650-680 nm) were recorded at low temperature. Co-localization of images showed spatial heterogeneity of PSI, PSII and PBSs over the thylakoid membrane, and three dominant areas were identified: PSI-PSII-PBS supercomplex area, PSII-PBS supercomplex area and PSI area. The observed results were discussed with regard to light-harvesting regulation in cyanobacteria.

  17. Differential responses of photosystems I and II to seasonal drought in two Ficus species

    NASA Astrophysics Data System (ADS)

    Zhang, Shubin; Huang, Wei; Zhang, Jiaolin; Cao, Kunfang

    2016-05-01

    Hemiepiphytic Ficus species exhibit more conservative water use strategy and are more drought-tolerant compared with their non-hemiepiphytic congeners, but a difference in the response of photosystem I (PSI) and photosystem II (PSII) to drought stress has not been documented to date. The enhancement of non-photochemical quenching (NPQ) and cyclic electron flow (CEF) have been identified as important mechanisms that protect the photosystems under drought conditions. Using the hemiepiphytic Ficus tinctoria and the non-hemiepiphytic Ficus racemosa, we studied the water status and the electron fluxes through PSI and PSII under seasonal water stress. Our results clearly indicated that the decline in the leaf predawn water potential (ψpd), the maximum photosynthetic rate (Amax) and the predawn maximum quantum yield of PSII (Fv/Fm) were more pronounced in F. racemosa than in F. tinctoria at peak drought. The Fv/Fm of F. racemosa was reduced to 0.69, indicating net photoinhibition of PSII. Concomitantly, the maximal photo-oxidizable P700 (Pm) decreased significantly in F. racemosa but remained stable in F. tinctoria. The fraction of non-photochemical quenching [Y(NPQ)] and the ratio of effective quantum yield of PSI to PSII [Y(I)/Y(II)] increased for both Ficus species at peak drought, with a stronger increase in F. racemosa. These results indicated that the enhancement of NPQ and the activation of CEF contributed to the photoprotection of PSI and PSII for both Ficus species under seasonal drought, particularly for F. racemosa.

  18. Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis[W

    PubMed Central

    Samol, Iga; Shapiguzov, Alexey; Ingelsson, Björn; Fucile, Geoffrey; Crèvecoeur, Michèle; Vener, Alexander V.; Rochaix, Jean-David; Goldschmidt-Clermont, Michel

    2012-01-01

    Reversible protein phosphorylation plays a major role in the acclimation of the photosynthetic apparatus to changes in light. Two paralogous kinases phosphorylate subsets of thylakoid membrane proteins. STATE TRANSITION7 (STN7) phosphorylates LHCII, the light-harvesting antenna of photosystem II (PSII), to balance the activity of the two photosystems through state transitions. STN8, which is mainly involved in phosphorylation of PSII core subunits, influences folding of the thylakoid membranes and repair of PSII after photodamage. The rapid reversibility of these acclimatory responses requires the action of protein phosphatases. In a reverse genetic screen, we identified the chloroplast PP2C phosphatase, PHOTOSYSTEM II CORE PHOSPHATASE (PBCP), which is required for efficient dephosphorylation of PSII proteins. Its targets, identified by immunoblotting and mass spectrometry, largely coincide with those of the kinase STN8. The recombinant phosphatase is active in vitro on a synthetic substrate or on isolated thylakoids. Thylakoid folding is affected in the absence of PBCP, while its overexpression alters the kinetics of state transitions. PBCP and STN8 form an antagonistic kinase and phosphatase pair whose substrate specificity and physiological functions are distinct from those of STN7 and the counteracting phosphatase PROTEIN PHOSPHATASE1/THYLAKOID-ASSOCIATED PHOSPHATASE38, but their activities may overlap to some degree. PMID:22706287

  19. Structure of spinach photosystem II-LHCII supercomplex at 3.2 Å resolution.

    PubMed

    Wei, Xuepeng; Su, Xiaodong; Cao, Peng; Liu, Xiuying; Chang, Wenrui; Li, Mei; Zhang, Xinzheng; Liu, Zhenfeng

    2016-06-01

    During photosynthesis, the plant photosystem II core complex receives excitation energy from the peripheral light-harvesting complex II (LHCII). The pathways along which excitation energy is transferred between them, and their assembly mechanisms, remain to be deciphered through high-resolution structural studies. Here we report the structure of a 1.1-megadalton spinach photosystem II-LHCII supercomplex solved at 3.2 Å resolution through single-particle cryo-electron microscopy. The structure reveals a homodimeric supramolecular system in which each monomer contains 25 protein subunits, 105 chlorophylls, 28 carotenoids and other cofactors. Three extrinsic subunits (PsbO, PsbP and PsbQ), which are essential for optimal oxygen-evolving activity of photosystem II, form a triangular crown that shields the Mn4CaO5-binding domains of CP43 and D1. One major trimeric and two minor monomeric LHCIIs associate with each core-complex monomer, and the antenna-core interactions are reinforced by three small intrinsic subunits (PsbW, PsbH and PsbZ). By analysing the closely connected interfacial chlorophylls, we have obtained detailed insights into the energy-transfer pathways between the antenna and core complexes.

  20. The antenna system of photosystem II from Thermosynechococcus elongatus at 3.2 A resolution.

    PubMed

    Loll, Bernhard; Kern, Jan; Zouni, Athina; Saenger, Wolfram; Biesiadka, Jacek; Irrgang, Klaus-Dieter

    2005-11-01

    The content and type of cofactors harboured in the Photosystem II core complex (PS IIcc) of the cyanobacterium Thermosynechococcus elongatus has been determined by biochemical and spectroscopic methods. 17 +/- 1 chlorophyll a per pheophytin a and 0.25 beta-carotene per chlorophyll a have been found in re-dissolved crystals of dimeric PS IIcc. The X-ray crystal structure of PS IIcc from Thermosynechococcus elongatus at 3.2 A resolution clearly shows chlorophyll a molecules arranged in two layers close to the cytoplasmic and lumenal sides of the thylakoid membrane. Each of the cytoplasmic layers contains 9 chlorophyll a, whose positions and orientations are related by a local twofold rotation pseudo-C2 axis passing through the non-haem Fe2+. These chlorophyll a are arranged comparably to those in the antenna domains of PsaA and PsaB of cyanobacterial Photosystem I affirming an evolutionary relation. The chlorophyll a in the lumenal layer are less well conserved between Photosystems I and II and even between CP43 and CP47 with 4 chlorophyll a in the former and 7 in the latter.

  1. Type IV secretion: intercellular transfer of macromolecules by systems ancestrally related to conjugation machines.

    PubMed

    Christie, P J

    2001-04-01

    Bacterial conjugation systems are highly promiscuous macromolecular transfer systems that impact human health significantly. In clinical settings, conjugation is exceptionally problematic, leading to the rapid dissemination of antibiotic resistance genes and other virulence traits among bacterial populations. Recent work has shown that several pathogens of plants and mammals - Agrobacterium tumefaciens, Bordetella pertussis, Helicobacter pylori and Legionella pneumophila - have evolved secretion pathways ancestrally related to conjugation systems for the purpose of delivering effector molecules to eukaryotic target cells. Each of these systems exports distinct DNA or protein substrates to effect a myriad of changes in host cell physiology during infection. Collectively, secretion pathways ancestrally related to bacterial conjugation systems are now referred to as the type IV secretion family. The list of putative type IV family members is increasing rapidly, suggesting that macromolecular transfer by these systems is a widespread phenomenon in nature. PMID:11309113

  2. Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.

    PubMed

    Medina, Edgar M; Turner, Jonathan J; Gordân, Raluca; Skotheim, Jan M; Buchler, Nicolas E

    2016-01-01

    Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast. PMID:27162172

  3. Unmasking the ancestral activity of integron integrases reveals a smooth evolutionary transition during functional innovation

    PubMed Central

    Escudero, Jose Antonio; Loot, Celine; Parissi, Vincent; Nivina, Aleksandra; Bouchier, Christiane; Mazel, Didier

    2016-01-01

    Tyrosine (Y)-recombinases have evolved to deliver mechanistically different reactions on a variety of substrates, but these evolutionary transitions are poorly understood. Among them, integron integrases are hybrid systems recombining single- and double-stranded DNA partners. These reactions are asymmetric and need a replicative resolution pathway, an exception to the canonical second strand exchange model of Y-recombinases. Integron integrases possess a specific domain for this specialized pathway. Here we show that despite this, integrases are still capable of efficiently operating the ancestral second strand exchange in symmetrical reactions between double-stranded substrates. During these reactions, both strands are reactive and Holliday junction resolution can follow either pathway. A novel deep-sequencing approach allows mapping of the crossover point for the second strand exchange. The persistence of the ancestral activity in integrases illustrates their robustness and shows that innovation towards new recombination substrates and resolution pathways was a smooth evolutionary process. PMID:26961432

  4. Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi

    PubMed Central

    Medina, Edgar M; Turner, Jonathan J; Gordân, Raluca; Skotheim, Jan M; Buchler, Nicolas E

    2016-01-01

    Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast. DOI: http://dx.doi.org/10.7554/eLife.09492.001 PMID:27162172

  5. Responses of Photosystem I Compared with Photosystem II to Fluctuating Light in the Shade-Establishing Tropical Tree Species Psychotria henryi

    PubMed Central

    Huang, Wei; Yang, Ying-Jie; Hu, Hong; Zhang, Shi-Bao

    2016-01-01

    Shade-establishing plants growing in the forest understory are exposed to constant high light or fluctuating light when gaps are created by fallen trees. Our previous studies indicate that photosystem I (PSI) is sensitive to constant high light in shade-establishing tree species, however, the effects of fluctuating light on PSI and photosystem II (PSII) in shade-establishing species are little known. In the present study, we examined the responses of PSI and PSII to fluctuating light in comparison to constant high light in the shade-establishing species Psychotria henryi. Accompanying with significant activation of cyclic electron flow (CEF), the P700 oxidation ratio was maintained at high levels when exposed to strong light either under fluctuating light or constant high light. Under moderate fluctuating light, PSI and PSII activities were remained stable in P. henryi. Interestingly, PSI was insusceptible to fluctuating light but sensitive to constant high light in P. henryi. Furthermore, both PSI and PSII were more sensitive to constant high light than fluctuating light. These results suggest that CEF is essential for photoprotection of PSI under fluctuating light in P. henryi. Furthermore, photoinhibition of PSI under high light in P. henryi is more related to the accumulation of reactive oxygen species rather than to P700 redox state, which is different from the mechanisms of PSI photoinhibition in Arabidopsis thaliana and rice. Taking together, PSI is a key determiner of photosynthetic responses to fluctuating light and constant high light in the shade-establishing species P. henryi. PMID:27799937

  6. Inactivation of a Synechocystis sp strain PCC 6803 gene with homology to conserved chloroplast open reading frame 184 increases the photosystem II-to-photosystem I ratio.

    PubMed Central

    Wilde, A; Härtel, H; Hübschmann, T; Hoffmann, P; Shestakov, S V; Börner, T

    1995-01-01

    A gene of the unicellular cyanobacterium Synechocystis sp strain PCC 6803 that is homologous to the conserved chloroplast open reading frame orf184 has been cloned and sequenced. The nucleotide sequence of the gene predicts a protein of 184 amino acids with a calculated molecular mass of 21.5 kD and two membrane-spanning regions. Amino acid sequence analysis showed 46 to 37% homology of the cyanobacterial orf184 with tobacco orf184, rice orf185, liverwort orf184, and Euglena gracilis orf206 sequences. Two orf184-specific mutants of Synechocystis sp PCC 6803 were constructed by insertion mutagenesis. Cells of mutants showed growth characteristics similar to those of the wild type. Their pigment composition was distinctly different from the wild type, as indicated by an increase in the phycocyanin-to-chlorophyll ratio. In addition, mutants also had a two- to threefold increase in photosynthetic electron transfer rates as well as in photosystem II-to-photosystem I ratio-a phenomenon hitherto not reported for mutants with altered photosynthetic characteristics. The observed alterations in the orf184-specific mutants provide strong evidence for a functional role of the orf184 gene product in photosynthetic processes. PMID:7780311

  7. Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor

    PubMed Central

    Carroll, Sean Michael; Ortlund, Eric A.; Thornton, Joseph W.

    2011-01-01

    Understanding the genetic, structural, and biophysical mechanisms that caused protein functions to evolve is a central goal of molecular evolutionary studies. Ancestral sequence reconstruction (ASR) offers an experimental approach to these questions. Here we use ASR to shed light on the earliest functions and evolution of the glucocorticoid receptor (GR), a steroid-activated transcription factor that plays a key role in the regulation of vertebrate physiology. Prior work showed that GR and its paralog, the mineralocorticoid receptor (MR), duplicated from a common ancestor roughly 450 million years ago; the ancestral functions were largely conserved in the MR lineage, but the functions of GRs—reduced sensitivity to all hormones and increased selectivity for glucocorticoids—are derived. Although the mechanisms for the evolution of glucocorticoid specificity have been identified, how reduced sensitivity evolved has not yet been studied. Here we report on the reconstruction of the deepest ancestor in the GR lineage (AncGR1) and demonstrate that GR's reduced sensitivity evolved before the acquisition of restricted hormone specificity, shortly after the GR–MR split. Using site-directed mutagenesis, X-ray crystallography, and computational analyses of protein stability to recapitulate and determine the effects of historical mutations, we show that AncGR1's reduced ligand sensitivity evolved primarily due to three key substitutions. Two large-effect mutations weakened hydrogen bonds and van der Waals interactions within the ancestral protein, reducing its stability. The degenerative effect of these two mutations is extremely strong, but a third permissive substitution, which has no apparent effect on function in the ancestral background and is likely to have occurred first, buffered the effects of the destabilizing mutations. Taken together, our results highlight the potentially creative role of substitutions that partially degrade protein structure and function and

  8. Late Paleozoic deformation of interior North America: The greater Ancestral Rocky Mountains

    SciTech Connect

    Ye, Hongzhuan |; Royden, L.; Burchfiel, C.; Schuepbach, M.

    1996-09-01

    Late Paleozoic deformation within interior North America has produced a series of north-northwest- to northwest-trending elongate basins that cover much of Oklahoma, Texas, New Mexico, Colorado, and Utah. Each basin thickens asymmetrically toward an adjacent region of coeval basement uplift from which it is separated by synsedimentary faults with great vertical relief. The remarkable coincidence in timing, geometry, and apparent structural style throughout the region of late Paleozoic deformation strongly suggests that these paired regions of basin subsidence and basement uplift form a unified system of regional deformation, the greater Ancestral Rocky Mountains. Over this region, basin subsidence and basement uplift were approximately synchronous, beginning in the Chesterian-Morrowan, continuing through the Pennsylvanian, and ending in the Wolfcampian (although minor post-Wolfcampian deformation occurs locally). The basement uplifts show evidence for folding and faulting in the Pennsylvanian and Early Permian. Reverse faults and thrust faults have been drilled over many of the uplifts, but only in the Anadarko region has thrusting of the basement uplifts over the adjacent basin been clearly documented. Extensive basement-involved thrusting also occurs along the margins of the Delaware and Midland basins, and suggests that the entire greater Ancestral Rocky Mountains region probably formed as the result of northeast-southwest-directed-intraplate shortening. Deformation within the greater Ancestral Rocky Mountains was coeval with late Paleozoic subduction along much of the North American plate margin, and has traditionally been related to emplacement of thrust sheets within the Ouachita-Marathon orogenic belt. The nature, timing, and orientation of events along the Ouachita-Marathon belt make it difficult to drive the deformation of the greater Ancestral Rocky Mountains by emplacement of the Ouachita-Marathon belt along the southern margin of North America.

  9. Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor

    SciTech Connect

    Carroll, Sean Michael; Ortlund, Eric A; Thornton, Joseph W.

    2012-03-16

    Understanding the genetic, structural, and biophysical mechanisms that caused protein functions to evolve is a central goal of molecular evolutionary studies. Ancestral sequence reconstruction (ASR) offers an experimental approach to these questions. Here we use ASR to shed light on the earliest functions and evolution of the glucocorticoid receptor (GR), a steroid-activated transcription factor that plays a key role in the regulation of vertebrate physiology. Prior work showed that GR and its paralog, the mineralocorticoid receptor (MR), duplicated from a common ancestor roughly 450 million years ago; the ancestral functions were largely conserved in the MR lineage, but the functions of GRs - reduced sensitivity to all hormones and increased selectivity for glucocorticoids - are derived. Although the mechanisms for the evolution of glucocorticoid specificity have been identified, how reduced sensitivity evolved has not yet been studied. Here we report on the reconstruction of the deepest ancestor in the GR lineage (AncGR1) and demonstrate that GR's reduced sensitivity evolved before the acquisition of restricted hormone specificity, shortly after the GR-MR split. Using site-directed mutagenesis, X-ray crystallography, and computational analyses of protein stability to recapitulate and determine the effects of historical mutations, we show that AncGR1's reduced ligand sensitivity evolved primarily due to three key substitutions. Two large-effect mutations weakened hydrogen bonds and van der Waals interactions within the ancestral protein, reducing its stability. The degenerative effect of these two mutations is extremely strong, but a third permissive substitution, which has no apparent effect on function in the ancestral background and is likely to have occurred first, buffered the effects of the destabilizing mutations. Taken together, our results highlight the potentially creative role of substitutions that partially degrade protein structure and function and

  10. Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins.

    PubMed

    Rolland, Morgane; Jensen, Mark A; Nickle, David C; Yan, Jian; Learn, Gerald H; Heath, Laura; Weiner, David; Mullins, James I

    2007-08-01

    The extensive diversity of human immunodeficiency virus type 1 (HIV-1) and its capacity to mutate and escape host immune responses are major challenges for AIDS vaccine development. Ancestral sequences, which minimize the genetic distance to circulating strains, provide an opportunity to design immunogens with the potential to elicit broad recognition of HIV epitopes. We developed a phylogenetics-informed algorithm to reconstruct ancestral HIV sequences, called Center of Tree (COT). COT sequences have potentially significant benefits over isolate-based strategies, as they minimize the evolutionary distances to circulating strains. COT sequences are designed to surmount the potential pitfalls stemming from sampling bias with the consensus method and outlier bias with the most-recent-common-ancestor approach. We computationally derived COT sequences from circulating HIV-1 subtype B sequences for the genes encoding the major viral structural protein (Gag) and two regulatory proteins, Tat and Nef. COT genes were synthesized de novo and expressed in mammalian cells, and the proteins were characterized. COT Gag was shown to generate virus-like particles, while COT Tat transactivated gene expression from the HIV-1 long terminal repeat and COT Nef mediated downregulation of cell surface major histocompatibility complex class I. Thus, retrodicted ancestral COT proteins can retain the biological functions of extant HIV-1 proteins. Additionally, COT proteins were immunogenic, as they elicited antigen-specific cytotoxic T-lymphocyte responses in mice. These data support the utility of the COT approach to create novel and biologically active ancestral proteins as a starting point for studies of the structure, function, and biological fitness of highly variable genes, as well as for the rational design of globally relevant vaccine candidates.

  11. Defining the ancestral eutherian karyotype: a cladistic interpretation of chromosome painting and genome sequence assembly data.

    PubMed

    Robinson, Terence J; Ruiz-Herrera, Aurora

    2008-01-01

    A cladistic analysis of genome assemblies (syntenic associations) for eutherian mammals against two distant outgroup species--opossum and chicken--permitted a refinement of the 46-chromosome karyotype formerly inferred in the ancestral eutherian. We show that two intact chromosome pairs (corresponding to human chromosomes 13 and 18) and three conserved chromosome segments (10q, 19p and 8q in the human karyotype) are probably symplesiomorphic for Eutheria because they are also present as unaltered orthologues in one or both outgroups. Seven additional syntenies (4q/8p/4pq, 3p/21, 14/15, 10p/12pq/22qt, 19q/16q, 16p/7a and 12qt/22q), each involving human chromosomal segments that in various combinations correspond to complete chromosomes in the ancestral eutherian karyotype, are also present in one or both outgroup taxa and thus are probable symplesiomorphies for Eutheria. Interestingly, several of the symplesiomorphic characters identified in chicken and/or opossum are present in more distant outgroups such as pufferfish and zebrafish (for example 3p/21, 14/15, 19q/16q and 16p/7a), suggesting their retention since vertebrate common ancestry approximately 450 million years ago. However, eight intact pairs (corresponding to human chromosomes 1, 5, 6, 9, 11, 17, 20 and the X) and three chromosome segments (7b, 2p-q13 and 2q13-qter) are derived characters potentially consistent with eutherian monophyly. Our analyses clarify the distinction between shared-ancestral and shared-derived homology in the eutherian ancestral karyotype.

  12. Photosystem II photochemistry and phycobiliprotein of the red algae Kappaphycus alvarezii and their implications for light adaptation.

    PubMed

    Guan, Xiangyu; Wang, Jinfeng; Zhu, Jianyi; Yao, Chunyan; Liu, Jianguo; Qin, Song; Jiang, Peng

    2013-01-01

    Photosystem II photochemistry and phycobiliprotein (PBP) genes of red algae Kappaphycus alvarezii, raw material of κ -carrageenan used in food and pharmaceutical industries, were analyzed in this study. Minimum saturating irradiance (I k) of this algal species was less than 115 μmol m(-2) s(-1). Its actual PSII efficiency (yield II) increased when light intensity enhanced and decreased when light intensity reached 200 μmol m(-2) s(-1). Under dim light, yield II declined at first and then increased on the fourth day. Under high light, yield II retained a stable value. These results indicate that K. alvarezii is a low-light-adapted species but possesses regulative mechanisms in response to both excessive and deficient light. Based on the PBP gene sequences, K. alvarezii, together with other red algae, assembled faster and showed a closer relationship with LL-Prochlorococcus compared to HL-Prochlorococcus. Many amino acid loci in PBP sequences of K. alvarezii were conserved with those of LL-Prochlorococcus. However, loci conserved with HL-Prochlorococcus but divergent with LL-Prochlorococcus were also found. The diversities of PE and PC are proposed to have played some roles during the algal evolution and divergence of light adaption.

  13. MET1 is a thylakoid-associated TPR protein involved in photosystem II supercomplex formation and repair in Arabidopsis.

    PubMed

    Bhuiyan, Nazmul H; Friso, Giulia; Poliakov, Anton; Ponnala, Lalit; van Wijk, Klaas J

    2015-01-01

    Photosystem II (PSII) requires constant disassembly and reassembly to accommodate replacement of the D1 protein. Here, we characterize Arabidopsis thaliana MET1, a PSII assembly factor with PDZ and TPR domains. The maize (Zea mays) MET1 homolog is enriched in mesophyll chloroplasts compared with bundle sheath chloroplasts, and MET1 mRNA and protein levels increase during leaf development concomitant with the thylakoid machinery. MET1 is conserved in C3 and C4 plants and green algae but is not found in prokaryotes. Arabidopsis MET1 is a peripheral thylakoid protein enriched in stroma lamellae and is also present in grana. Split-ubiquitin assays and coimmunoprecipitations showed interaction of MET1 with stromal loops of PSII core components CP43 and CP47. From native gels, we inferred that MET1 associates with PSII subcomplexes formed during the PSII repair cycle. When grown under fluctuating light intensities, the Arabidopsis MET1 null mutant (met1) showed conditional reduced growth, near complete blockage in PSII supercomplex formation, and concomitant increase of unassembled CP43. Growth of met1 in high light resulted in loss of PSII supercomplexes and accelerated D1 degradation. We propose that MET1 functions as a CP43/CP47 chaperone on the stromal side of the membrane during PSII assembly and repair. This function is consistent with the observed differential MET1 accumulation across dimorphic maize chloroplasts.

  14. Photosystem II Photochemistry and Phycobiliprotein of the Red Algae Kappaphycus alvarezii and Their Implications for Light Adaptation

    PubMed Central

    Wang, Jinfeng; Zhu, Jianyi; Yao, Chunyan; Liu, Jianguo; Qin, Song; Jiang, Peng

    2013-01-01

    Photosystem II photochemistry and phycobiliprotein (PBP) genes of red algae Kappaphycus alvarezii, raw material of κ-carrageenan used in food and pharmaceutical industries, were analyzed in this study. Minimum saturating irradiance (Ik) of this algal species was less than 115 μmol m−2 s−1. Its actual PSII efficiency (yield II) increased when light intensity enhanced and decreased when light intensity reached 200 μmol m−2 s−1. Under dim light, yield II declined at first and then increased on the fourth day. Under high light, yield II retained a stable value. These results indicate that K. alvarezii is a low-light-adapted species but possesses regulative mechanisms in response to both excessive and deficient light. Based on the PBP gene sequences, K. alvarezii, together with other red algae, assembled faster and showed a closer relationship with LL-Prochlorococcus compared to HL-Prochlorococcus. Many amino acid loci in PBP sequences of K. alvarezii were conserved with those of LL-Prochlorococcus. However, loci conserved with HL-Prochlorococcus but divergent with LL-Prochlorococcus were also found. The diversities of PE and PC are proposed to have played some roles during the algal evolution and divergence of light adaption. PMID:24380080

  15. Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change.

    PubMed

    Martinez, Carlos; Rest, Joshua S; Kim, Ah-Ram; Ludwig, Michael; Kreitman, Martin; White, Kevin; Reinitz, John

    2014-04-01

    Upstream regulatory sequences that control gene expression evolve rapidly, yet the expression patterns and functions of most genes are typically conserved. To address this paradox, we have reconstructed computationally and resurrected in vivo the cis-regulatory regions of the ancestral Drosophila eve stripe 2 element and evaluated its evolution using a mathematical model of promoter function. Our feed-forward transcriptional model predicts gene expression patterns directly from enhancer sequence. We used this functional model along with phylogenetics to generate a set of possible ancestral eve stripe 2 sequences for the common ancestors of 1) D. simulans and D. sechellia; 2) D. melanogaster, D. simulans, and D. sechellia; and 3) D. erecta and D. yakuba. These ancestral sequences were synthesized and resurrected in vivo. Using a combination of quantitative and computational analysis, we find clear support for functional compensation between the binding sites for Bicoid, Giant, and Krüppel over the course of 40-60 My of Drosophila evolution. We show that this compensation is driven by a coupling interaction between Bicoid activation and repression at the anterior and posterior border necessary for proper placement of the anterior stripe 2 border. A multiplicity of mechanisms for binding site turnover exemplified by Bicoid, Giant, and Krüppel sites, explains how rapid sequence change may occur while maintaining the function of the cis-regulatory element.

  16. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction.

    PubMed

    Whitfield, Jason H; Zhang, William H; Herde, Michel K; Clifton, Ben E; Radziejewski, Johanna; Janovjak, Harald; Henneberger, Christian; Jackson, Colin J

    2015-09-01

    Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 µM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue.

  17. Something for nothing? Reconstruction of ancestral character states in asterinid sea star development.

    PubMed

    Keever, Carson C; Hart, Michael W

    2008-01-01

    Traits from early development mapped onto phylogenetic trees can potentially offer insight into the evolutionary history of development by inferring the states of those characters among ancestors at nodes in the phylogeny. A key and often-overlooked aspect of such mapping is the underlying model of character evolution. Without a well-supported and realistic model ("nothing"), character mapping of ancestral traits onto phylogenetic trees might often return results ("something") that lack a sound basis. Here we reconsider a challenging case study in this area of evolutionary developmental biology: the inference of ancestral states for ecological and morphological characters in the reproduction and larval development of asterinid sea stars. We apply improved analytical methods to an expanded set of asterinid phylogenetic data and developmental character states. This analysis shows that the new methods might generally offer some independent insight into choice of a model of character evolution, but that in the specific case of asterinid sea stars the quantitative features of the model (especially the relative probabilities of different directions of change) have an important effect on the results. We suggest caution in applying ancestral state reconstructions in the absence of an independently corroborated model of character evolution, and highlight the need for such modeling in evolutionary developmental biology.

  18. A Cooperative Co-Evolutionary Genetic Algorithm for Tree Scoring and Ancestral Genome Inference.

    PubMed

    Gao, Nan; Zhang, Yan; Feng, Bing; Tang, Jijun

    2015-01-01

    Recent advances of technology have made it easy to obtain and compare whole genomes. Rearrangements of genomes through operations such as reversals and transpositions are rare events that enable researchers to reconstruct deep evolutionary history among species. Some of the popular methods need to search a large tree space for the best scored tree, thus it is desirable to have a fast and accurate method that can score a given tree efficiently. During the tree scoring procedure, the genomic structures of internal tree nodes are also provided, which provide important information for inferring ancestral genomes and for modeling the evolutionary processes. However, computing tree scores and ancestral genomes are very difficult and a lot of researchers have to rely on heuristic methods which have various disadvantages. In this paper, we describe the first genetic algorithm for tree scoring and ancestor inference, which uses a fitness function considering co-evolution, adopts different initial seeding methods to initialize the first population pool, and utilizes a sorting-based approach to realize evolution. Our extensive experiments show that compared with other existing algorithms, this new method is more accurate and can infer ancestral genomes that are much closer to the true ancestors. PMID:26671797

  19. AAV ancestral reconstruction library enables selection of broadly infectious viral variants.

    PubMed

    Santiago-Ortiz, J; Ojala, D S; Westesson, O; Weinstein, J R; Wong, S Y; Steinsapir, A; Kumar, S; Holmes, I; Schaffer, D V

    2015-12-01

    Adeno-associated virus (AAV) vectors have achieved clinical efficacy in treating several diseases. However, enhanced vectors are required to extend these landmark successes to other indications and protein engineering approaches may provide the necessary vector improvements to address such unmet medical needs. To generate new capsid variants with potentially enhanced infectious properties and to gain insights into AAV's evolutionary history, we computationally designed and experimentally constructed a putative ancestral AAV library. Combinatorial variations at 32 amino acid sites were introduced to account for uncertainty in their identities. We then analyzed the evolutionary flexibility of these residues, the majority of which have not been previously studied, by subjecting the library to iterative selection on a representative cell line panel. The resulting variants exhibited transduction efficiencies comparable to the most efficient extant serotypes and, in general, ancestral libraries were broadly infectious across the cell line panel, indicating that they favored promiscuity over specificity. Interestingly, putative ancestral AAVs were more thermostable than modern serotypes and did not use sialic acids, galactose or heparan sulfate proteoglycans for cellular entry. Finally, variants mediated 19- to 31-fold higher gene expression in the muscle compared with AAV1, a clinically used serotype for muscle delivery, highlighting their promise for gene therapy.

  20. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction

    PubMed Central

    Whitfield, Jason H; Zhang, William H; Herde, Michel K; Clifton, Ben E; Radziejewski, Johanna; Janovjak, Harald; Henneberger, Christian; Jackson, Colin J

    2015-01-01

    Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding “core” that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 µM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue. PMID:26061224

  1. Ancestral state reconstruction, rate heterogeneity, and the evolution of reptile viviparity.

    PubMed

    King, Benedict; Lee, Michael S Y

    2015-05-01

    Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. However, this assumption is unlikely to hold in many situations, particularly as ancestral state reconstructions are being performed on increasingly large phylogenies. Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. The random local clock method, implemented in BEAST, estimates the position and magnitude of rate changes on the tree; split BiSSE estimates separate rate parameters for pre-specified clades; and the hidden rates model partitions each character state into a number of rate categories. Simulations show the inadequacy of traditional models when characters evolve with both asymmetry (different rates of change between states within a character) and heterotachy (different rates of character evolution across different clades). The importance of accounting for rate heterogeneity in ancestral state reconstruction is highlighted empirically with a new analysis of the evolution of viviparity in squamate reptiles, which reveal a predominance of forward (oviparous-viviparous) transitions and very few reversals.

  2. Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins.

    PubMed

    Clifton, Ben E; Jackson, Colin J

    2016-02-18

    The promiscuous functions of proteins are an important reservoir of functional novelty in protein evolution, but the molecular basis for binding promiscuity remains elusive. We used ancestral protein reconstruction to experimentally characterize evolutionary intermediates in the functional expansion of the polar amino acid-binding protein family, which has evolved to bind a variety of amino acids with high affinity and specificity. High-resolution crystal structures of an ancestral arginine-binding protein in complex with l-arginine and l-glutamine show that the promiscuous binding of l-glutamine is enabled by multi-scale conformational plasticity, water-mediated interactions, and selection of an alternative conformational substate productive for l-glutamine binding. Evolution of specialized glutamine-binding proteins from this ancestral protein was achieved by displacement of water molecules from the protein-ligand interface, reducing the entropic penalty associated with the promiscuous interaction. These results provide a structural and thermodynamic basis for the co-option of a promiscuous interaction in the evolution of binding specificity.

  3. Preliminary appraisal of ground water in and near the ancestral Missouri River Valley, northeastern Montana

    USGS Publications Warehouse

    Levings, G.W.

    1986-01-01

    A preliminary appraisal was conducted in and near the ancestral Missouri River valley in northeastern Montana to describe the groundwater resources and to establish a data base for the area. The data base then could be used for future evaluation of possible changes in water levels or water quality. In this area, consolidated aquifers are the Upper Cretaceous Fox Hills-lower Hell Creek aquifer and the overlying Paleocene Fort Union Formation. Unconsolidated aquifers are Pleistocene terrace gravel and glacial deposits and Holocene alluvial deposits. Aquifers are recharged by precipitation, infiltration of streamflow, and possibly leakage from lakes and potholes. Groundwater moves from topographically higher areas to the ancestral valley, then along the ancestral valley to the southwest. Water is discharged from aquifers by evapotranspiration, springs and seeps, movement directly into streams and lakes, and from pumping wells. Average well yields are greatest for irrigation wells completed in outwash gravel (886 gallons/min). Eighteen wells were completed in various aquifers to monitor potential long-term changes in water levels and water quality. Measured water levels declined about 2 ft. or less during the study (1982-85). Chemical analysis of groundwater samples indicated that concentrations of some dissolved constituents exceeded U.S. Environmental Protection Agency standards for drinking water. (USGS)

  4. A general modeling framework for genome ancestral origins in multiparental populations.

    PubMed

    Zheng, Chaozhi; P Boer, Martin; van Eeuwijk, Fred A

    2014-09-01

    The next generation of QTL (quantitative trait loci) mapping populations have been designed with multiple founders, where one to a number of generations of intercrossing are introduced prior to the inbreeding phase to increase accumulated recombinations and thus mapping resolution. Examples of such populations are Collaborative Cross (CC) in mice and Multiparent Advanced Generation Inter-Cross (MAGIC) lines in Arabidopsis. The genomes of the produced inbred lines are fine-grained random mosaics of the founder genomes. In this article, we present a novel framework for modeling ancestral origin processes along two homologous autosomal chromosomes from mapping populations, which is a major component in the reconstruction of the ancestral origins of each line for QTL mapping. We construct a general continuous time Markov model for ancestral origin processes, where the rate matrix is deduced from the expected densities of various types of junctions (recombination breakpoints). The model can be applied to monoecious populations with or without self-fertilizations and to dioecious populations with two separate sexes. The analytic expressions for map expansions and expected junction densities are obtained for mapping populations that have stage-wise constant mating schemes, such as CC and MAGIC. Our studies on the breeding design of MAGIC populations show that the intercross mating schemes do not matter much for large population size and that the overall expected junction density, and thus map resolution, are approximately proportional to the inverse of the number of founders.

  5. Patterns of Ancestral Human Diversity: An Analysis of Alu-Insertion and Restriction-Site Polymorphisms

    PubMed Central

    Watkins, W. S.; Ricker, C. E.; Bamshad, M. J.; Carroll, M. L.; Nguyen, S. V.; Batzer, M. A.; Harpending, H. C.; Rogers, A. R.; Jorde, L. B.

    2001-01-01

    We have analyzed 35 widely distributed, polymorphic Alu loci in 715 individuals from 31 world populations. The average frequency of Alu insertions (the derived state) is lowest in Africa (.42) but is higher and similar in India (.55), Europe (.56), and Asia (.57). A comparison with 30 restriction-site polymorphisms (RSPs) for which the ancestral state has been determined shows that the frequency of derived RSP alleles is also lower in Africa (.35) than it is in Asia (.45) and in Europe (.46). Neighbor-joining networks based on Alu insertions or RSPs are rooted in Africa and show African populations as separate from other populations, with high statistical support. Correlations between genetic distances based on Alu and nuclear RSPs, short tandem-repeat polymorphisms, and mtDNA, in the same individuals, are high and significant. For the 35 loci, Alu gene diversity and the diversity attributable to population subdivision is highest in Africa but is lower and similar in Europe and Asia. The distribution of ancestral alleles is consistent with an origin of early modern human populations in sub-Saharan Africa, the isolation and preservation of ancestral alleles within Africa, and an expansion out of Africa into Eurasia. This expansion is characterized by increasing frequencies of Alu inserts and by derived RSP alleles with reduced genetic diversity in non-African populations. PMID:11179020

  6. Ancestral sleep.

    PubMed

    de la Iglesia, Horacio O; Moreno, Claudia; Lowden, Arne; Louzada, Fernando; Marqueze, Elaine; Levandovski, Rosa; Pilz, Luisa K; Valeggia, Claudia; Fernandez-Duque, Eduardo; Golombek, Diego A; Czeisler, Charles A; Skene, Debra J; Duffy, Jeanne F; Roenneberg, Till

    2016-04-01

    While we do not yet understand all the functions of sleep, its critical role for normal physiology and behaviour is evident. Its amount and temporal pattern depend on species and condition. Humans sleep about a third of the day with the longest, consolidated episode during the night. The change in lifestyle from hunter-gatherers via agricultural communities to densely populated industrialized centres has certainly affected sleep, and a major concern in the medical community is the impact of insufficient sleep on health [1,2]. One of the causal mechanisms leading to insufficient sleep is altered exposure to the natural light-dark cycle. This includes the wide availability of electric light, attenuated exposure to daylight within buildings, and evening use of light-emitting devices, all of which decrease the strength of natural light-dark signals that entrain circadian systems [3].

  7. Ancestral sleep.

    PubMed

    de la Iglesia, Horacio O; Moreno, Claudia; Lowden, Arne; Louzada, Fernando; Marqueze, Elaine; Levandovski, Rosa; Pilz, Luisa K; Valeggia, Claudia; Fernandez-Duque, Eduardo; Golombek, Diego A; Czeisler, Charles A; Skene, Debra J; Duffy, Jeanne F; Roenneberg, Till

    2016-04-01

    While we do not yet understand all the functions of sleep, its critical role for normal physiology and behaviour is evident. Its amount and temporal pattern depend on species and condition. Humans sleep about a third of the day with the longest, consolidated episode during the night. The change in lifestyle from hunter-gatherers via agricultural communities to densely populated industrialized centres has certainly affected sleep, and a major concern in the medical community is the impact of insufficient sleep on health [1,2]. One of the causal mechanisms leading to insufficient sleep is altered exposure to the natural light-dark cycle. This includes the wide availability of electric light, attenuated exposure to daylight within buildings, and evening use of light-emitting devices, all of which decrease the strength of natural light-dark signals that entrain circadian systems [3]. PMID:27046809

  8. Toward synthetic models for high oxidation state forms of the photosystem II active site metal cluster: the first tetranuclear manganese cluster containing a [Mn4(mu-O)5]6+ core.

    PubMed

    Mukhopadhyay, Sumitra; Staples, Richard J; Armstrong, William H

    2002-04-21

    The first tetrameric high valent manganese complex consisting of a MnIV4(mu-O)5 bridged core, [Mn4(mu-O)5(dmb)4(dmbO)2](ClO4)4, [symbol: see text] was isolated via dimanganese (III,IV) and (IV,IV) intermediates in presence of the oxidant tert-butyl hydroperoxide and was characterized by X-ray crystallography, electrochemistry, infrared, UV-visible, 1H NMR, and mass spectroscopy; the structure found differs greatly from a proposal for the putative Mn4O5 aggregate found in Photosystem II.

  9. Can an ancestral condition for milk oligosaccharides be determined? Evidence from the Tasmanian echidna (Tachyglossus aculeatus setosus).

    PubMed

    Oftedal, Olav T; Nicol, Stewart C; Davies, Noel W; Sekii, Nobuhiro; Taufik, Epi; Fukuda, Kenji; Saito, Tadao; Urashima, Tadasu

    2014-09-01

    The monotreme pattern of egg-incubation followed by extended lactation represents the ancestral mammalian reproductive condition, suggesting that monotreme milk may include saccharides of an ancestral type. Saccharides were characterized from milk of the Tasmanian echidna Tachyglossus aculeatus setosus. Oligosaccharides in pooled milk from late lactation were purified by gel filtration and high-performance liquid chromatography using a porous graphitized carbon column and characterized by (1)H NMR spectroscopy; oligosaccharides in smaller samples from early and mid-lactation were separated by ultra-performance liquid chromatography and characterized by negative electrospray ionization mass spectrometry (ESI-MS) and tandem collision mass spectroscopy (MS/MS) product ion patterns. Eight saccharides were identified by (1)H NMR: lactose, 2'-fucosyllactose, difucosyllactose (DFL), B-tetrasaccharide, B-pentasaccharide, lacto-N-fucopentaose III (LNFP3), 4-O-acetyl-3'-sialyllactose [Neu4,5Ac(α2-3)Gal(β1-4)Glc] and 4-O-acetyl-3'-sialyl-3-fucosyllactose [Neu4,5Ac(α2-3)Gal(β1-4)[Fuc(α1-3)]Glc]. Six of these (all except DFL and LNFP3) were present in early and mid-lactation per ESI-MS, although some at trace levels. Four additional oligosaccharides examined by ESI-MS and MS/MS are proposed to be 3'-sialyllactose [Neu5Ac(α2-3)Gal(β1-4)Glc], di-O-acetyl-3'-sialyllactose [Neu4,5,UAc3(α2-3)Gal(β1-4)Glc where U = 7, 8 or 9], 4-O-acetyl-3'-sialyllactose sulfate [Neu4,5Ac(α2-3)Gal(β1-4)GlcS, where position of the sulfate (S) is unknown] and an unidentified 800 Da oligosaccharide containing a 4-O-acetyl-3'-sialyllactose core. 4-O-acetyl-3'-sialyllactose was the predominant saccharide at all lactation stages. 4-O-Acetylation is known to protect sialyllactose from bacterial sialidases and may be critical to prevent microbial degradation on the mammary areolae and/or in the hatchling digestive tract so that sialyllactose can be available for enterocyte uptake. The ability to

  10. Can an ancestral condition for milk oligosaccharides be determined? Evidence from the Tasmanian echidna (Tachyglossus aculeatus setosus).

    PubMed

    Oftedal, Olav T; Nicol, Stewart C; Davies, Noel W; Sekii, Nobuhiro; Taufik, Epi; Fukuda, Kenji; Saito, Tadao; Urashima, Tadasu

    2014-09-01

    The monotreme pattern of egg-incubation followed by extended lactation represents the ancestral mammalian reproductive condition, suggesting that monotreme milk may include saccharides of an ancestral type. Saccharides were characterized from milk of the Tasmanian echidna Tachyglossus aculeatus setosus. Oligosaccharides in pooled milk from late lactation were purified by gel filtration and high-performance liquid chromatography using a porous graphitized carbon column and characterized by (1)H NMR spectroscopy; oligosaccharides in smaller samples from early and mid-lactation were separated by ultra-performance liquid chromatography and characterized by negative electrospray ionization mass spectrometry (ESI-MS) and tandem collision mass spectroscopy (MS/MS) product ion patterns. Eight saccharides were identified by (1)H NMR: lactose, 2'-fucosyllactose, difucosyllactose (DFL), B-tetrasaccharide, B-pentasaccharide, lacto-N-fucopentaose III (LNFP3), 4-O-acetyl-3'-sialyllactose [Neu4,5Ac(α2-3)Gal(β1-4)Glc] and 4-O-acetyl-3'-sialyl-3-fucosyllactose [Neu4,5Ac(α2-3)Gal(β1-4)[Fuc(α1-3)]Glc]. Six of these (all except DFL and LNFP3) were present in early and mid-lactation per ESI-MS, although some at trace levels. Four additional oligosaccharides examined by ESI-MS and MS/MS are proposed to be 3'-sialyllactose [Neu5Ac(α2-3)Gal(β1-4)Glc], di-O-acetyl-3'-sialyllactose [Neu4,5,UAc3(α2-3)Gal(β1-4)Glc where U = 7, 8 or 9], 4-O-acetyl-3'-sialyllactose sulfate [Neu4,5Ac(α2-3)Gal(β1-4)GlcS, where position of the sulfate (S) is unknown] and an unidentified 800 Da oligosaccharide containing a 4-O-acetyl-3'-sialyllactose core. 4-O-acetyl-3'-sialyllactose was the predominant saccharide at all lactation stages. 4-O-Acetylation is known to protect sialyllactose from bacterial sialidases and may be critical to prevent microbial degradation on the mammary areolae and/or in the hatchling digestive tract so that sialyllactose can be available for enterocyte uptake. The ability to

  11. Food-Nonfood Discrimination in Ancestral Vertebrates: Gamete Cannibalism and the Origin of the Adaptive Immune System.

    PubMed

    Corcos, D

    2015-11-01

    Adaptive immunity is a complex system that appeared twice in vertebrates (in gnathostomes and in jawless fish) although it is not required for invertebrate defence. The adaptive immune system is tightly associated with self-non-self discrimination, and it is now clear that this interplay is not limited to the prevention of autoreactivity. Micro-organisms are usually considered for their pathogenicity or symbiotic ability, but, for most small metazoans, they mainly constitute food. Vertebrates are characterized by feeding by predation on larger preys, when compared to their ancestors who were filter feeders and ate micro-organisms. Predation gives a strong selective advantage, not only due to the availability of new food resources but also by the ability to eliminate competitors for environmental resources (intraguild predation (IGP)). Unlike size-structured IGP, intraspecific predation of juveniles, zygotes or gametes can be detrimental for species fitness in some circumstances. The ability of individuals to recognize highly polymorphic molecules on the surface of gametes present in the plankton and so distinguish self versus non-self gametes might have constituted a strong selective advantage in intraspecific competition. Here, I propose the theory that the capacity to rearrange receptors has been selected in ancestral vertebrates as a consequence of this strong need for discriminating between hetero-cannibalism versus filial cannibalism. This evolutionary origin sheds light on presently unexplained features of the immune system, including the existence of regulatory T cells and of non-pathogenic natural autoimmunity. PMID:26286030

  12. Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators

    PubMed Central

    Fumeaux, Coralie; Radhakrishnan, Sunish Kumar; Ardissone, Silvia; Théraulaz, Laurence; Frandi, Antonio; Martins, Daniel; Nesper, Jutta; Abel, Sören; Jenal, Urs; Viollier, Patrick H.

    2014-01-01

    Zinc-finger domain transcriptional regulators regulate a myriad of functions in eukaryotes. Interestingly, ancestral versions (MucR) from Alpha-proteobacteria control bacterial virulence/symbiosis. Whether virulence regulators can also control cell cycle transcription is unknown. Here we report that MucR proteins implement a hitherto elusive primordial S→G1 transcriptional switch. After charting G1-specific promoters in the cell cycle model Caulobacter crescentus by comparative ChIP-seq, we use one such promoter as genetic proxy to unearth two MucR paralogs, MucR1/2, as constituents of a quadripartite and homeostatic regulatory module directing the S→G1 transcriptional switch. Surprisingly, MucR orthologues that regulate virulence and symbiosis gene transcription in Brucella, Agrobacterium or Sinorhizobium support this S→G1 switch in Caulobacter. Pan-genomic ChIP-seq analyses in Sinorhizobium and Caulobacter show that this module indeed targets orthologous genes. We propose that MucR proteins and possibly other virulence regulators primarily control bacterial cell cycle (G1-phase) transcription, rendering expression of target (virulence) genes periodic and in tune with the cell cycle. PMID:24939058

  13. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage

    PubMed Central

    Yeoh, Yun Kit; Sekiguchi, Yuji; Parks, Donovan H.; Hugenholtz, Philip

    2016-01-01

    Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0–1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms. PMID:26615204

  14. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.

    PubMed

    Yeoh, Yun Kit; Sekiguchi, Yuji; Parks, Donovan H; Hugenholtz, Philip

    2016-04-01

    Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0-1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms.

  15. Ancestral association between HLA and HFE H63D and C282Y gene mutations from northwest Colombia

    PubMed Central

    Rodriguez, Libia M; Giraldo, Mabel C; Velasquez, Laura I; Alvarez, Cristiam M; Garcia, Luis F; Jimenez-Del-Rio, Marlene; Velez-Pardo, Carlos

    2015-01-01

    A significant association between HFE gene mutations and the HLA-A*03-B*07 and HLA-A*29-B*44 haplotypes has been reported in the Spanish population. It has been proposed that these mutations are probably connected with Celtic and North African ancestry, respectively. We aimed to find the possible ancestral association between HLA alleles and haplotypes associated with the HFE gene (C282Y and H63D) mutations in 214 subjects from Antioquia, Colombia. These were 18 individuals with presumed hereditary hemochromatosis (“HH”) and 196 controls. The HLA-B*07 allele was in linkage disequilibrium (LD) with C282Y, while HLA-A*23, A*29, HLA-B*44, and B*49 were in LD with H63D. Altogether, our results show that, although the H63D mutation is more common in the Antioquia population, it is not associated with any particular HLA haplotype, whereas the C282Y mutation is associated with HLA-A*03-B*07, this supporting a northern Spaniard ancestry. PMID:25983618

  16. Testing the museum versus cradle tropical biological diversity hypothesis: phylogeny, diversification, and ancestral biogeographic range evolution of the ants.

    PubMed

    Moreau, Corrie S; Bell, Charles D

    2013-08-01

    Ants are one of the most ecologically and numerically dominant group of terrestrial organisms with most species diversity currently found in tropical climates. Several explanations for the disparity of biological diversity in the tropics compared to temperate regions have been proposed including that the tropics may act as a "museum" where older lineages persist through evolutionary time or as a "cradle" where new species continue to be generated. We infer the molecular phylogenetic relationships of 295 ant specimens including members of all 21 extant subfamilies to explore the evolutionary diversification and biogeography of the ants. By constraining the topology and age of the root node while using 45 fossils as minimum constraints, we converge on an age of 139-158 Mya for the modern ants. Further diversification analyses identified 10 periods with a significant change in the tempo of diversification of the ants, although these shifts did not appear to correspond to ancestral biogeographic range shifts. Likelihood-based historical biogeographic reconstructions suggest that the Neotropics were important in early ant diversification (e.g., Cretaceous). This finding coupled with the extremely high-current species diversity suggests that the Neotropics have acted as both a museum and cradle for ant diversity.

  17. New Sicydiinae phylogeny (Teleostei: Gobioidei) inferred from mitochondrial and nuclear genes: insights on systematics and ancestral areas.

    PubMed

    Taillebois, Laura; Castelin, Magalie; Lord, Clara; Chabarria, Ryan; Dettaï, Agnès; Keith, Philippe

    2014-01-01

    The Sicydiinae subfamily (Teleostei: Gobioidei) is the biggest contributor to the diversity of fish communities in river systems of tropical islands. These species are found in the Indo-Pacific area, the Caribbean region and West Africa. They spawn in freshwater, their planktotrophic larvae drift downstream to the sea where they develop, before returning to the rivers to grow and reproduce. Hence, they are called amphidromous. Their phylogeny has been explored using a total of 3545 sites from 5 molecular markers (mitochondrial DNA: 16S rDNA, cytochrome oxidase I, cytochrome b; nuclear DNA: rhodopsin gene and a nuclear marker specially developed for this study, the interferon regulatory factor 2 binding protein 1-IRF2PB1). Sequences were obtained for 59 Sicydiinae specimens of 9 known genera. The Bayesian and maximum likelihood analyses support the monophyly of the subfamily as well as the monophylyof all genera except Sicydium, which is paraphyletic. Five major clades were identified within this subfamily. One clade contained the genus Stiphodon. Another clade contained Sicyopterus, Sicydium and Parasicydium with Sicyopterus as sister genus of Sicydium. The non-monophyly of Sicydium subclade, because it includes the monotypic genus Parasicydium, challenged the validity of Parasicydium genus. Ancestral area reconstruction showed that the subfamily emerged in the Central West Pacific region implying that previous hypotheses proposing a dispersal route for Sicydiinae into the Atlantic Ocean are unsupported by the present analysis. Our results suggest that the hypotheses for the dispersal route of the genus Sicydium should be reconsidered.

  18. Development and use of domain-specific antibodies in a characterization of the large subunits of soybean photosystem 1

    NASA Technical Reports Server (NTRS)

    Henry, R. L.; Takemoto, L. J.; Murphy, J.; Gallegos, G. L.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

    1992-01-01

    The molecular architecture of the soybean photosystem 1 reaction center complex was examined using a combination of surface labeling and immunological methodology on isolated thylakoid membranes. Synthetic peptides (12 to 14 amino acids in length) were prepared which correspond to the N-terminal regions of the 83 and 82.4 kDa subunits of photosystem 1 (the PsaA and PsaB proteins, respectively). Similarly, a synthetic peptide was prepared corresponding to the C-terminal region of the PsaB subunit. These peptides were conjugated to a carrier protein, and were used for the production of polyclonal antibodies in rabbits. The resulting sera could distinguish between the PsaA and PsaB photosystem 1 subunits by Western blot analysis, and could identify appropriate size classes of cyanogen bromide cleavage fragments as predicted from the primary sequences of these two subunits. When soybean thylakoid membranes were surface-labeled with N-hydroxysuccinimidobiotin, several subunits of the complete photosystem 1 lipid/protein complex incorporated label. These included the light harvesting chlorophyll proteins of photosystem 1, and peptides thought to aid in the docking of ferredoxin to the complex during photosynthetic electron transport. However, the PsaA and PsaB subunits showed very little biotinylation. When these subunits were examined for the domains to which biotin did attach, most of the observed label was associated with the N-terminal domain of the PsaA subunit, as identified using a domain-specific polyclonal antisera.

  19. Phosphorylation of Photosystem II Controls Functional Macroscopic Folding of Photosynthetic Membranes in Arabidopsis[C][W][OA

    PubMed Central

    Fristedt, Rikard; Willig, Adrian; Granath, Pontus; Crèvecoeur, Michèle; Rochaix, Jean-David; Vener, Alexander V.

    2009-01-01

    Photosynthetic thylakoid membranes in plants contain highly folded membrane layers enriched in photosystem II, which uses light energy to oxidize water and produce oxygen. The sunlight also causes quantitative phosphorylation of major photosystem II proteins. Analysis of the Arabidopsis thaliana stn7xstn8 double mutant deficient in thylakoid protein kinases STN7 and STN8 revealed light-independent phosphorylation of PsbH protein and greatly reduced N-terminal phosphorylation of D2 protein. The stn7xstn8 and stn8 mutants deficient in light-induced phosphorylation of photosystem II had increased thylakoid membrane folding compared with wild-type and stn7 plants. Significant enhancement in the size of stacked thylakoid membranes in stn7xstn8 and stn8 accelerated gravity-driven sedimentation of isolated thylakoids and was observed directly in plant leaves by transmission electron microscopy. Increased membrane folding, caused by the loss of light-induced protein phosphorylation, obstructed lateral migration of the photosystem II reaction center protein D1 and of processing protease FtsH between the stacked and unstacked membrane domains, suppressing turnover of damaged D1 in the leaves exposed to high light. These findings show that the high level of photosystem II phosphorylation in plants is required for adjustment of macroscopic folding of large photosynthetic membranes modulating lateral mobility of membrane proteins and sustained photosynthetic activity. PMID:20028840

  20. Atrazine and Methyl Viologen Effects on Chlorophyll-a Fluorescence Revisited-Implications in Photosystems Emission and Ecotoxicity Assessment.

    PubMed

    Iriel, Analia; Novo, Johanna M; Cordon, Gabriela B; Lagorio, María G

    2014-01-01

    In this work, we use the effect of herbicides that affect the photosynthetic chain at defined sites in the photosynthetic reaction steps to derive information about the fluorescence emission of photosystems. The interpretation of spectral data from treated and control plants, after correction for light reabsorption processes, allowed us to elucidate current controversies in the subject. Results were compatible with the fact that a nonnegligible Photosystem I contribution to chlorophyll fluorescence in plants at room temperature does exist. In another aspect, variable and nonvariable chlorophyll fluorescence were comparatively tested as bioindicators for detection of both herbicides in aquatic environment. Both methodologies were appropriate tools for this purpose. However, they showed better sensitivity for pollutants disconnecting Photosystem II-Photosystem I by blocking the electron transport between them as Atrazine. Specifically, changes in the (experimental and corrected by light reabsorption) red to far red fluorescence ratio, in the maximum photochemical quantum yield and in the quantum efficiency of Photosytem II for increasing concentrations of herbicides have been measured and compared. The most sensitive bioindicator for both herbicides was the quantum efficiency of Photosystem II.

  1. Atrazine and Methyl Viologen Effects on Chlorophyll-a Fluorescence Revisited-Implications in Photosystems Emission and Ecotoxicity Assessment.

    PubMed

    Iriel, Analia; Novo, Johanna M; Cordon, Gabriela B; Lagorio, María G

    2014-01-01

    In this work, we use the effect of herbicides that affect the photosynthetic chain at defined sites in the photosynthetic reaction steps to derive information about the fluorescence emission of photosystems. The interpretation of spectral data from treated and control plants, after correction for light reabsorption processes, allowed us to elucidate current controversies in the subject. Results were compatible with the fact that a nonnegligible Photosystem I contribution to chlorophyll fluorescence in plants at room temperature does exist. In another aspect, variable and nonvariable chlorophyll fluorescence were comparatively tested as bioindicators for detection of both herbicides in aquatic environment. Both methodologies were appropriate tools for this purpose. However, they showed better sensitivity for pollutants disconnecting Photosystem II-Photosystem I by blocking the electron transport between them as Atrazine. Specifically, changes in the (experimental and corrected by light reabsorption) red to far red fluorescence ratio, in the maximum photochemical quantum yield and in the quantum efficiency of Photosytem II for increasing concentrations of herbicides have been measured and compared. The most sensitive bioindicator for both herbicides was the quantum efficiency of Photosystem II. PMID:23869421

  2. Fluorescence F 0 of photosystems II and I in developing C3 and C 4 leaves, and implications on regulation of excitation balance.

    PubMed

    Peterson, Richard B; Oja, Vello; Eichelmann, Hillar; Bichele, Irina; Dall'Osto, Luca; Laisk, Agu

    2014-10-01

    This work addresses the question of occurrence and function of photosystem II (PSII) in bundle sheath (BS) cells of leaves possessing NADP-malic enzyme-type C4 photosynthesis (Zea mays). Although no requirement for PSII activity in the BS has been established, several component proteins of PSII have been detected in BS cells of developing maize leaves exhibiting O2-insensitive photosynthesis. We used the basal fluorescence emissions of PSI (F 0I) and PSII (F 0II) as quantitative indicators of the respective relative photosystem densities. Chl fluorescence induction was measured simultaneously at 680 and 750 nm. In mature leaves, the F m(680)/F 0(680) ratio was 10.5 but less in immature leaves. We propose that the lower ratio was caused by the presence of a distinct non-variable component, F c, emitting at 680 and 750 nm. After F c was subtracted, the fluorescence of PSI (F 0I) was detected as a non-variable component at 750 nm and was undetectably low at 680 nm. Contents of Chls a and b were measured in addition to Chl fluorescence. The Chl b/(a + b) was relatively stable in developing sunflower leaves (0.25-0.26), but in maize it increased from 0.09 to 0.21 with leaf tissue age. In sunflower, the F 0I/(F 0I + F 0II) was 0.39 ± 0.01 independent of leaf age, but in maize, this parameter was 0.65 in young tissue of very low Chl content (20-50 mg m(-2)) falling to a stable level of 0.53 ± 0.01 at Chl contents >100 mg m(-2). The values of F 0I/(F 0I + F 0II) showed that in sunflower, excitation was partitioned between PSII and PSI in a ratio of 2:1, but the same ratio was 1:1 in the C4 plant. The latter is consistent with a PSII:PSI ratio of 2:1 in maize mesophyll cells and PSI only in BS cells (2:1:1 distribution). We suggest, moreover, that redox mediation of Chl synthesis, rather than protein accumulation, regulates photosystem assembly to ensure optimum excitation balance between functional PSII and PSI. Indeed, the apparent necessity for two

  3. Photosystem I shows a higher tolerance to sorbitol-induced osmotic stress than photosystem II in the intertidal macro-algae Ulva prolifera (Chlorophyta).

    PubMed

    Gao, Shan; Zheng, Zhenbing; Gu, Wenhui; Xie, Xiujun; Huan, Li; Pan, Guanghua; Wang, Guangce

    2014-10-01

    The photosynthetic performance of the desiccation-tolerant, intertidal macro-algae Ulva prolifera was significantly affected by sorbitol-induced osmotic stress. Our results showed that photosynthetic activity decreased significantly with increases in sorbitol concentration. Although the partial activity of both photosystem I (PS I) and photosystem II (PS II) was able to recover after 30 min of rehydration, the activity of PS II decreased more rapidly than PS I. At 4 M sorbitol concentration, the activity of PS II was almost 0 while that of PS I was still at about one third of normal levels. Following prolonged treatment with 1 and 2 M sorbitol, the activity of PS I and PS II decreased slowly, suggesting that the effects of moderate concentrations of sorbitol on PS I and PS II were gradual. Interestingly, an increase in non-photochemical quenching occurred under these conditions in response to moderate osmotic stress, whereas it declined significantly under severe osmotic stress. These results suggest that photoprotection in U. prolifera could also be induced by moderate osmotic stress. In addition, the oxidation of PS I was significantly affected by osmotic stress. P700(+) in the thalli treated with high concentrations of sorbitol could still be reduced, as PS II was inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), but it could not be fully oxidized. This observation may be caused by the higher quantum yield of non-photochemical energy dissipation in PS I due to acceptor-side limitation (Y(NA)) during rehydration in seawater containing DCMU.

  4. Absence of the major light harvesting antenna proteins alters the redox properties of photosystem II reaction centres in the chlorine F2 mutant of barley

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the chlorina F2 mutant of barley specifically exhibits reduced levels of the major light harvesting polypeptides (Lhcb) associated with photosystem II, thermoluminescence measurements of photosystem reaction centre photochemistry revealed that S2/S3QB- charge recombinations were shifted to ...

  5. Analysis of Ancestral and Functionally Relevant CD5 Variants in Systemic Lupus Erythematosus Patients

    PubMed Central

    Consuegra, Marta; Bonet, Lizette; Carnero-Montoro, Elena; Armiger, Noelia; Caballero-Baños, Miguel; Arias, Maria Teresa; Benitez, Daniel; Ortego-Centeno, Norberto; de Ramón, Enrique; Sabio, José Mario; García–Hernández, Francisco J.; Tolosa, Carles; Suárez, Ana; González-Gay, Miguel A.; Bosch, Elena; Martín, Javier; Lozano, Francisco

    2014-01-01

    Objective CD5 plays a crucial role in autoimmunity and is a well-established genetic risk factor of developing RA. Recently, evidence of positive selection has been provided for the CD5 Pro224-Val471 haplotype in East Asian populations. The aim of the present work was to further analyze the functional relevance of non-synonymous CD5 polymorphisms conforming the ancestral and the newly derived haplotypes (Pro224-Ala471 and Pro224-Val471, respectively) as well as to investigate the potential role of CD5 on the development of SLE and/or SLE nephritis. Methods The CD5 SNPs rs2241002 (C/T; Pro224Leu) and rs2229177 (C/T; Ala471Val) were genotyped using TaqMan allelic discrimination assays in a total of 1,324 controls and 681 SLE patients of Spanish origin. In vitro analysis of CD3-mediated T cell proliferative and cytokine response profiles of healthy volunteers homozygous for the above mentioned CD5 haplotypes were also analyzed. Results T-cell proliferation and cytokine release were significantly increased showing a bias towards to a Th2 profile after CD3 cross-linking of peripheral mononuclear cells from healthy individuals homozygous for the ancestral Pro224-Ala471 (CC) haplotype, compared to the more recently derived Pro224-Val471 (CT). The same allelic combination was statistically associated with Lupus nephritis. Conclusion The ancestral Ala471 CD5 allele confers lymphocyte hyper-responsiveness to TCR/CD3 cross-linking and is associated with nephritis in SLE patients. PMID:25402503

  6. Evolution of sexes from an ancestral mating-type specification pathway.

    PubMed

    Geng, Sa; De Hoff, Peter; Umen, James G

    2014-07-01

    Male and female sexes have evolved repeatedly in eukaryotes but the origins of dimorphic sexes and their relationship to mating types in unicellular species are not understood. Volvocine algae include isogamous species such as Chlamydomonas reinhardtii, with two equal-sized mating types, and oogamous multicellular species such as Volvox carteri with sperm-producing males and egg-producing females. Theoretical work predicts genetic linkage of a gamete cell-size regulatory gene(s) to an ancestral mating-type locus as a possible step in the evolution of dimorphic gametes, but this idea has not been tested. Here we show that, contrary to predictions, a single conserved mating locus (MT) gene in volvocine algae-MID, which encodes a RWP-RK domain transcription factor-evolved from its ancestral role in C. reinhardtii as a mating-type specifier, to become a determinant of sperm and egg development in V. carteri. Transgenic female V. carteri expressing male MID produced functional sperm packets during sexual development. Transgenic male V. carteri with RNA interference (RNAi)-mediated knockdowns of VcMID produced functional eggs, or self-fertile hermaphrodites. Post-transcriptional controls were found to regulate cell-type-limited expression and nuclear localization of VcMid protein that restricted its activity to nuclei of developing male germ cells and sperm. Crosses with sex-reversed strains uncoupled sex determination from sex chromosome identity and revealed gender-specific roles for male and female mating locus genes in sexual development, gamete fitness and reproductive success. Our data show genetic continuity between the mating-type specification and sex determination pathways of volvocine algae, and reveal evidence for gender-specific adaptations in the male and female mating locus haplotypes of Volvox. These findings will enable a deeper understanding of how a master regulator of mating-type determination in an ancestral unicellular species was reprogrammed to

  7. Evolution of Sexes from an Ancestral Mating-Type Specification Pathway

    PubMed Central

    Geng, Sa; De Hoff, Peter; Umen, James G.

    2014-01-01

    Male and female sexes have evolved repeatedly in eukaryotes but the origins of dimorphic sexes and their relationship to mating types in unicellular species are not understood. Volvocine algae include isogamous species such as Chlamydomonas reinhardtii, with two equal-sized mating types, and oogamous multicellular species such as Volvox carteri with sperm-producing males and egg-producing females. Theoretical work predicts genetic linkage of a gamete cell-size regulatory gene(s) to an ancestral mating-type locus as a possible step in the evolution of dimorphic gametes, but this idea has not been tested. Here we show that, contrary to predictions, a single conserved mating locus (MT) gene in volvocine algae—MID, which encodes a RWP-RK domain transcription factor—evolved from its ancestral role in C. reinhardtii as a mating-type specifier, to become a determinant of sperm and egg development in V. carteri. Transgenic female V. carteri expressing male MID produced functional sperm packets during sexual development. Transgenic male V. carteri with RNA interference (RNAi)-mediated knockdowns of VcMID produced functional eggs, or self-fertile hermaphrodites. Post-transcriptional controls were found to regulate cell-type–limited expression and nuclear localization of VcMid protein that restricted its activity to nuclei of developing male germ cells and sperm. Crosses with sex-reversed strains uncoupled sex determination from sex chromosome identity and revealed gender-specific roles for male and female mating locus genes in sexual development, gamete fitness and reproductive success. Our data show genetic continuity between the mating-type specification and sex determination pathways of volvocine algae, and reveal evidence for gender-specific adaptations in the male and female mating locus haplotypes of Volvox. These findings will enable a deeper understanding of how a master regulator of mating-type determination in an ancestral unicellular species was reprogrammed

  8. Clumped isotope paleothermometry of the Mio-Pliocene freshwater Lake Mohave. Lower ancestral Colorado River, USA

    NASA Astrophysics Data System (ADS)

    Lang, K. A.; Huntington, K. W.

    2015-12-01

    The fluvio-lacustrine deposits of the Bouse Formation are an archive of ancestral Colorado River integration in the Late Miocene and Early Pliocene. In Mohave Valley along the California-Arizona-Nevada border, exposures of the Bouse Formation are observed ~400 m above the modern river elevation, which has been interpreted as evidence of tectonic uplift following a regionally extensive marine incursion and integration of the ancestral Colorado River by capture. However, recent investigations instead favor a "top-down" process of river integration by sequential infilling of freshwater lakes that does not require subsequent tectonic uplift. Accurate interpretation of the Bouse Formation's depositional environment is needed to test these models and ultimately, constrain the timing and mechanism of southwestern Colorado Plateau uplift. To further constrain interpretations of depositional environment, we present new clumped isotope analyses with major and trace element geochemistry and scanning electron microscopy of carbonate samples from the Bouse Formation in Mohave Valley. Here the Bouse Formation contains three distinct facies: basal marl and limestone overlain by thick beds of calcareous claystone interbedded with siltstone and sandstone and locally overlain by tufa. Bulk geochemistry of all facies is consistent with a similar freshwater source yet each facies is isotopically distinct, potentially indicating a strong influence of facies-specific fractionation processes. Carbonate formation temperatures measured in tufa samples are variable, suggesting multiple generations of calcite precipitation. Formation temperatures from basal marl and claystone samples are generally consistent with near-surface lake temperatures, broadly supporting a lacustrine depositional environment and "top-down" process of ancestral Colorado River integration. More broadly, our results quantify the variability in carbonate formation temperatures with different lacustrine facies and

  9. Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms.

    PubMed

    Lowery, Robert K; Uribe, Gabriel; Jimenez, Eric B; Weiss, Mark A; Herrera, Kristian J; Regueiro, Maria; Herrera, Rene J

    2013-11-01

    Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1-4% of the non-Sub-Saharan African gene pool may be Neanderthal derived, while 6-8% of the Melanesian gene pool may be the product of admixture between the Denisovans and the direct ancestors of Melanesians. In the present study, we analyzed single nucleotide polymorphism (SNP) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee). We partitioned SNPs into subsets, including those that are derived in both archaic lineages, those that are ancestral in both archaic lineages and those that are only derived in one archaic lineage. By doing this, we have conducted separate examinations of subsets of mutations with higher probabilities of divergent phylogenetic origins. While previous investigations have excluded SNPs from common ancestors in principal component analyses, we included common ancestral SNPs in our analyses to visualize the relative placement of the Neanderthal and Denisova among human populations. To assess the genetic similarities among the various hominin lineages, we performed genetic structure analyses to provide a comparison of genetic patterns found within contemporary human genomes that may have archaic or common ancestral roots. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Our results suggest that Neanderthal genetic associations with contemporary non-Sub-Saharan African populations, as well as the genetic affinities observed between Denisovans and Melanesians most likely result from the retention of ancient mutations in these populations. PMID:23872234

  10. Contrasting determinants of abundance in ancestral and colonized ranges of an invasive brood parasite

    USGS Publications Warehouse

    Hahn, D.C.; O'Connor, R.J.; Scott, J. Michael; Heglund, Patricia J.; Morrison, Michael L.; Haufler, Jonathan B.; Wall, William A.

    2002-01-01

    Avian species distributions are typically regarded as constrained by spatially extensive variables such as climate, habitat, spatial patchiness, and microhabitat attributes. We hypothesized that the distribution of a brood parasite depends as strongly on host distribution patterns as on biophysical factors and examined this hypothesis with respect to the national distribution of the Brown-headed Cowbird (Molothrus ater). We applied a classification and regression (CART) analysis to data from the Breeding Bird Survey (BBS) and the Christmas Bird Count (CBC) and derived hierarchically organized statistical models of the influence of climate and weather, cropping and land use, and host abundance and distribution on the distribution of the Brown-headed Cowbird within the conterminous United States. The model accounted for 47.2% of the variation in cowbird incidence, and host abundance was the top predictor with an R2 of 18.9%. The other predictors identified by the model (crops 15.7%, weather and climate 14.3%, and region 9.6%) fit the ecological profile of this cowbird. We showed that host abundance was independent of these environmental predictors of cowbird distribution. At the regional scale host abundance played a very strong role in determining cowbird abundance in the cowbird?s colonized range east and west of their ancestral range in the Great Plains (26.6%). Crops were not a major predictor for cowbirds in their ancestral range, although they are the most important predictive factor (33%) for the grassland passerines that are the cowbird?s ancestral hosts. Consequently our findings suggest that the distribution of hosts does indeed take precedence over habitat attributes in shaping the cowbird?s distribution at a national scale, within an envelope of constraint set by biophysical factors.

  11. The evolution of virulence in primate malaria parasites based on Bayesian reconstructions of ancestral states.

    PubMed

    Garamszegi, László Zsolt

    2011-02-01

    Plasmodium parasites, the causative agents of malaria, are generally considered as harmful parasites, but many of them cause mild symptoms. Little is known about the evolutionary history and phylogenetic constraints that generate this interspecific variation in virulence due to uncertainties about the phylogenetic associations of parasites. Here, to account for such phylogenetic uncertainty, phylogenetic methods based on Bayesian statistics were followed in combination with sequence data from five genes to estimate the ancestral state of virulence in primate Plasmodium parasites. When recent parasites were categorised according to the damage caused to the host, Bayesian estimates of ancestral states indicated that the acquisition of a harmful host exploitation strategy is more likely to be a recent evolutionary event than a result of an ancient change in a character state altering virulence. On the contrary, there was more evidence for moderate host exploitation having a deep origin along the phylogenetic tree. Moreover, the evolution of host severity is determined by the phylogenetic relationships of parasites, as severity gains did not appear randomly on the evolutionary tree. Such phylogenetic constraints can be mediated by the acquisition of virulence genes. As the impact of a parasite on a host is the result of both the parasite's investment in reproduction and host sensitivity, virulence was also estimated by calculating peak parasitemia after eliminating host effects. A directional random-walk evolutionary model showed that the ancestral primate malarias reproduced at very low parasitemia in their hosts. Consequently, the extreme variation in the outcome of malaria infection in different host species can be better understood in light of the phylogeny of parasites.

  12. Isolation of a photosystem II reaction center consisting of D-1 and D-2 polypeptides and cytochrome b-559

    SciTech Connect

    Nanba, O.; Satoh, K.

    1987-01-01

    A photosystem II reaction center complex consisting of D-1 and D-2 polypeptides and cytochrome b-559 was isolated from spinach grana thylakoids, treated with 4% (wt/vol) Triton X-100, by ion-exchange chromatography using DEAE-Toyopearl 650S. The isolated complex appears to contain five chlorophyll a, two pheophytin a, one ..beta..-carotene, and one or two cytochrome b-559 heme(s) (molar ratio) and exhibits a reversible absorbance change attributable to the photochemical accumulation of reduced pheophytin typical for the intermediary electron acceptor of photosystem II reaction center. These results strongly suggest that the site of primary charge separation in photosystem II is located on the heterodimer composed of D-1 and D-2 subunits.

  13. Heat- and light-induced detachment of the light harvesting complex from isolated photosystem I supercomplexes.

    PubMed

    Nellaepalli, Sreedhar; Zsiros, Ottó; Tóth, Tünde; Yadavalli, Venkateswarlu; Garab, Győző; Subramanyam, Rajagopal; Kovács, László

    2014-08-01

    In a previous study, using photosystem I enriched stroma thylakoid membrane vesicles, we have shown that the light harvesting complexes of this photosystem are prone to heat- and light-induced, thermo-optically driven detachment from the supercomplex [43]. We have also shown that the splitting of the supercomplex occurs in a gradual and specific manner, selectively affecting the different constituents of the antenna complexes. Here we further analyse these heat- and light-induced processes in isolated Photosystem I supercomplex using circular dichroism and 77K fluorescence emission spectroscopy and immuno blotting, and obtain further details on the sequence of events of the dissociation process as well as on the thermal stability of the different components. Our absorption and circular dichroism spectroscopy and immuno blotting data show that the dissociation of LHCI from PSI-LHCI supercomplex starts above 50°C. Also, the low temperature fluorescence emission spectra depicts decrease of maximum fluorescence emission at 730nm and an increase of the intensity at 685nm, and about 10nm blue-shifts, from 730 to 720nm and from 685 to 676nm, respectively, indicating the heat (50°C) induced detachment of LHCI from PSI core complexes. The reaction centre proteins are highly stable even at high temperatures. Lhca2 is more heat stable than the other light harvesting protein complexes of PSI, whereas Lhca4 and Lhca3 are rather labile. Combined heat and light treatments significantly enhances the disorganization of PSI-LHCI supercomplexes, indicating a thermo-optic mechanism, which might have significant role under combined heat and light stress conditions.

  14. Light-induced gradual activation of photosystem II in dark-grown Norway spruce seedlings.

    PubMed

    Pavlovič, Andrej; Stolárik, Tibor; Nosek, Lukáš; Kouřil, Roman; Ilík, Petr

    2016-06-01

    Gymnosperms, unlike angiosperms, are able to synthesize chlorophyll and form photosystems in complete darkness. Photosystem I (PSI) formed under such conditions is fully active, but photosystem II (PSII) is present in its latent form with inactive oxygen evolving complex (OEC). In this work we have studied light-induced gradual changes in PSII function in dark-grown cotyledons of Norway spruce (Picea abies) via the measurement of chlorophyll a fluorescence rise, absorption changes at 830 nm, thermoluminescence glow curves (TL) and protein analysis. The results indicate that in dark-grown cotyledons, alternative reductants were able to act as electron donors to PSII with inactive OEC. Illumination of cotyledons for 5 min led to partial activation of PSII, which was accompanied by detectable oxygen evolution, but still a substantial number of PSII centers remained in the so called PSII-Q(B)-non-reducing form. Interestingly, even 24 h long illumination was not sufficient for the full activation of PSII centers. This was evidenced by a weak attachment of PsbP protein and the absence of PsbQ protein in PSII particles, the absence of PSII supercomplexes, the suboptimal maximum yield of PSII photochemistry, the presence of C band in TL curve and also the presence of up-shifted Q band in TL in DCMU-treated cotyledons. This slow light-induced activation of PSII in dark-grown cotyledons could contribute to the prevention of PSII overexcitation before the light-induced increase in PSI/PSII ratio allows effective operation of linear electron flow. PMID:26901522

  15. Light-induced gradual activation of photosystem II in dark-grown Norway spruce seedlings.

    PubMed

    Pavlovič, Andrej; Stolárik, Tibor; Nosek, Lukáš; Kouřil, Roman; Ilík, Petr

    2016-06-01

    Gymnosperms, unlike angiosperms, are able to synthesize chlorophyll and form photosystems in complete darkness. Photosystem I (PSI) formed under such conditions is fully active, but photosystem II (PSII) is present in its latent form with inactive oxygen evolving complex (OEC). In this work we have studied light-induced gradual changes in PSII function in dark-grown cotyledons of Norway spruce (Picea abies) via the measurement of chlorophyll a fluorescence rise, absorption changes at 830 nm, thermoluminescence glow curves (TL) and protein analysis. The results indicate that in dark-grown cotyledons, alternative reductants were able to act as electron donors to PSII with inactive OEC. Illumination of cotyledons for 5 min led to partial activation of PSII, which was accompanied by detectable oxygen evolution, but still a substantial number of PSII centers remained in the so called PSII-Q(B)-non-reducing form. Interestingly, even 24 h long illumination was not sufficient for the full activation of PSII centers. This was evidenced by a weak attachment of PsbP protein and the absence of PsbQ protein in PSII particles, the absence of PSII supercomplexes, the suboptimal maximum yield of PSII photochemistry, the presence of C band in TL curve and also the presence of up-shifted Q band in TL in DCMU-treated cotyledons. This slow light-induced activation of PSII in dark-grown cotyledons could contribute to the prevention of PSII overexcitation before the light-induced increase in PSI/PSII ratio allows effective operation of linear electron flow.

  16. Changes in antenna of photosystem II induced by short-term heating.

    PubMed

    Kochubey, Svetlana M

    2010-12-01

    Changes in antenna of photosystem II, induced by short-term heating, were studied using characteristics of a short-wavelength band in low-temperature fluorescence spectra (77 K) of pea chloroplasts. Heating for 5 min was carried out at 25 and 45°C in the darkness or in the presence of white light with intensity of 260 or 1,400 μmol/m(2)s. Most modes of thermal treating induced a decrease in integral intensity of the band and an increase of its half-width. The changes were more prominent at high-temperature heating. The second derivative of the contour of a short-wavelength band showed its three components around 680, 685, and 693 nm, the first of which belongs to emission of the outer antenna of Photosystem II, and the other two to its inner antenna. As the fourth derivative shows, high-temperature heating in the presence of light evokes an appearance of some additional components in a short-wavelength region (654, 658, 661, 666, 672, and 675 nm) as well as of two additional components, 682 and 689 nm, in the region of 685-nm peak. Two subcomponents, 692 and 694 nm, can be detected in the 693-nm component. The results are discussed on the basis of the data concerning energy levels and pathways of energy transfer in pigment-protein complexes of the outer and the inner antennas of photosystem II. It is assumed that a protective role of low light relates to inducing of an essential disarrangement in the outer and the inner antennas and of a subsequent decrease in energy funneling to reaction centers, which, in turn, lowers the extent of photoinhibition.

  17. The search for ancestral nervous systems: an integrative and comparative approach.

    PubMed

    Satterlie, Richard A

    2015-02-15

    Even the most basal multicellular nervous systems are capable of producing complex behavioral acts that involve the integration and combination of simple responses, and decision-making when presented with conflicting stimuli. This requires an understanding beyond that available from genomic investigations, and calls for a integrative and comparative approach, where the power of genomic/transcriptomic techniques is coupled with morphological, physiological and developmental experimentation to identify common and species-specific nervous system properties for the development and elaboration of phylogenomic reconstructions. With careful selection of genes and gene products, we can continue to make significant progress in our search for ancestral nervous system organizations. PMID:25696824

  18. Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila

    PubMed Central

    Zhou, Qi; Bachtrog, Doris

    2015-01-01

    Sex chromosomes evolve distinctive types of chromatin from a pair of ancestral autosomes that are usually euchromatic. In Drosophila, the dosage-compensated X becomes enriched for hyperactive chromatin in males (mediated by H4K16ac), while the Y chromosome acquires silencing heterochromatin (enriched for H3K9me2/3). Drosophila autosomes are typically mostly euchromatic but the small dot chromosome has evolved a heterochromatin-like milieu (enriched for H3K9me2/3) that permits the normal expression of dot-linked genes, but which is different from typical pericentric heterochromatin. In Drosophila busckii, the dot chromosomes have fused to the ancestral sex chromosomes, creating a pair of ‘neo-sex’ chromosomes. Here we collect genomic, transcriptomic and epigenomic data from D. busckii, to investigate the evolutionary trajectory of sex chromosomes from a largely heterochromatic ancestor. We show that the neo-sex chromosomes formed <1 million years ago, but nearly 60% of neo-Y linked genes have already become non-functional. Expression levels are generally lower for the neo-Y alleles relative to their neo-X homologs, and the silencing heterochromatin mark H3K9me2, but not H3K9me3, is significantly enriched on silenced neo-Y genes. Despite rampant neo-Y degeneration, we find that the neo-X is deficient for the canonical histone modification mark of dosage compensation (H4K16ac), relative to autosomes or the compensated ancestral X chromosome, possibly reflecting constraints imposed on evolving hyperactive chromatin in an originally heterochromatic environment. Yet, neo-X genes are transcriptionally more active in males, relative to females, suggesting the evolution of incipient dosage compensation on the neo-X. Our data show that Y degeneration proceeds quickly after sex chromosomes become established through genomic and epigenetic changes, and are consistent with the idea that the evolution of sex-linked chromatin is influenced by its ancestral configuration. PMID

  19. Ancestral heritage saves tribes during 1 April 2007 Solomon Islands tsunami

    NASA Astrophysics Data System (ADS)

    Fritz, Hermann M.; Kalligeris, Nikos

    2008-01-01

    The 1 April 2007 magnitude Ms 8.1 earthquake off the New Georgia Group in the Solomon Islands generated a tsunami that killed 52 with locally focused run-up heights of 12 m, local flow depths of 5 m as well as tectonic uplift up to 3.6 m and subsidence down to -1.5 m. A reconnaissance team deployed within one week investigated 65 coastal settlements on 13 remote Islands. The ancestral heritage ``run to high ground after an earthquake'' passed on to younger generations by survivors of smaller historic tsunamis triggered an immediate spontaneous self evacuation containing the death toll.

  20. Sedimentation, volcanism, and ancestral lakes in the Valles Marineris: Clues from topography

    NASA Astrophysics Data System (ADS)

    Lucchitta, B. K.; Isbell, N. K.; Howington-Kraus, A.

    1993-03-01

    Compilation of a simplified geologic/geomorphic map onto a digital terrain model of Valles Marineris has permitted quantitative evaluations of topographic parameters. The study showed that, if their interior layered deposits are lacustrine, the ancestral Valles Marineris must have consisted of isolated basins. If, on the other hand, the troughs were interconnected as they are today, the deposits are most likely to volcanic origin, and the mesas in the peripheral troughs may be table mountains. The material eroded from the trough walls was probably not sufficient to form all of the interior layered deposits, but it may have contributed significantly to their formation.

  1. Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila.

    PubMed

    Zhou, Qi; Bachtrog, Doris

    2015-06-01

    Sex chromosomes evolve distinctive types of chromatin from a pair of ancestral autosomes that are usually euchromatic. In Drosophila, the dosage-compensated X becomes enriched for hyperactive chromatin in males (mediated by H4K16ac), while the Y chromosome acquires silencing heterochromatin (enriched for H3K9me2/3). Drosophila autosomes are typically mostly euchromatic but the small dot chromosome has evolved a heterochromatin-like milieu (enriched for H3K9me2/3) that permits the normal expression of dot-linked genes, but which is different from typical pericentric heterochromatin. In Drosophila busckii, the dot chromosomes have fused to the ancestral sex chromosomes, creating a pair of 'neo-sex' chromosomes. Here we collect genomic, transcriptomic and epigenomic data from D. busckii, to investigate the evolutionary trajectory of sex chromosomes from a largely heterochromatic ancestor. We show that the neo-sex chromosomes formed <1 million years ago, but nearly 60% of neo-Y linked genes have already become non-functional. Expression levels are generally lower for the neo-Y alleles relative to their neo-X homologs, and the silencing heterochromatin mark H3K9me2, but not H3K9me3, is significantly enriched on silenced neo-Y genes. Despite rampant neo-Y degeneration, we find that the neo-X is deficient for the canonical histone modification mark of dosage compensation (H4K16ac), relative to autosomes or the compensated ancestral X chromosome, possibly reflecting constraints imposed on evolving hyperactive chromatin in an originally heterochromatic environment. Yet, neo-X genes are transcriptionally more active in males, relative to females, suggesting the evolution of incipient dosage compensation on the neo-X. Our data show that Y degeneration proceeds quickly after sex chromosomes become established through genomic and epigenetic changes, and are consistent with the idea that the evolution of sex-linked chromatin is influenced by its ancestral configuration.

  2. The search for ancestral nervous systems: an integrative and comparative approach.

    PubMed

    Satterlie, Richard A

    2015-02-15

    Even the most basal multicellular nervous systems are capable of producing complex behavioral acts that involve the integration and combination of simple responses, and decision-making when presented with conflicting stimuli. This requires an understanding beyond that available from genomic investigations, and calls for a integrative and comparative approach, where the power of genomic/transcriptomic techniques is coupled with morphological, physiological and developmental experimentation to identify common and species-specific nervous system properties for the development and elaboration of phylogenomic reconstructions. With careful selection of genes and gene products, we can continue to make significant progress in our search for ancestral nervous system organizations.

  3. Molecular dynamics studies of pathways of water movement in cyanobacterial photosystem II

    SciTech Connect

    Gabdulkhakov, A. G. Kljashtorny, V. G.; Dontsova, M. V.

    2015-01-15

    Photosystem II (PSII) catalyzes the light-induced generation of oxygen from water. The oxygen-evolving complex is buried deep in the protein on the lumenal side of PSII, and water molecules need to pass through protein subunits to reach the active site—the manganese cluster. Previous studies on the elucidation of water channels in PSII were based on an analysis of the cavities in the static PSII structure determined by X-ray diffraction. In the present study, we perform molecular dynamics simulations of the water movement in the transport system of PSII.

  4. Concentric-Flow Electrokinetic Injector Enables Serial Crystallography of Ribosome and Photosystem-II

    PubMed Central

    Sierra, Raymond G.; Gati, Cornelius; Laksmono, Hartawan; Dao, E. Han; Gul, Sheraz; Fuller, Franklin; Kern, Jan; Chatterjee, Ruchira; Ibrahim, Mohamed; Brewster, Aaron S.; Young, Iris D.; Michels-Clark, Tara; Aquila, Andrew; Liang, Mengning; Hunter, Mark S.; Koglin, Jason E.; Boutet, Sébastien; Junco, Elia A.; Hayes, Brandon; Bogan, Michael J.; Hampton, Christina Y.; Puglisi, Elisabetta V.; Sauter, Nicholas K.; Stan, Claudiu A.; Zouni, Athina; Yano, Junko; Yachandra, Vittal K.; Soltis, S. Michael; Puglisi, Joseph D.; DeMirci, Hasan

    2016-01-01

    In this work, a concentric-flow electrokinetic injector delivered microcrystals of Geobacillus stearothermophilus thermolysin (2.2 Å structure), Thermosynechococcus elongatus photosystem II (< 3 Å diffraction) and Thermus thermophilus small ribosomal subunit (3.4 Å structure). The first ambient-temperature X-ray crystal structure of the 30S subunit bound to the antibiotic paromomycin was obtained in its native mother liquor. Compared to previous cryo-cooled structures, this new structure showed that paromomycin binds to the decoding center in a different conformation. PMID:26619013

  5. Isolation of monomeric photosystem II that retains the subunit PsbS.

    PubMed

    Haniewicz, Patrycja; De Sanctis, Daniele; Büchel, Claudia; Schröder, Wolfgang P; Loi, Maria Cecilia; Kieselbach, Thomas; Bochtler, Matthias; Piano, Dario

    2013-12-01

    Photosystem II has been purified from a transplastomic strain of Nicotiana tabacum according to two different protocols. Using the procedure described in Piano et al. (Photosynth Res 106:221-226, 2010) it was possible to isolate highly active PSII composed of monomers and dimers but depleted in their PsbS protein content. A "milder" procedure than the protocol reported by Fey et al. (Biochim Biophys Acta 1777:1501-1509, 2008) led to almost exclusively monomeric PSII complexes which in part still bind the PsbS protein. This finding might support a role for PSII monomers in higher plants.

  6. Arbuscular mycorrhizal symbiosis ameliorates the optimum quantum yield of photosystem II and reduces non-photochemical quenching in rice plants subjected to salt stress.

    PubMed

    Porcel, Rosa; Redondo-Gómez, Susana; Mateos-Naranjo, Enrique; Aroca, Ricardo; Garcia, Rosalva; Ruiz-Lozano, Juan Manuel

    2015-08-01

    Rice is the most important food crop in the world and is a primary source of food for more than half of the world population. However, salinity is considered the most common abiotic stress reducing its productivity. Soil salinity inhibits photosynthetic processes, which can induce an over-reduction of the reaction centres in photosystem II (PSII), damaging the photosynthetic machinery. The arbuscular mycorrhizal (AM) symbiosis may improve host plant tolerance to salinity, but it is not clear how the AM symbiosis affects the plant photosynthetic capacity, particularly the efficiency of PSII. This study aimed at determining the influence of the AM symbiosis on the performance of PSII in rice plants subjected to salinity. Photosynthetic activity, plant gas-exchange parameters, accumulation of photosynthetic pigments and rubisco activity and gene expression were also measured in order to analyse comprehensively the response of the photosynthetic processes to AM symbiosis and salinity. Results showed that the AM symbiosis enhanced the actual quantum yield of PSII photochemistry and reduced the quantum yield of non-photochemical quenching in rice plants subjected to salinity. AM rice plants maintained higher net photosynthetic rate, stomatal conductance and transpiration rate than nonAM plants. Thus, we propose that AM rice plants had a higher photochemical efficiency for CO2 fixation and solar energy utilization and this increases plant salt tolerance by preventing the injury to the photosystems reaction centres and by allowing a better utilization of light energy in photochemical processes. All these processes translated into higher photosynthetic and rubisco activities in AM rice plants and improved plant biomass production under salinity.

  7. Acceleration of cyclic electron flow in rice plants (Oryza sativa L.) deficient in the PsbS protein of Photosystem II.

    PubMed

    Zulfugarov, Ismayil S; Tovuu, Altanzaya; Lee, Choon-Hwan

    2014-11-01

    When compared with Photosystem I (PSI) in wild-type (WT) rice plants, PSI in PsbS-knockout (KO) plants that lack the energy-dependent component of nonphotochemical quenching (NPQ) was less sensitive to photoinhibition. Therefore, we investigated the relationship between NPQ and cyclic electron flow (CEF) around PSI as a photoprotective mechanism. Activities of two CEF routes (PGR5-dependent or NDH-dependent) were compared between those genotypes by using both dark-adapted plants and pre-illuminated plants, i.e., those in which the Calvin-Benson cycle is de-activated and activated, respectively. In dark-adapted leaves activity of the PGR5-dependent route was determined as the rate of P700 photooxidation. Activity was higher in the mutants than in the WT. However, no difference was noted when plants of either genotype were pre-illuminated. When the electron transport pathway was switched to the cyclic mode by infiltrating leaf segments with 150 mM sorbitol, 40 μM DCMU, and 2 mM hydroxylamine, the rate of P700 oxidation was faster in the mutant. That difference disappeared when leaves were infiltrated with antimycin A to inhibit the PGR5-dependent route. Chlorophyll fluorescence (Fo) was also evaluated. To achieve an Fo level comparable to that of the WT, activation of the NDH-dependent route in the mutant required pre-illumination at a certain dose. Therefore, we propose that, as an alternate pathway for the photoprotection of photosystems in the absence of energy-dependent quenching, this PGR5-dependent route is more highly activated in the PsbS-KO mutants than in the WT. Moreover, that stronger activity is probably responsible for slower activation of the NDH-dependent route in the mutant.

  8. Probing S-state advancements and recombination pathways in photosystem II with a global fit program for flash-induced oxygen evolution pattern.

    PubMed

    Pham, Long Vo; Messinger, Johannes

    2016-06-01

    The oxygen-evolving complex (OEC) in photosystem II catalyzes the oxidation of water to molecular oxygen. Four decades ago, measurements of flash-induced oxygen evolution have shown that the OEC steps through oxidation states S(0), S(1), S(2), S(3) and S(4) before O(2) is released and the S(0) state is reformed. The light-induced transitions between these states involve misses and double hits. While it is widely accepted that the miss parameter is S state dependent and may be further modulated by the oxidation state of the acceptor side, the traditional way of analyzing each flash-induced oxygen evolution pattern (FIOP) individually did not allow using enough free parameters to thoroughly test this proposal. Furthermore, this approach does not allow assessing whether the presently known recombination processes in photosystem II fully explain all measured oxygen yields during Si state lifetime measurements. Here we present a global fit program that simultaneously fits all flash-induced oxygen yields of a standard FIOP (2 Hz flash frequency) and of 11-18 FIOPs each obtained while probing the S(0), S(2) and S(3) state lifetimes in spinach thylakoids at neutral pH. This comprehensive data treatment demonstrates the presence of a very slow phase of S(2) decay, in addition to the commonly discussed fast and slow reduction of S(2) by YD and QB(-), respectively. Our data support previous suggestions that the S(0)→S(1) and S(1)→S(2) transitions involve low or no misses, while high misses occur in the S(2)→S(3) or S(3)→S(0) transitions. PMID:27033305

  9. Probing S-state advancements and recombination pathways in photosystem II with a global fit program for flash-induced oxygen evolution pattern.

    PubMed

    Pham, Long Vo; Messinger, Johannes

    2016-06-01

    The oxygen-evolving complex (OEC) in photosystem II catalyzes the oxidation of water to molecular oxygen. Four decades ago, measurements of flash-induced oxygen evolution have shown that the OEC steps through oxidation states S(0), S(1), S(2), S(3) and S(4) before O(2) is released and the S(0) state is reformed. The light-induced transitions between these states involve misses and double hits. While it is widely accepted that the miss parameter is S state dependent and may be further modulated by the oxidation state of the acceptor side, the traditional way of analyzing each flash-induced oxygen evolution pattern (FIOP) individually did not allow using enough free parameters to thoroughly test this proposal. Furthermore, this approach does not allow assessing whether the presently known recombination processes in photosystem II fully explain all measured oxygen yields during Si state lifetime measurements. Here we present a global fit program that simultaneously fits all flash-induced oxygen yields of a standard FIOP (2 Hz flash frequency) and of 11-18 FIOPs each obtained while probing the S(0), S(2) and S(3) state lifetimes in spinach thylakoids at neutral pH. This comprehensive data treatment demonstrates the presence of a very slow phase of S(2) decay, in addition to the commonly discussed fast and slow reduction of S(2) by YD and QB(-), respectively. Our data support previous suggestions that the S(0)→S(1) and S(1)→S(2) transitions involve low or no misses, while high misses occur in the S(2)→S(3) or S(3)→S(0) transitions.

  10. Induction of efficient energy dissipation in the isolated light-harvesting complex of Photosystem II in the absence of protein aggregation.

    PubMed

    Ilioaia, Cristian; Johnson, Matthew P; Horton, Peter; Ruban, Alexander V

    2008-10-24

    Under excess illumination, the Photosystem II light-harvesting antenna of higher plants has the ability to switch into an efficient photoprotective mode, allowing safe dissipation of excitation energy into heat. In this study, we show induction of the energy dissipation state, monitored by chlorophyll fluorescence quenching, in the isolated major light-harvesting complex (LHCII) incorporated into a solid gel system. Removal of detergent caused strong fluorescence quenching, which was totally reversible. Singlet-singlet annihilation and gel electrophoresis experiments suggested that the quenched complexes were in the trimeric not aggregated state. Both the formation and recovery of this quenching state were inhibited by a cross-linker, implying involvement of conformational changes. Absorption and CD measurements performed on the samples in the quenched state revealed specific alterations in the spectral bands assigned to the red forms of chlorophyll a, neoxanthin, and lutein 1 molecules. The majority of these alterations were similar to those observed during LHCII aggregation. This suggests that not the aggregation process as such but rather an intrinsic conformational transition in the complex is responsible for establishment of quenching. 77 K fluorescence measurements showed red-shifted chlorophyll a fluorescence in the 690-705 nm region, previously observed in aggregated LHCII. The fact that all spectral changes associated with the dissipative mode observed in the gel were different from those of the partially denatured complex strongly argues against the involvement of protein denaturation in the observed quenching. The implications of these findings for proposed mechanisms of energy dissipation in the Photosystem II antenna are discussed.

  11. The role of phosphatidylglycerol as a functional effector and membrane anchor of the D1-core peptide from photosystem II-particles of the cyanobacterium Oscillatoria chalybea.

    PubMed

    Kruse, O; Schmid, G H

    1995-01-01

    The intrinsic polypeptide D1, isolated from photosystem (PS) II-particles of the cyanobacterium Oscillatoria chalybea, was obtained by electroelution and fractionated extraction with organic solvents. Purification was demonstrated by Western blotting and amino acid sequencing. By carrying out D1-immunization in rabbits a polyclonal monospecific D1-antiserum was obtained. For the qualitative characterization of D1 as a lipid-binding peptide, the effect of the lipids phosphatidylglycerol (PG), monogalactosyldiacylglyceride (MGDG) and phosphatidylcholine (PC) on PSII-oxygen evolution was analysed in reconstitution experiments. In these experiments purified photosystem II (PSII)-particle preparations were treated with the enzyme phospholipase A2 and supplemented with lipid emulsions. We were able to show that the inhibition of electron transport, as the consequence of this lipase treatment, was only relieved, if phosphatidylglycerol was added to the preparation. A model was proposed, in which phosphatidylglycerol is a functional effector for the optimal conformation of D1 in the PSII core complex. Phosphatidylglycerol molecules are unusually tightly bound to the D1 peptide by hydrophobic interactions. A covalent binding seems not probable. The localisation of phosphatidylglycerol binding sites was found by trypsin treatment of D1 and analysis of the obtained oligopeptides with HPLC and immunoblotting. The binding sites could be confined to the hydrophobic amino acid section between arginine 27 and arginine 225, which is known to be the membrane anchor of D1. This has led us to the conclusion that the phospholipid phosphatidylglycerol plays an important role for anchoring the D1-peptide and for its orientation in the thylakoid membrane. Phosphatidylglycerol with its high amount of palmitic acid has in prokaryotic cyanobacteria apparently a role in stabilization and orientation. The high turn-over of D1 and the spatial separation of the synthesis- and incorporation

  12. Arbuscular mycorrhizal symbiosis ameliorates the optimum quantum yield of photosystem II and reduces non-photochemical quenching in rice plants subjected to salt stress.

    PubMed

    Porcel, Rosa; Redondo-Gómez, Susana; Mateos-Naranjo, Enrique; Aroca, Ricardo; Garcia, Rosalva; Ruiz-Lozano, Juan Manuel

    2015-08-01

    Rice is the most important food crop in the world and is a primary source of food for more than half of the world population. However, salinity is considered the most common abiotic stress reducing its productivity. Soil salinity inhibits photosynthetic processes, which can induce an over-reduction of the reaction centres in photosystem II (PSII), damaging the photosynthetic machinery. The arbuscular mycorrhizal (AM) symbiosis may improve host plant tolerance to salinity, but it is not clear how the AM symbiosis affects the plant photosynthetic capacity, particularly the efficiency of PSII. This study aimed at determining the influence of the AM symbiosis on the performance of PSII in rice plants subjected to salinity. Photosynthetic activity, plant gas-exchange parameters, accumulation of photosynthetic pigments and rubisco activity and gene expression were also measured in order to analyse comprehensively the response of the photosynthetic processes to AM symbiosis and salinity. Results showed that the AM symbiosis enhanced the actual quantum yield of PSII photochemistry and reduced the quantum yield of non-photochemical quenching in rice plants subjected to salinity. AM rice plants maintained higher net photosynthetic rate, stomatal conductance and transpiration rate than nonAM plants. Thus, we propose that AM rice plants had a higher photochemical efficiency for CO2 fixation and solar energy utilization and this increases plant salt tolerance by preventing the injury to the photosystems reaction centres and by allowing a better utilization of light energy in photochemical processes. All these processes translated into higher photosynthetic and rubisco activities in AM rice plants and improved plant biomass production under salinity. PMID:26291919

  13. Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure.

    PubMed

    DeGiorgio, Michael; Rosenberg, Noah A

    2016-08-01

    In the last few years, several statistically consistent consensus methods for species tree inference have been devised that are robust to the gene tree discordance caused by incomplete lineage sorting in unstructured ancestral populations. One source of gene tree discordance that has only recently been identified as a potential obstacle for phylogenetic inference is ancestral population structure. In this article, we describe a general model of ancestral population structure, and by relying on a single carefully constructed example scenario, we show that the consensus methods Democratic Vote, STEAC, STAR, R(∗) Consensus, Rooted Triple Consensus, Minimize Deep Coalescences, and Majority-Rule Consensus are statistically inconsistent under the model. We find that among the consensus methods evaluated, the only method that is statistically consistent in the presence of ancestral population structure is GLASS/Maximum Tree. We use simulations to evaluate the behavior of the various consensus methods in a model with ancestral population structure, showing that as the number of gene trees increases, estimates on the basis of GLASS/Maximum Tree approach the true species tree topology irrespective of the level of population structure, whereas estimates based on the remaining methods only approach the true species tree topology if the level of structure is low. However, through simulations using species trees both with and without ancestral population structure, we show that GLASS/Maximum Tree performs unusually poorly on gene trees inferred from alignments with little information. This practical limitation of GLASS/Maximum Tree together with the inconsistency of other methods prompts the need for both further testing of additional existing methods and development of novel methods under conditions that incorporate ancestral population structure.

  14. Was Australopithecus anamensis ancestral to A. afarensis? A case of anagenesis in the hominin fossil record.

    PubMed

    Kimbel, William H; Lockwood, Charles A; Ward, Carol V; Leakey, Meave G; Rak, Yoel; Johanson, Donald C

    2006-08-01

    We tested the hypothesis that early Pliocene Australopithecus anamensis was ancestral to A. afarensis by conducting a phylogenetic analysis of four temporally successive fossil samples assigned to these species (from earliest to latest: Kanapoi, Allia Bay, Laetoli, Hadar) using polarized character-state data from 20 morphological characters of the dentition and jaws. If the hypothesis that A. anamensis is ancestral to A. afarensis is true, then character-state changes between the temporally ordered site-samples should be congruent with hypothesized polarity transformations based on outgroup (African great ape) conditions. The most parsimonious reconstruction of character-state evolution suggests that each of the hominin OTUs shares apomorphies only with geologically younger OTUs, as predicted by the hypothesis of ancestry (tree length=31; Consistency Index=0.903). This concordance of stratigraphic and character-state data supports the idea that the A. anamensis and A. afarensis samples represent parts of an anagenetically evolving lineage, or evolutionary species. Each site-sample appears to capture a different point along this evolutionary trajectory. We discuss the implications of this conclusion for the taxonomy and adaptive evolution of these early-middle Pliocene hominins.

  15. Style and origin of mid-Carboniferous deformation in the Illinois Basin, USA - Ancestral rockies deformation?

    USGS Publications Warehouse

    McBride, J.H.; Nelson, W.J.

    1999-01-01

    The integration of outcrop, borehole, and seismic reflection data from the Illinois Basin and adjacent eastern Ozark Dome in Illinois and Missouri sheds new light on the style and origin of intra-cratonic deformation. Typical structures of this region are high-angle reverse faults in Precambrian basement that propagated upward to monoclines and asymmetrical anticlines in Paleozoic sedimentary cover. These are compressive-block structures directly analogous to (although smaller than) 'Laramide-style' structures of the Colorado Plateau and Rocky Mountain foreland. Central Illinois Basin structures were active chiefly during late Chesterian through Atokan (i.e., late Mississippian to middle Pennsylvanian; mid-Carboniferous) time, with continued intermittent movement through the late Pennsylvanian. Both the style and timing of deformation match those of the 'Ancestral Rocky Mountains' orogeny of the southern Midcontinent and Rocky Mountain region of the USA. Deformation in the central Illinois Basin has generally been attributed to the nearby late Paleozoic Appalachian-Ouachita orogeny, even though the Illinois Basin's compressive block structural style is foreign to the Appalachian foreland. We suggest that the Ancestral Rockies event may have played a significant role in the development of Pennsylvanian-age compressive-block structures in Illinois and Missouri.

  16. Bearing the unbearable: ancestral transmission through dreams and moving metaphors in the analtyic field.

    PubMed

    Pickering, Judith

    2012-11-01

    This paper explores how untold and unresolved intergenerational trauma may be transmitted through unconscious channels of communication, manifesting in the dreams of descendants. Unwitting carriers for that which was too horrific for their ancestors to bear, descendants may enter analysis through an unconscious need to uncover past secrets, piece together ancestral histories before the keys to comprehending their terrible inheritance die with their forebears. They seek the relational containment of the analytic relationship to provide psychological conditions to bear the unbearable, know the unknowable, speak the unspeakable and redeem the unredeemable. In the case of 'Rachael', initial dreams gave rise to what Hobson (1984) called 'moving metaphors of self' in the analytic field. Dream imagery, projective and introjective processes in the transference-countertransference dynamics gradually revealed an unknown ancestral history. I clarify the back and forth process from dream to waking dream thoughts to moving metaphors and differentiate the moving metaphor from a living symbol. I argue that the containment of the analytic relationship nested within the security of the analytic space is a necessary precondition for such healing processes to occur.

  17. Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution

    PubMed Central

    Rothschild, Jeremy B.; Tsimiklis, Panagiotis; Siggia, Eric D.; François, Paul

    2016-01-01

    Molecular evolution is an established technique for inferring gene homology but regulatory DNA turns over so rapidly that inference of ancestral networks is often impossible. In silico evolution is used to compute the most parsimonious path in regulatory space for anterior-posterior patterning linking two Dipterian species. The expression pattern of gap genes has evolved between Drosophila (fly) and Anopheles (mosquito), yet one of their targets, eve, has remained invariant. Our model predicts that stripe 5 in fly disappears and a new posterior stripe is created in mosquito, thus eve stripe modules 3+7 and 4+6 in fly are homologous to 3+6 and 4+5 in mosquito. We can place Clogmia on this evolutionary pathway and it shares the mosquito homologies. To account for the evolution of the other pair-rule genes in the posterior we have to assume that the ancestral Dipterian utilized a dynamic method to phase those genes in relation to eve. PMID:27227405

  18. Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple.

    PubMed

    Ismail, Siti Izera; Batzer, Jean Carlson; Harrington, Thomas C; Crous, Pedro W; Lavrov, Dennis V; Li, Huanyu; Gleason, Mark L

    2016-01-01

    Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi.

  19. RNA–DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA

    PubMed Central

    Bar-Yaacov, Dan; Avital, Gal; Levin, Liron; Richards, Allison L.; Hachen, Naomi; Rebolledo Jaramillo, Boris; Nekrutenko, Anton; Zarivach, Raz; Mishmar, Dan

    2013-01-01

    RNA transcripts are generally identical to the underlying DNA sequences. Nevertheless, RNA–DNA differences (RDDs) were found in the nuclear human genome and in plants and animals but not in human mitochondria. Here, by deep sequencing of human mitochondrial DNA (mtDNA) and RNA, we identified three RDD sites at mtDNA positions 295 (C-to-U), 13710 (A-to-U, A-to-G), and 2617 (A-to-U, A-to-G). Position 2617, within the 16S rRNA, harbored the most prevalent RDDs (>30% A-to-U and ∼15% A-to-G of the reads in all tested samples). The 2617 RDDs appeared already at the precursor polycistrone mitochondrial transcript. By using traditional Sanger sequencing, we identified the A-to-U RDD in six different cell lines and representative primates (Gorilla gorilla, Pongo pigmaeus, and Macaca mulatta), suggesting conservation of the mechanism generating such RDD. Phylogenetic analysis of more than 1700 vertebrate mtDNA sequences supported a thymine as the primate ancestral allele at position 2617, suggesting that the 2617 RDD recapitulates the ancestral 16S rRNA. Modeling U or G (the RDDs) at position 2617 stabilized the large ribosomal subunit structure in contrast to destabilization by an A (the pre-RDDs). Hence, these mitochondrial RDDs are likely functional. PMID:23913925

  20. A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences.

    PubMed

    Groussin, M; Boussau, B; Gouy, M

    2013-07-01

    Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.

  1. Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome.

    PubMed

    Rahman, Imran A; Zamora, Samuel; Falkingham, Peter L; Phillips, Jeremy C

    2015-11-01

    Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding and active pharyngeal filter feeding. The results demonstrate that an orientation with the mouth facing downstream of the current was optimal for drag and lift reduction. Moreover, they show that there was almost no flow to the mouth and associated marginal groove under simulations of passive feeding, whereas considerable flow towards the animal was observed for active feeding, which would have enhanced the transport of suspended particles to the mouth. This strongly suggests that cinctans were active pharyngeal filter feeders, like modern enteropneust hemichordates and urochordates, indicating that the ancestral deuterostome employed a similar feeding strategy.

  2. Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome.

    PubMed

    Rahman, Imran A; Zamora, Samuel; Falkingham, Peter L; Phillips, Jeremy C

    2015-11-01

    Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding and active pharyngeal filter feeding. The results demonstrate that an orientation with the mouth facing downstream of the current was optimal for drag and lift reduction. Moreover, they show that there was almost no flow to the mouth and associated marginal groove under simulations of passive feeding, whereas considerable flow towards the animal was observed for active feeding, which would have enhanced the transport of suspended particles to the mouth. This strongly suggests that cinctans were active pharyngeal filter feeders, like modern enteropneust hemichordates and urochordates, indicating that the ancestral deuterostome employed a similar feeding strategy. PMID:26511049

  3. Evolution of steroid receptors from an estrogen-sensitive ancestral receptor.

    PubMed

    Eick, Geeta N; Thornton, Joseph W

    2011-03-01

    Members of the steroid hormone receptor (SR) family activate transcription from different DNA response elements and are regulated by distinct hormonal ligands. Understanding the evolutionary process by which this diversity arose can provide insight into how and why SRs function as they do. Here we review the characteristics of the ancient receptor protein from which the SR family descends by a process of gene duplication and divergence. Several orthogonal lines of evidence - bioinformatic, phylogenetic, and experimental - indicate that this ancient SR had the capacity to activate transcription from DNA estrogen response elements in response to estrogens. Duplication and divergence of the ancestral SR gene subsequently generated new receptors that were activated by other steroid hormones, including progestagens, androgens, and corticosteroids. The androgen and progesterone receptors recruited as their ligands steroids that were previously present as biochemical intermediates in the synthesis of estrogens. This process is an example of molecular exploitation--the evolution of new molecular interactions when an older molecule, which previously had a different function, is co-opted as a binding partner by a newly evolved molecule. The primordial interaction between the ancestral steroid receptor and estrogens may itself have evolved due to an early molecular exploitation event.

  4. Sexually dimorphic effects of ancestral exposure to vinclozolin on stress reactivity in rats.

    PubMed

    Gillette, Ross; Miller-Crews, Isaac; Nilsson, Eric E; Skinner, Michael K; Gore, Andrea C; Crews, David

    2014-10-01

    How an individual responds to the environment depends upon both personal life history as well as inherited genetic and epigenetic factors from ancestors. Using a 2-hit, 3 generations apart model, we tested how F3 descendants of rats given in utero exposure to the environmental endocrine-disrupting chemical (EDC) vinclozolin reacted to stress during adolescence in their own lives, focusing on sexually dimorphic phenotypic outcomes. In adulthood, male and female F3 vinclozolin- or vehicle-lineage rats, stressed or nonstressed, were behaviorally characterized on a battery of tests and then euthanized. Serum was used for hormone assays, and brains were used for quantitative PCR and transcriptome analyses. Results showed that the effects of ancestral exposure to vinclozolin converged with stress experienced during adolescence in a sexually dimorphic manner. Debilitating effects were seen at all levels of the phenotype, including physiology, behavior, brain metabolism, gene expression, and genome-wide transcriptome modifications in specific brain nuclei. Additionally, females were significantly more vulnerable than males to transgenerational effects of vinclozolin on anxiety but not sociality tests. This fundamental transformation occurs in a manner not predicted by the ancestral exposure or the proximate effects of stress during adolescence, an interaction we refer to as synchronicity. PMID:25051444

  5. On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins.

    PubMed

    Trudeau, Devin L; Kaltenbach, Miriam; Tawfik, Dan S

    2016-10-01

    Ancestral reconstruction provides instrumental insights regarding the biochemical and biophysical characteristics of past proteins. A striking observation relates to the remarkably high thermostability of reconstructed ancestors. The latter has been linked to high environmental temperatures in the Precambrian era, the era relating to most reconstructed proteins. We found that inferred ancestors of the serum paraoxonase (PON) enzyme family, including the mammalian ancestor, exhibit dramatically increased thermostabilities compared with the extant, human enzyme (up to 30 °C higher melting temperature). However, the environmental temperature at the time of emergence of mammals is presumed to be similar to the present one. Additionally, the mammalian PON ancestor has superior folding properties (kinetic stability)-unlike the extant mammalian PONs, it expresses in E. coli in a soluble and functional form, and at a high yield. We discuss two potential origins of this unexpectedly high stability. First, ancestral stability may be overestimated by a "consensus effect," whereby replacing amino acids that are rare in contemporary sequences with the amino acid most common in the family increases protein stability. Comparison to other reconstructed ancestors indicates that the consensus effect may bias some but not all reconstructions. Second, we note that high stability may relate to factors other than high environmental temperature such as oxidative stress or high radiation levels. Foremost, intrinsic factors such as high rates of genetic mutations and/or of transcriptional and translational errors, and less efficient protein quality control systems, may underlie the high kinetic and thermodynamic stability of past proteins.

  6. On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins.

    PubMed

    Trudeau, Devin L; Kaltenbach, Miriam; Tawfik, Dan S

    2016-10-01

    Ancestral reconstruction provides instrumental insights regarding the biochemical and biophysical characteristics of past proteins. A striking observation relates to the remarkably high thermostability of reconstructed ancestors. The latter has been linked to high environmental temperatures in the Precambrian era, the era relating to most reconstructed proteins. We found that inferred ancestors of the serum paraoxonase (PON) enzyme family, including the mammalian ancestor, exhibit dramatically increased thermostabilities compared with the extant, human enzyme (up to 30 °C higher melting temperature). However, the environmental temperature at the time of emergence of mammals is presumed to be similar to the present one. Additionally, the mammalian PON ancestor has superior folding properties (kinetic stability)-unlike the extant mammalian PONs, it expresses in E. coli in a soluble and functional form, and at a high yield. We discuss two potential origins of this unexpectedly high stability. First, ancestral stability may be overestimated by a "consensus effect," whereby replacing amino acids that are rare in contemporary sequences with the amino acid most common in the family increases protein stability. Comparison to other reconstructed ancestors indicates that the consensus effect may bias some but not all reconstructions. Second, we note that high stability may relate to factors other than high environmental temperature such as oxidative stress or high radiation levels. Foremost, intrinsic factors such as high rates of genetic mutations and/or of transcriptional and translational errors, and less efficient protein quality control systems, may underlie the high kinetic and thermodynamic stability of past proteins. PMID:27413048

  7. Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences

    PubMed Central

    Ettwiller, Laurence; Budd, Aidan; Spitz, François; Wittbrodt, Joachim

    2008-01-01

    Background Changes in gene regulation are suspected to comprise one of the driving forces for evolution. To address the extent of cis-regulatory changes and how they impact on gene regulatory networks across eukaryotes, we systematically analyzed the evolutionary dynamics of target gene batteries controlled by 16 different transcription factors. Results We found that gene batteries show variable conservation within vertebrates, with slow and fast evolving modules. Hence, while a key gene battery associated with the cell cycle is conserved throughout metazoans, the POU5F1 (Oct4) and SOX2 batteries in embryonic stem cells show strong conservation within mammals, with the striking exception of rodents. Within the genes composing a given gene battery, we could identify a conserved core that likely reflects the ancestral function of the corresponding transcription factor. Interestingly, we show that the association between a transcription factor and its target genes is conserved even when we exclude conserved sequence similarities of their promoter regions from our analysis. This supports the idea that turnover, either of the transcription factor binding site or its direct neighboring sequence, is a pervasive feature of proximal regulatory sequences. Conclusions Our study reveals the dynamics of evolutionary changes within metazoan gene networks, including both the composition of gene batteries and the architecture of target gene promoters. This variation provides the playground required for evolutionary innovation around conserved ancestral core functions. PMID:19087242

  8. A FORTRAN subroutine to compute inbreeding and kinship coefficients according to the number of ancestral generations.

    PubMed

    Vu Tien Khang, J

    1989-07-01

    This paper presents a FORTRAN IV subroutine to calculate inbreeding and kinship coefficients from pedigree information in a diploid population without self-fertilization. The user can specify the number of ancestral generations to be taken into account. It is thus possible to determine contributions of succeeding ancestral generations to the inbreeding and kinship coefficients under consideration. The subroutine is based on a recursive procedure that generates systematically all paths connecting two individuals. NP and NM, whose kinship coefficient is to be calculated (or between the father NP and the mother NM of the individual whose inbreeding coefficient is to be calculated). These paths obey the following conditions: (i) a given path does not contain the same parent-offspring link more than once; (ii) the vertex of a path is an ancestor common to individuals NP and NM, with a rank lower or equal to the parameter specified in input. Constraints regarding the size of the corpus of genealogical data and the storage method are discussed, as well as the interest of this subroutine compared to the existing ones. An example of application is given.

  9. Sexually Dimorphic Effects of Ancestral Exposure to Vinclozolin on Stress Reactivity in Rats

    PubMed Central

    Gillette, Ross; Miller-Crews, Isaac; Nilsson, Eric E.; Skinner, Michael K.; Gore, Andrea C.

    2014-01-01

    How an individual responds to the environment depends upon both personal life history as well as inherited genetic and epigenetic factors from ancestors. Using a 2-hit, 3 generations apart model, we tested how F3 descendants of rats given in utero exposure to the environmental endocrine-disrupting chemical (EDC) vinclozolin reacted to stress during adolescence in their own lives, focusing on sexually dimorphic phenotypic outcomes. In adulthood, male and female F3 vinclozolin- or vehicle-lineage rats, stressed or nonstressed, were behaviorally characterized on a battery of tests and then euthanized. Serum was used for hormone assays, and brains were used for quantitative PCR and transcriptome analyses. Results showed that the effects of ancestral exposure to vinclozolin converged with stress experienced during adolescence in a sexually dimorphic manner. Debilitating effects were seen at all levels of the phenotype, including physiology, behavior, brain metabolism, gene expression, and genome-wide transcriptome modifications in specific brain nuclei. Additionally, females were significantly more vulnerable than males to transgenerational effects of vinclozolin on anxiety but not sociality tests. This fundamental transformation occurs in a manner not predicted by the ancestral exposure or the proximate effects of stress during adolescence, an interaction we refer to as synchronicity. PMID:25051444

  10. Internal structural variations in a debris-avalanche deposit from ancestral Mount Shasta, California, USA

    NASA Astrophysics Data System (ADS)

    Ui, Tadahide; Glicken, Harry

    1986-08-01

    Various parameters of the internal structure of a debris-avalanche deposit from ancestral Mount Shasta (size and percentage of block facies in each exposure, number and width of jigsaw cracks, and number of rounded clasts in matrix facies) were measured in order to study flow and emplacement mechanisms. Three types of coherent blocks were identified: blocks of massive or brecciated lava flows or domes, blocks of layered volcaniclastic deposits, and blocks of accidental material, typically from sedimentary units underlying Shasta Valley. The mean maximum dimension of the three largest blocks of layered volcaniclastic material is 220 m, and that of the lava blocks, 110 m. This difference may reflect plastic deformation of blocks of layered volcaniclastic material; blocks of massive or brecciated volcanic rock deformated brittly and may have split into several smaller blocks. The blocks in the deposit are one order of magnitude larger, and the height of collapse 1100 m higher, than the Pungarehu debris-avalanche deposit at Mount Egmont, New Zealand, although the degree of fracturing is about the same.This suggests either that the Shasta source material was less broken, or that the intensity of any accompanying explosion was smaller at ancestral Mount Shasta. The Shasta debris-avalanche deposit covered the floor of a closed basin; the flanks of the basin may have retarded the opening of jigsaw cracks and the formation of stretched and deformed blocks such as those of the Pungarehu debris-avalanche deposit.

  11. Internal structural variations in a debris-avalanche deposit from ancestral Mount Shasta, California, USA

    USGS Publications Warehouse

    Ui, T.; Glicken, H.

    1986-01-01

    Various parameters of the internal structure of a debris-avalanche deposit from ancestral Mount Shasta (size and percentage of block facies in each exposure, number and width of jigsaw cracks, and number of rounded clasts in matrix facies) were measured in order to study flow and emplacement mechanisms. Three types of coherent blocks were identified: blocks of massive or brecciated lava flows or domes, blocks of layered volcaniclastic deposits, and blocks of accidental material, typically from sedimentary units underlying Shasta Valley. The mean maximum dimension of the three largest blocks of layered volcaniclastic material is 220 m, and that of the lava blocks, 110 m. This difference may reflect plastic deformation of blocks of layered volcaniclastic material; blocks of massive or brecciated volcanic rock deformated brittly and may have split into several smaller blocks. The blocks in the deposit are one order of magnitude larger, and the height of collapse 1100 m higher, than the Pungarehu debris-avalanche deposit at Mount Egmont, New Zealand, although the degree of fracturing is about the same.This suggests either that the Shasta source material was less broken, or that the intensity of any accompanying explosion was smaller at ancestral Mount Shasta. The Shasta debris-avalanche deposit covered the floor of a closed basin; the flanks of the basin may have retarded the opening of jigsaw cracks and the formation of stretched and deformed blocks such as those of the Pungarehu debris-avalanche deposit. ?? 1986 Springer-Verlag.

  12. The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome.

    PubMed

    Nelson, Matthew N; Parkin, Isobel A P; Lydiate, Derek J

    2011-01-01

    The organisation of the Sinapis alba genome, comprising 12 linkage groups (n = 12), was compared with the Brassicaceae ancestral karyotype (AK) genomic blocks previously described in other crucifer species. Most of the S. alba genome falls into conserved triplicated genomic blocks that closely match the AK-defined genomic blocks found in other crucifer species including the A, B, and C genomes of closely related Brassica species. In one instance, an S. alba linkage group (S05) was completely collinear with one AK chromosome (AK1), the first time this has been observed in a member of the Brassiceae tribe. However, as observed for other members of the Brassiceae tribe, ancestral genomic blocks were fragmented in the S. alba genome, supporting previously reported comparative chromosome painting describing rearrangements of the AK karyotype prior to the divergence of the Brassiceae from other crucifers. The presented data also refute previous phylogenetic reports that suggest S. alba was more closely related to Brassica nigra (B genome) than to B. rapa (A genome) and B. oleracea (C genome). A comparison of the S. alba and Arabidopsis thaliana genomes revealed many regions of conserved gene order, which will facilitate access to the rich genomic resources available in the model species A. thaliana for genetic research in the less well-resourced crop species S. alba.

  13. Functional Analyses of the Plant Photosystem I–Light-Harvesting Complex II Supercomplex Reveal That Light-Harvesting Complex II Loosely Bound to Photosystem II Is a Very Efficient Antenna for Photosystem I in State II[W

    PubMed Central

    Galka, Pierre; Santabarbara, Stefano; Khuong, Thi Thu Huong; Degand, Hervé; Morsomme, Pierre; Jennings, Robert C.; Boekema, Egbert J.; Caffarri, Stefano

    2012-01-01

    State transitions are an important photosynthetic short-term response that allows energy distribution balancing between photosystems I (PSI) and II (PSII). In plants when PSII is preferentially excited compared with PSI (State II), part of the major light-harvesting complex LHCII migrates to PSI to form a PSI-LHCII supercomplex. So far, little is known about this complex, mainly due to purification problems. Here, a stable PSI-LHCII supercomplex is purified from Arabidopsis thaliana and maize (Zea mays) plants. It is demonstrated that LHCIIs loosely bound to PSII in State I are the trimers mainly involved in state transitions and become strongly bound to PSI in State II. Specific Lhcb1-3 isoforms are differently represented in the mobile LHCII compared with S and M trimers. Fluorescence analyses indicate that excitation energy migration from mobile LHCII to PSI is rapid and efficient, and the quantum yield of photochemical conversion of PSI-LHCII is substantially unaffected with respect to PSI, despite a sizable increase of the antenna size. An updated PSI-LHCII structural model suggests that the low-energy chlorophylls 611 and 612 in LHCII interact with the chlorophyll 11145 at the interface of PSI. In contrast with the common opinion, we suggest that the mobile pool of LHCII may be considered an intimate part of the PSI antenna system that is displaced to PSII in State I. PMID:22822202

  14. Pathway for Mn-cluster oxidation by tyrosine-Z in the S2 state of photosystem II

    PubMed Central

    Narzi, Daniele; Bovi, Daniele; Guidoni, Leonardo

    2014-01-01

    Water oxidation in photosynthetic organisms occurs through the five intermediate steps S0–S4 of the Kok cycle in the oxygen evolving complex of photosystem II (PSII). Along the catalytic cycle, four electrons are subsequently removed from the Mn4CaO5 core by the nearby tyrosine Tyr-Z, which is in turn oxidized by the chlorophyll special pair P680, the photo-induced primary donor in PSII. Recently, two Mn4CaO5 conformations, consistent with the S2 state (namely, S2A and S2B models) were suggested to exist, perhaps playing a different role within the S2-to-S3 transition. Here we report multiscale ab initio density functional theory plus U simulations revealing that upon such oxidation the relative thermodynamic stability of the two previously proposed geometries is reversed, the S2B state becoming the leading conformation. In this latter state a proton coupled electron transfer is spontaneously observed at ∼100 fs at room temperature dynamics. Upon oxidation, the Mn cluster, which is tightly electronically coupled along dynamics to the Tyr-Z tyrosyl group, releases a proton from the nearby W1 water molecule to the close Asp-61 on the femtosecond timescale, thus undergoing a conformational transition increasing the available space for the subsequent coordination of an additional water molecule. The results can help to rationalize previous spectroscopic experiments and confirm, for the first time to our knowledge, that the water-splitting reaction has to proceed through the S2B conformation, providing the basis for a structural model of the S3 state. PMID:24889635

  15. Cationic screening of charged surface groups (carboxylates) affects electron transfer steps in photosystem-II water oxidation and quinone reduction.

    PubMed

    Karge, Oliver; Bondar, Ana-Nicoleta; Dau, Holger

    2014-10-01

    The functional or regulatory role of long-distance interactions between protein surface and interior represents an insufficiently understood aspect of protein function. Cationic screening of surface charges determines the morphology of thylakoid membrane stacks. We show that it also influences directly the light-driven reactions in the interior of photosystem II (PSII). After laser-flash excitation of PSII membrane particles from spinach, time courses of the delayed recombination fluorescence (10μs-10ms) and the variable chlorophyll-fluorescence yield (100μs-1s) were recorded in the presence of chloride salts. At low salt-concentrations, a stimulating effect was observed for the S-state transition efficiency, the time constant of O2-formation at the Mn4Ca-complex of PSII, and the halftime of re-oxidation of the primary quinone acceptor (Qa) by the secondary quinone acceptor (Qb). The cation valence determined the half-effect concentrations of the stimulating salt effect, which were around 6μM, 200μM and 10mM for trivalent (LaCl3), bivalent (MgCl2, CaCl2), and monovalent cations (NaCl, KCl), respectively. A depressing high-salt effect also depended strongly on the cation valence (onset concentrations around 2mM, 50mM, and 500mM). These salt effects are proposed to originate from electrostatic screening of negatively charged carboxylate sidechains, which are found in the form of carboxylate clusters at the solvent-exposed protein surface. We conclude that the influence of electrostatic screening by solvent cations manifests a functionally relevant long-distance interaction between protein surface and electron-transfer reactions in the protein interior. A relation to regulation and adaptation in response to environmental changes is conceivable.

  16. Protons bound to the Mn cluster in photosystem II oxygen evolving complex detected by proton matrix ENDOR.

    PubMed

    Yamada, Hiroiku; Mino, Hiroyuki; Itoh, Shigeru

    2007-03-01

    Protons in the vicinity of the oxygen-evolving manganese cluster in photosystem II were studied by proton matrix ENDOR. Six pairs of proton ENDOR signals were detected in both the S(0) and S(2) states of the Mn-cluster. Two pairs of signals that show hyperfine constants of 2.3/2.2 and 4.0 MHz, respectively, disappeared after D(2)O incubation in both states. The signals with 2.3/2.2 MHz hyperfine constants in S(0) and S(2) state multiline disappeared after 3 h of D(2)O incubation in the S(0) and S(1) states, respectively. The signal with 4.0 MHz hyperfine constants in S(0) state multiline disappeared after 3 h of D(2)O incubation in the S(0) state, while the similar signal in S(2) state multiline disappeared only after 24 h of D(2)O incubation in the S(1) state. The different proton exchange rates seem to be ascribable to the change in affinities of water molecules to the variation in oxidation state of the Mn cluster during the water oxidation cycle. Based on the point dipole approximation, the distances between the center of electronic spin of the Mn cluster and the exchangeable protons were estimated to be 3.3/3.2 and 2.7 A, respectively. These short distances suggest the protons belong to the water molecules ligated to the manganese cluster. We propose a model for the binding of water to the manganese cluster based on these results.

  17. Photosystem II Activity of Wild Type Synechocystis PCC 6803 and Its Mutants with Different Plastoquinone Pool Redox States.

    PubMed

    Voloshina, O V; Bolychevtseva, Y V; Kuzminov, F I; Gorbunov, M Y; Elanskaya, I V; Fadeev, V V

    2016-08-01

    To assess the role of redox state of photosystem II (PSII) acceptor side electron carriers in PSII photochemical activity, we studied sub-millisecond fluorescence kinetics of the wild type Synechocystis PCC 6803 and its mutants with natural variability in the redox state of the plastoquinone (PQ) pool. In cyanobacteria, dark adaptation tends to reduce PQ pool and induce a shift of the cyanobacterial photosynthetic apparatus to State 2, whereas illumination oxidizes PQ pool, leading to State 1 (Mullineaux, C. W., and Holzwarth, A. R. (1990) FEBS Lett., 260, 245-248). We show here that dark-adapted Ox(-) mutant with naturally reduced PQ is characterized by slower QA(-) reoxidation and O2 evolution rates, as well as lower quantum yield of PSII primary photochemical reactions (Fv/Fm) as compared to the wild type and SDH(-) mutant, in which the PQ pool remains oxidized in the dark. These results indicate a large portion of photochemically inactive PSII reaction centers in the Ox(-) mutant after dark adaptation. While light adaptation increases Fv/Fm in all tested strains, indicating PSII activation, by far the greatest increase in Fv/Fm and O2 evolution rates is observed in the Ox(-) mutant. Continuous illumination of Ox(-) mutant cells with low-intensity blue light, that accelerates QA(-) reoxidation, also increases Fv/Fm and PSII functional absorption cross-section (590 nm); this effect is almost absent in the wild type and SDH(-) mutant. We believe that these changes are caused by the reorganization of the photosynthetic apparatus during transition from State 2 to State 1. We propose that two processes affect the PSII activity during changes of light conditions: 1) reversible inactivation of PSII, which is associated with the reduction of electron carriers on the PSII acceptor side in the dark, and 2) PSII activation under low light related to the increase in functional absorption cross-section at 590 nm.

  18. Photoinhibitory damage is modulated by the rate of photosynthesis and by the photosystem II light-harvesting chlorophyll antenna size.

    PubMed

    Baroli, I; Melis, A

    1998-06-01

    We investigated the effect of photosynthetic electron transport and of the photosystem II (PSII) chlorophyll (Chl) antenna size on the rate of PSII photoinhibitory damage. To modulate the rate of photosynthesis and the light-harvesting capacity in the unicellular chlorophyte Dunaliella salina Teod., we varied the amount of inorganic carbon in the culture medium. Cells were grown under high irradiance either with a limiting supply of inorganic carbon, provided by an initial concentration of 25 mM NaHCO3, or with supplemental CO2 bubbled in the form of 3% CO2 in air. The NaHCO3-grown cells displayed slow rates of photosynthesis and had a small PSII light-harvesting Chl antenna size (60 Chl molecules). The half-time of PSII photodamage was 40 min. When switched to supplemental CO2 conditions, the rate of photodamage was retarded to a t1/2 = 70 min. Conversely, CO2-supplemented cells displayed faster rates of photosynthesis and a larger PSII light-harvesting Chl antenna size (500 Chl molecules). They also showed a rate of photodamage with t1/2 = 40 min. When depleted of CO2, the rate of photodamage was accelerated (t1/2 = 20 min). These results indicate that the in-vivo susceptibility to photodamage is modulated by the rate of forward electron transport through PSII. Moreover, a large Chl antenna size enhances the rate of light absorption and photodamage and, therefore, counters the mitigating effect of forward electron transport. We propose that under steady-state photosynthesis, the rate of light absorption (determined by incident light intensity and PS Chl antenna size) and the rate of forward electron transport (determined by CO2 availability) modulate the oxidation/reduction state of the primary PSII acceptor QA, which in turn defines the low/high probability for photodamage in the PSII reaction center.

  19. Defining the far-red limit of photosystem I: the primary charge separation is functional to 840 nm.

    PubMed

    Mokvist, Fredrik; Mamedov, Fikret; Styring, Stenbjörn

    2014-08-29

    The far-red limit of photosystem I (PS I) photochemistry was studied by EPR spectroscopy using laser flashes between 730 and 850 nm. In manganese-depleted spinach thylakoid membranes, the primary donor in PS I, P700, was oxidized simultaneously with tyrosine Z, the secondary donor in PS II. It was found that at 295 K PS I photochemistry, observed as P700 (+) formation, was functional up to 840 nm. This is 30 nm further to the red region than was reported for PS II photochemistry (Thapper, A., Mamedov, F., Mokvist, F., Hammarström, L., and Styring, S. (2009) Plant Cell 21, 2391-2401). The same far-red limit for the P700 (+) formation was observed in a PS I reaction center core preparation from Nostoc punctiforme. The reduction of the acceptor side of PS I, observed as reduction of the iron-sulfur centers FA and FB by low temperature EPR measurements, was also functional at 15 K with light up to >830 nm. Taken together, these results, obtained from both plants and cyanobacteria, most likely rule out involvement of the red-absorbing antenna chlorophylls in this reaction. Instead we propose the existence of weak charge transfer bands absorbing in the far-red region in the ensemble of excitonically coupled chlorophyll a molecules around P700 similar to what has been found in the reaction center of PS II. These charge transfer bands could be responsible for the far-red light absorption leading to PS I photochemistry at wavelengths up to 840 nm.

  20. Photosystem II Activity of Wild Type Synechocystis PCC 6803 and Its Mutants with Different Plastoquinone Pool Redox States.

    PubMed

    Voloshina, O V; Bolychevtseva, Y V; Kuzminov, F I; Gorbunov, M Y; Elanskaya, I V; Fadeev, V V

    2016-08-01

    To assess the role of redox state of photosystem II (PSII) acceptor side electron carriers in PSII photochemical activity, we studied sub-millisecond fluorescence kinetics of the wild type Synechocystis PCC 6803 and its mutants with natural variability in the redox state of the plastoquinone (PQ) pool. In cyanobacteria, dark adaptation tends to reduce PQ pool and induce a shift of the cyanobacterial photosynthetic apparatus to State 2, whereas illumination oxidizes PQ pool, leading to State 1 (Mullineaux, C. W., and Holzwarth, A. R. (1990) FEBS Lett., 260, 245-248). We show here that dark-adapted Ox(-) mutant with naturally reduced PQ is characterized by slower QA(-) reoxidation and O2 evolution rates, as well as lower quantum yield of PSII primary photochemical reactions (Fv/Fm) as compared to the wild type and SDH(-) mutant, in which the PQ pool remains oxidized in the dark. These results indicate a large portion of photochemically inactive PSII reaction centers in the Ox(-) mutant after dark adaptation. While light adaptation increases Fv/Fm in all tested strains, indicating PSII activation, by far the greatest increase in Fv/Fm and O2 evolution rates is observed in the Ox(-) mutant. Continuous illumination of Ox(-) mutant cells with low-intensity blue light, that accelerates QA(-) reoxidation, also increases Fv/Fm and PSII functional absorption cross-section (590 nm); this effect is almost absent in the wild type and SDH(-) mutant. We believe that these changes are caused by the reorganization of the photosynthetic apparatus during transition from State 2 to State 1. We propose that two processes affect the PSII activity during changes of light conditions: 1) reversible inactivation of PSII, which is associated with the reduction of electron carriers on the PSII acceptor side in the dark, and 2) PSII activation under low light related to the increase in functional absorption cross-section at 590 nm. PMID:27677553

  1. Entangled quantum electronic wavefunctions of the Mn4CaO5 cluster in photosystem II

    NASA Astrophysics Data System (ADS)

    Kurashige, Yuki; Chan, Garnet Kin-Lic; Yanai, Takeshi

    2013-08-01

    It is a long-standing goal to understand the reaction mechanisms of catalytic metalloenzymes at an entangled many-electron level, but this is hampered by the exponential complexity of quantum mechanics. Here, by exploiting the special structure of physical quantum states and using the density matrix renormalization group, we compute near-exact many-electron wavefunctions of the Mn4CaO5 cluster of photosystem II, with more than 1 × 1018 quantum degrees of freedom. This is the first treatment of photosystem II beyond the single-electron picture of density functional theory. Our calculations support recent modifications to the structure determined by X-ray crystallography. We further identify multiple low-lying energy surfaces associated with the structural distortion seen using X-ray crystallography, highlighting multistate reactivity in the chemistry of the cluster. Direct determination of Mn spin-projections from our wavefunctions suggests that current candidates that have been recently distinguished using parameterized spin models should be reassessed. Through entanglement maps, we reveal rich information contained in the wavefunctions on bonding changes in the cycle.

  2. Advanced unidirectional photocurrent generation via cytochrome c as reaction partner for directed assembly of photosystem I.

    PubMed

    Stieger, Kai R; Feifel, Sven C; Lokstein, Heiko; Lisdat, Fred

    2014-08-01

    Conversion of light into an electrical current based on biohybrid systems mimicking natural photosynthesis is becoming increasingly popular. Photosystem I (PSI) is particularly useful in such photo-bioelectrochemical devices. Herein, we report on a novel biomimetic approach for an effective assembly of photosystem I with the electron transfer carrier cytochrome c (cyt c), deposited on a thiol-modified gold-surface. Atomic force microscopy and surface plasmon resonance measurements have been used for characterization of the assembly process. Photoelectrochemical experiments demonstrate a cyt c mediated generation of an enhanced unidirectional cathodic photocurrent. Here, cyt c can act as a template for the assembly of an oriented and dense layer of PSI and as wiring agent to direct the electrons from the electrode towards the photosynthetic reaction center of PSI. Furthermore, three-dimensional protein architectures have been formed via the layer-by-layer deposition technique resulting in a successive increase in photocurrent densities. An intermittent cyt c layer is essential for an efficient connection of PSI layers with the electrode and for an improvement of photocurrent densities. PMID:24957935

  3. Co-assembly of photosystem II/reduced graphene oxide multilayered biohybrid films for enhanced photocurrent

    NASA Astrophysics Data System (ADS)

    Cai, Peng; Feng, Xiyun; Fei, Jinbo; Li, Guangle; Li, Jiao; Huang, Jianguo; Li, Junbai

    2015-06-01

    A new type of biohybrid photo-electrochemical cell was fabricated by layer-by-layer assembly of photosystem II and reduced graphene oxide. We demonstrate that the photocurrent in the direct electron transfer is enhanced about two fold with improved stability. The assembly strategy without any cross-linker or additional electron mediators makes the cell fabrication and operation much simpler as compared to previous approaches. This work may open new routes for the construction of solar energy conversion systems based on photoactive proteins and graphene materials.A new type of biohybrid photo-electrochemical cell was fabricated by layer-by-layer assembly of photosystem II and reduced graphene oxide. We demonstrate that the photocurrent in the direct electron transfer is enhanced about two fold with improved stability. The assembly strategy without any cross-linker or additional electron mediators makes the cell fabrication and operation much simpler as compared to previous approaches. This work may open new routes for the construction of solar energy conversion systems based on photoactive proteins and graphene materials. Electronic supplementary information (ESI) available: Detailed experimental procedures, XRD patterns, UV-vis spectra, XPS spectra, SDS-PAGE patterns, AFM images and SEM images. See DOI: 10.1039/c5nr02322j

  4. Isolated photosystem I reaction centers on a functionalized gated high electron mobility transistor.

    PubMed

    Eliza, Sazia A; Lee, Ida; Tulip, Fahmida S; Mostafa, Salwa; Greenbaum, Elias; Ericson, M Nance; Islam, Syed K

    2011-09-01

    In oxygenic plants, photons are captured with high quantum efficiency by two specialized reaction centers (RC) called Photosystem I (PS I) and Photosystem II (PS II). The captured photon triggers rapid charge separation and the photon energy is converted into an electrostatic potential across the nanometer-scale (~6 nm) reaction centers. The exogenous photovoltages from a single PS I RC have been previously measured using the technique of Kelvin force probe microscopy (KFM). However, biomolecular photovoltaic applications require two-terminal devices. This paper presents for the first time, a micro-device for detection and characterization of isolated PS I RCs. The device is based on an AlGaN/GaN high electron mobility transistor (HEMT) structure. AlGaN/GaN HEMTs show high current throughputs and greater sensitivity to surface charges compared to other field-effect devices. PS I complexes immobilized on the floating gate of AlGaN/GaN HEMTs resulted in significant changes in the device characteristics under illumination. An analytical model has been developed to estimate the RCs of a major orientation on the functionalized gate surface of the HEMTs. PMID:21926029

  5. Organization of photosystem I polypeptides examined by chemical cross-linking

    NASA Technical Reports Server (NTRS)

    Armbrust, T. S.; Chitnis, P. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

    1996-01-01

    Photosystem I from the cyanobacterium Synechocystis sp. PCC 6803 was examined using the chemical cross-linkers glutaraldehyde and N-ethyl-1-3-[3-(dimethylamino)propyl]carbodiimide to investigate the organization of the polypeptide subunits. Thylakoid membranes and photosystem I, which was isolated by Triton X-100 fractionation, were treated with cross-linking reagents and were resolved using a Tricine/urea low-molecular-weight resolution gel system. Subunit-specific antibodies and western blotting analysis were used to identify the components of cross-linked species. These analyses identified glutaraldehyde-dependent cross-linking products composed of small amounts of PsaD and PsaC, PsaC and PsaE, and PsaE and PsaF. The novel cross-link between PsaE and PsaF was also observed following treatment with N-ethyl-1-3-[3-(dimethylamino)propyl]carbodiimide. These cross-linking results suggest a structural interaction between PsaE and PsaF and predict a transmembrane topology for PsaF.

  6. Isolated photosystem I reaction centers on a functionalized gated high electron mobility transistor.

    PubMed

    Eliza, Sazia A; Lee, Ida; Tulip, Fahmida S; Mostafa, Salwa; Greenbaum, Elias; Ericson, M Nance; Islam, Syed K

    2011-09-01

    In oxygenic plants, photons are captured with high quantum efficiency by two specialized reaction centers (RC) called Photosystem I (PS I) and Photosystem II (PS II). The captured photon triggers rapid charge separation and the photon energy is converted into an electrostatic potential across the nanometer-scale (~6 nm) reaction centers. The exogenous photovoltages from a single PS I RC have been previously measured using the technique of Kelvin force probe microscopy (KFM). However, biomolecular photovoltaic applications require two-terminal devices. This paper presents for the first time, a micro-device for detection and characterization of isolated PS I RCs. The device is based on an AlGaN/GaN high electron mobility transistor (HEMT) structure. AlGaN/GaN HEMTs show high current throughputs and greater sensitivity to surface charges compared to other field-effect devices. PS I complexes immobilized on the floating gate of AlGaN/GaN HEMTs resulted in significant changes in the device characteristics under illumination. An analytical model has been developed to estimate the RCs of a major orientation on the functionalized gate surface of the HEMTs.

  7. Effect of light state transitions on the apparent absorption cross section of Photosystem II in Chlorella

    SciTech Connect

    Falkowski, P.G.; Fujita, Yoshihiko

    1986-01-01

    The distribution of excitation energy between photosystems may profoundly affect the quantum yield of photosynthetic oxygen evolution. Excitation energy absorbed by pigment molecules is transferred to reaction centers, where it may potentially drive a photochemical event. To balance the photochemical events in PSII with those in PSI, excitation energy may be transferred between PSII and PSI. This type of energy transfer has been inferred primarily in the steady state quantum yield of oxygen evolution and/or fluorescence with changes in excitation wavelength. These so called ''state transitions'' have been attributed to changes in either the absorption cross section of PSII or ''spillover'' of excitation energy between the two photosystems. We report here on measurements of relative absorption cross sections of PSII under state I and state II light conditions. We simultaneously followed the yields of O/sub 2/ and the change in fluorescence yields, ..delta.. phi, as a function of flash energy using single turnover xenon flashes. Our data suggest that the effective absorption cross section of PSII does not change within +- 10% under physiological conditions in unpoisoned Chlorella pyrenoidosa. 13 refs., 3 figs.

  8. Detection of herbicide subclasses by an optical multibiosensor based on an array of photosystem II mutants.

    PubMed

    Giardi, Maria Teresa; Guzzella, Licia; Euzet, Pierre; Rouillon, Regis; Esposito, Dania

    2005-07-15

    Massive use of herbicides in agriculture over the last few decades has become a serious environmental problem. The residual concentration of these compounds frequently exceeds the maximum admissible concentration in drinking water for human consumption and is a real environmental risk for the aquatic ecosystem. Herbicides inhibiting photosynthesis via targeting photosystem II function still represent the basic means of weed control. A multibiosensor was constructed for detecting herbicides using as biosensing elements photosynthetic preparations coupled to an optical fluorescence transduction system (Giardi et al. EU patent EP1134585, 01830148.1-2204); this paper is about its application in the detection of herbicide subclasses in river water. Photosynthetic material was immobilized on a silicio septum inside a series of flow cells, close to diodes so as to activate photosystem II (PSII) fluorescence. The principle of the detection was based on the factthat herbicides selectively modify PSII fluorescence activity. The multibiosensor has the original feature of being able to distinguish the subclasses of the photosynthetic herbicides by using specific immobilized biomediators isolated from mutated organisms. This setup resulted in a reusable, portable multibiosensor for the detection of herbicide subclasses with a half-life of 54 h for spinach thylakoids and limit of detection of 3 x 10(-9) M for herbicides present in river water.

  9. Cyanobacterial Light-Harvesting Phycobilisomes Uncouple From Photosystem I During Dark-To-Light Transitions

    PubMed Central

    Chukhutsina, Volha; Bersanini, Luca; Aro, Eva-Mari; van Amerongen, Herbert

    2015-01-01

    Photosynthetic organisms cope with changes in light quality by balancing the excitation energy flow between photosystems I (PSI) and II (PSII) through a process called state transitions. Energy redistribution has been suggested to be achieved by movement of the light-harvesting phycobilisome between PSI and PSII, or by nanometre scale rearrangements of the recently discovered PBS-PSII-PSI megacomplexes. The alternative ‘spillover’ model, on the other hand, states that energy redistribution is achieved by mutual association/dissociation of PSI and PSII. State transitions have always been studied by changing the redox state of the electron carriers using electron transfer inhibitors, or by applying illumination conditions with different colours. However, the molecular events during natural dark-to-light transitions in cyanobacteria have largely been overlooked and still remain elusive. Here we investigated changes in excitation energy transfer from phycobilisomes to the photosystems upon dark-light transitions, using picosecond fluorescence spectroscopy. It appears that megacomplexes are not involved in these changes, and neither does spillover play a role. Instead, the phycobilisomes partly energetically uncouple from PSI in the light but hardly couple to PSII. PMID:26388233

  10. A Novel Redoxin in the Thylakoid Membrane Regulates the Titer of Photosystem I.

    PubMed

    Zhu, Yuehui; Liberton, Michelle; Pakrasi, Himadri B

    2016-09-01

    In photosynthetic organisms like cyanobacteria and plants, the main engines of oxygenic photosynthesis are the pigment-protein complexes photosystem I (PSI) and photosystem II (PSII) located in the thylakoid membrane. In the cyanobacterium Synechocystis sp. PCC 6803, the slr1796 gene encodes a single cysteine thioredoxin-like protein, orthologs of which are found in multiple cyanobacterial strains as well as chloroplasts of higher plants. Targeted inactivation of slr1796 in Synechocystis 6803 resulted in compromised photoautotrophic growth. The mutant displayed decreased chlorophyll a content. These changes correlated with a decrease in the PSI titer of the mutant cells, whereas the PSII content was unaffected. In the mutant, the transcript levels of genes for PSI structural and accessory proteins remained unaffected, whereas the levels of PSI structural proteins were severely diminished, indicating that Slr1796 acts at a posttranscriptional level. Biochemical analysis indicated that Slr1796 is an integral thylakoid membrane protein. We conclude that Slr1796 is a novel regulatory factor that modulates PSI titer.

  11. A Novel Redoxin in the Thylakoid Membrane Regulates the Titer of Photosystem I.

    PubMed

    Zhu, Yuehui; Liberton, Michelle; Pakrasi, Himadri B

    2016-09-01

    In photosynthetic organisms like cyanobacteria and plants, the main engines of oxygenic photosynthesis are the pigment-protein complexes photosystem I (PSI) and photosystem II (PSII) located in the thylakoid membrane. In the cyanobacterium Synechocystis sp. PCC 6803, the slr1796 gene encodes a single cysteine thioredoxin-like protein, orthologs of which are found in multiple cyanobacterial strains as well as chloroplasts of higher plants. Targeted inactivation of slr1796 in Synechocystis 6803 resulted in compromised photoautotrophic growth. The mutant displayed decreased chlorophyll a content. These changes correlated with a decrease in the PSI titer of the mutant cells, whereas the PSII content was unaffected. In the mutant, the transcript levels of genes for PSI structural and accessory proteins remained unaffected, whereas the levels of PSI structural proteins were severely diminished, indicating that Slr1796 acts at a posttranscriptional level. Biochemical analysis indicated that Slr1796 is an integral thylakoid membrane protein. We conclude that Slr1796 is a novel regulatory factor that modulates PSI titer. PMID:27382055

  12. Kinetics of the photoreduction of cytochrome b-559 by photosystem II in chloroplasts.

    PubMed

    Whitmarsh, J; Cramer, W A

    1977-05-11

    The kinetics of the photoreduction of cytochrome b-559 and plastoquinone were measured using well-coupled spinach chloroplasts. High potential (i.e, hydroquinone reducible) cytochrome b-559 was oxidized with low intensity far-red light in the presence of N-methyl phenazonium methosulfate or after preillumination with high intensity light. Using long flashes of red light, the half-reduction time of cytochrome b-559 was found to be 100 +/- 10 ms, compared to 6-10 ms for the photoreduction of the plastoquinone pool. Light saturation of the photoreduction of cytochrome b-559 occurred at a light intensity less than one-third of the intensity necessary for the saturation of ferricyanide reduction under identical illumination conditions. The photoreduction of cytochrome b-559 was accelerated in the presence of dibromothymoquinone with a t 1/2 = 25-35 ms. The addition of uncouplers, which caused stimulatory effect on ferricyanide reduction under the same experimental conditions resulted in a decrease in the rate of cytochrome b-559 reduction. The relatively slow photoreduction rate of cytochrome b-559 compared to the plastoquinone pool implies that electrons can be transferred efficiently from Photosystem II to plastoquinone without the involvement of cytochrome b-559 as an intermediate. These results indicate that it is unlikely that high potential cytochrome b-559 functions as an obligatory redox component in the main electron transport chain joining the two photosystems.

  13. Excitation energy transfer between Light-harvesting complex II and Photosystem I in reconstituted membranes.

    PubMed

    Akhtar, Parveen; Lingvay, Mónika; Kiss, Teréz; Deák, Róbert; Bóta, Attila; Ughy, Bettina; Garab, Győző; Lambrev, Petar H

    2016-04-01

    Light-harvesting complex II (LHCII), the major peripheral antenna of Photosystem II in plants, participates in several concerted mechanisms for regulation of the excitation energy and electron fluxes in thylakoid membranes. In part, these include interaction of LHCII with Photosystem I (PSI) enhancing the latter's absorption cross-section - for example in the well-known state 1 - state 2 transitions or as a long-term acclimation to high light. In this work we examined the capability of LHCII to deliver excitations to PSI in reconstituted membranes in vitro. Proteoliposomes with native plant thylakoid membrane lipids and different stoichiometric ratios of LHCII:PSI were reconstituted and studied by steady-state and time-resolved fluorescence spectroscopy. Fluorescence emission from LHCII was strongly decreased in PSI-LHCII membranes due to trapping of excitations by PSI. Kinetic modelling of the time-resolved fluorescence data revealed the existence of separate pools of LHCII distinguished by the time scale of energy transfer. A strongly coupled pool, equivalent to one LHCII trimer per PSI, transferred excitations to PSI with near-unity efficiency on a time scale of less than 10ps but extra LHCIIs also contributed significantly to the effective antenna size of PSI, which could be increased by up to 47% in membranes containing 3 LHCII trimers per PSI. The results demonstrate a remarkable competence of LHCII to increase the absorption cross-section of PSI, given the opportunity that the two types of complexes interact in the membrane.

  14. Enhanced photocurrent from Photosystem I upon in vitro truncation of the antennae chlorophyll.

    PubMed

    Carter, J Ridge; Baker, David R; Witt, T Austin; Bruce, Barry D

    2016-02-01

    Current effects on climate change and dwindling fossil fuel reserves require new materials and methods to convert solar energy into a viable clean energy source. Recent progress in the direct conversion of light into photocurrent has been well documented using Photosystem I. In plants, PSI consists of a core complex and multiple light-harvesting complexes, denoted LHCI and LHCII. Most of the methods for isolating PSI from plants involve a selective, detergent solubilization from thylakoids followed by sucrose gradient density centrifugation. These processes isolate one variant of PSI with a specific ratio of Chl:P700. In this study, we have developed a simple and potentially scalable method for isolating multiple PSI variants using Hydroxyapatite chromatography, which has been well documented in other Photosystem I isolation protocols. By varying the wash conditions, we show that it is possible to change the Chl:P700 ratios. These different PSI complexes were cast into a PSI-Nafion-osmium polymer film that enabled their photoactivity to be measured. Photocurrent increases nearly 400% between highly washed and untreated solutions based on equal chlorophyll content. Importantly, the mild washing conditions remove peripheral Chl and some LHCI without inhibiting the photochemical activity of PSI as suggested by SDS-PAGE analysis. This result could indicate that more P700 could be loaded per surface area for biohybrid devices. Compared with other PSI isolations, this protocol also allows isolation of multiple PSI variants without loss of photochemical activity. PMID:26031418

  15. Entangled quantum electronic wavefunctions of the Mn₄CaO₅ cluster in photosystem II.

    PubMed

    Kurashige, Yuki; Chan, Garnet Kin-Lic; Yanai, Takeshi

    2013-08-01

    It is a long-standing goal to understand the reaction mechanisms of catalytic metalloenzymes at an entangled many-electron level, but this is hampered by the exponential complexity of quantum mechanics. Here, by exploiting the special structure of physical quantum states and using the density matrix renormalization group, we compute near-exact many-electron wavefunctions of the Mn4CaO5 cluster of photosystem II, with more than 1 × 10(18) quantum degrees of freedom. This is the first treatment of photosystem II beyond the single-electron picture of density functional theory. Our calculations support recent modifications to the structure determined by X-ray crystallography. We further identify multiple low-lying energy surfaces associated with the structural distortion seen using X-ray crystallography, highlighting multistate reactivity in the chemistry of the cluster. Direct determination of Mn spin-projections from our wavefunctions suggests that current candidates that have been recently distinguished using parameterized spin models should be reassessed. Through entanglement maps, we reveal rich information contained in the wavefunctions on bonding changes in the cycle. PMID:23881496

  16. Light Driven CO2 Fixation by Using Cyanobacterial Photosystem I and NADPH-Dependent Formate Dehydrogenase

    PubMed Central

    Ihara, Masaki; Kawano, Yusuke; Urano, Miho; Okabe, Ayako

    2013-01-01

    The ultimate goal of this research is to construct a new direct CO2 fixation system using photosystems in living algae. Here, we report light-driven formate production from CO2 by using cyanobacterial photosystem I (PS I). Formate, a chemical hydrogen carrier and important industrial material, can be produced from CO2 by using the reducing power and the catalytic function of formate dehydrogenase (FDH). We created a bacterial FDH mutant that experimentally switched the cofactor specificity from NADH to NADPH, and combined it with an in vitro-reconstituted cyanobacterial light-driven NADPH production system consisting of PS I, ferredoxin (Fd), and ferredoxin-NADP+-reductase (FNR). Consequently, light-dependent formate production under a CO2 atmosphere was successfully achieved. In addition, we introduced the NADPH-dependent FDH mutant into heterocysts of the cyanobacterium Anabaena sp. PCC 7120 and demonstrated an increased formate concentration in the cells. These results provide a new possibility for photo-biological CO2 fixation. PMID:23936519

  17. Light induced changes in Raman scattering of carotenoid molecules in Photosystem I particles

    NASA Astrophysics Data System (ADS)

    Andreeva, Atanaska; Abarova, Silviya; Stoitchkova, Katerina; Velitchkova, Maya

    2007-03-01

    The photosynthetic antenna systems are able to regulate the light energy harvesting under different light conditions by dynamic changes in their protein structure protecting the reaction center complexes. The changes modulate the electronic structure of the main antenna pigments (chlorophylls and carotenoids) and distort the characteristic planar structure of carotenoids, allowing their forbidden out of plane vibrations. Electronic absorption and low-temperature resonance Raman spectroscopy were used to study the changes in composition and spectral properties of the major carotenoids in spinach Photosystem I particles due to high light treatment. The duration of the applied intensity of the white light (1800 μE m -2 s -1) was 30, 60 and 120 minutes. We used Raman scattering in an attempt to recognize the type and conformation of photobleached carotenoid molecules. The resonance Raman spectra were measured at 488 and 514.5 nm, coinciding with the absorption maximum positions of the carotenoids neoxanthin and lutein, correspondingly. The results revealed nearly a full photobleaching of the long wavelength lutein molecules, whereas the bleaching of neoxantin molecules is negligible. The involvement of these changes in the photoprotection and photoinactivation of the Photosystem I particles was discussed.

  18. Nanodomains of cytochrome b6f and photosystem II complexes in spinach grana thylakoid membranes.

    PubMed

    Johnson, Matthew P; Vasilev, Cvetelin; Olsen, John D; Hunter, C Neil

    2014-07-01

    The cytochrome b6f (cytb6f) complex plays a central role in photosynthesis, coupling electron transport between photosystem II (PSII) and photosystem I to the generation of a transmembrane proton gradient used for the biosynthesis of ATP. Photosynthesis relies on rapid shuttling of electrons by plastoquinone (PQ) molecules between PSII and cytb6f complexes in the lipid phase of the thylakoid membrane. Thus, the relative membrane location of these complexes is crucial, yet remains unknown. Here, we exploit the selective binding of the electron transfer protein plastocyanin (Pc) to the lumenal membrane surface of the cytb6f complex using a Pc-functionalized atomic force microscope (AFM) probe to identify the position of cytb6f complexes in grana thylakoid membranes from spinach (Spinacia oleracea). This affinity-mapping AFM method directly correlates membrane surface topography with Pc-cytb6f interactions, allowing us to construct a map of the grana thylakoid membrane that reveals nanodomains of colocalized PSII and cytb6f complexes. We suggest that the close proximity between PSII and cytb6f complexes integrates solar energy conversion and electron transfer by fostering short-range diffusion of PQ in the protein-crowded thylakoid membrane, thereby optimizing photosynthetic efficiency.

  19. Temperature dependence of antenna excitation transport in native photosystem I particles. [Electronic energy transport (EET)

    SciTech Connect

    Lyle, P.A.; Struve, W.S. )

    1991-05-16

    The temperature dependence of polarized photobleaching dynamics was investigated through 680-nm pump-probe experiments in the Chl a antenna of native photosystem 1 particles (Chl/P700 {approximately} 200) from spinach. The anisotropic decay time is lengthened by an order of magnitude (from {approximately}7 to {approximately}62 ps) when the temperature is reduced from 290 to 38 K; most of this increase occurs between 65 and 38 K. The occurrence of this transition temperature in the tens of kelvin reflects the participation of protein phonons in antenna EET. The isotopic decay kinetics are considerably less temperature sensitive, indicating that the anisotropic and isotropic decays stem from different energy-transfer processes with contrasting temperature dependence. The 38 K photobleaching spectrum at 5 ps exhibits considerably more weighting in the lower energy Chl a spectral forms than the room-temperature spectrum, suggesting that rapid spectral equilibration occurs in the photosystem 1 antenna. In light of the phonon frequency and electron-phonon coupling parameters determined in independent PSI-200 spectral hole-burning experiments, the quantitative temperature dependence int he anisotropic decay times is consistent with a theory for phonon-assisted EET in which the pertinent phonons are independent modes localized about the donor and acceptor chromophores.

  20. Cyanobacterial Light-Harvesting Phycobilisomes Uncouple From Photosystem I During Dark-To-Light Transitions.

    PubMed

    Chukhutsina, Volha; Bersanini, Luca; Aro, Eva-Mari; van Amerongen, Herbert

    2015-09-21

    Photosynthetic organisms cope with changes in light quality by balancing the excitation energy flow between photosystems I (PSI) and II (PSII) through a process called state transitions. Energy redistribution has been suggested to be achieved by movement of the light-harvesting phycobilisome between PSI and PSII, or by nanometre scale rearrangements of the recently discovered PBS-PSII-PSI megacomplexes. The alternative 'spillover' model, on the other hand, states that energy redistribution is achieved by mutual association/dissociation of PSI and PSII. State transitions have always been studied by changing the redox state of the electron carriers using electron transfer inhibitors, or by applying illumination conditions with different colours. However, the molecular events during natural dark-to-light transitions in cyanobacteria have largely been overlooked and still remain elusive. Here we investigated changes in excitation energy transfer from phycobilisomes to the photosystems upon dark-light transitions, using picosecond fluorescence spectroscopy. It appears that megacomplexes are not involved in these changes, and neither does spillover play a role. Instead, the phycobilisomes partly energetically uncouple from PSI in the light but hardly couple to PSII.

  1. A protein dynamics study of photosystem II: the effects of protein conformation on reaction center function.

    PubMed

    Vasil'ev, Sergej; Bruce, Doug

    2006-05-01

    Molecular dynamics simulations have been performed to study photosystem II structure and function. Structural information obtained from simulations was combined with ab initio computations of chromophore excited states. In contrast to calculations based on the x-ray structure, the molecular-dynamics-based calculations accurately predicted the experimental absorbance spectrum. In addition, our calculations correctly assigned the energy levels of reaction-center (RC) chromophores, as well as the lowest-energy antenna chlorophyll. The primary and secondary quinone electron acceptors, Q(A) and Q(B), exhibited independent changes in position over the duration of the simulation. Q(B) fluctuated between two binding sites similar to the proximal and distal sites previously observed in light- and dark-adapted RC from purple bacteria. Kinetic models were used to characterize the relative influence of chromophore geometry, site energies, and electron transport rates on RC efficiency. The fluctuating energy levels of antenna chromophores had a larger impact on quantum yield than did their relative positions. Variations in electron transport rates had the most significant effect and were sufficient to explain the experimentally observed multi-component decay of excitation in photosystem II. The implications of our results are discussed in the context of competing evolutionary selection pressures for RC structure and function.

  2. Molecular weight determination of an active photosystem I preparation from a thermophilic cyanobacterium, Synechococcus elongatus.

    PubMed

    Schafheutle, M E; Setliková, E; Timmins, P A; Johner, H; Gutgesell, P; Setlik, I; Welte, W

    1990-02-01

    An active photosystem I (PSI) complex was isolated from the thermophilic cyanobacterium Synechococcus elongatus by a procedure consisting of three steps: First, extraction of photosystem II from the thylakoids by a sulfobetaine detergent yields PSI-enriched membranes. Second, the latter are treated with Triton X-100 to extract PSI particles, which are further purified by preparative isoelectric focusing. Third, anion-exchange chromatography is used to remove contaminating phycobilisome polypeptides. The purified particles show three major bands in sodium dodecyl sulfate gel electrophoresis of apparent molecular mass of 110, 15, and 10 kDa. Charge separation was monitored by the kinetics of flash-induced absorption changes at 820 nm. A chlorophyll/P700 ratio of 60 was found. When the particles are stored at 4 degrees C, charge separation was stable for weeks. The molecular mass of the PSI particles, determined by measurement of zero-angle neutron scattering intensity, was 217,000 Da. The PSI particles thus consist of one heterodimer of the 60-80-kDa polypeptides and presumably one copy of the 15- and 10-kDa polypeptides, respectively.

  3. Isolated Photosystem I Reaction Centers on a Functionalized Gated High Electron Mobility Transistor

    SciTech Connect

    Eliza, Sazia A.; Lee, Ida; Tulip, Fahmida S; Islam, Syed K; Mostafa, Salwa; Greenbaum, Elias; Ericson, Milton Nance

    2011-01-01

    In oxygenic plants, photons are captured with high quantum efficiency by two specialized reaction centers (RC) called Photosystem I (PS I) and Photosystem II (PS II). The captured photon triggers rapid charge separation and the photon energy is converted into an electrostatic potential across the nanometer-scale nm reaction centers. The exogenous photovoltages from a single PS I RC have been previously measured using the technique of Kelvin force probe microscopy (KFM). However, biomolecular photovoltaic applications require two-terminal devices. This paper presents for the first time, a micro-device for detection and characterization of isolated PS I RCs. The device is based on an AlGaN/GaN high electron mobility transistor (HEMT) structure. AlGaN/GaN HEMTs show high current throughputs and greater sensitivity to surface charges compared to other field-effect devices. PS I complexes immobilized on the floating gate of AlGaN/GaN HEMTs resulted in significant changes in the device characteristics under illumination. An analytical model has been developed to estimate the RCs of a major orientation on the functionalized gate surface of the HEMTs.

  4. Ancestral amino acid substitution improves the thermal stability of recombinant lignin-peroxidase from white-rot fungi, Phanerochaete chrysosporium strain UAMH 3641.

    PubMed

    Semba, Yasuyuki; Ishida, Manabu; Yokobori, Shin-ichi; Yamagishi, Akihiko

    2015-07-01

    Stabilizing enzymes from mesophiles of industrial interest is one of the greatest challenges of protein engineering. The ancestral mutation method, which introduces inferred ancestral residues into a target enzyme, has previously been developed and used to improve the thermostability of thermophilic enzymes. In this report, we studied the ancestral mutation method to improve the chemical and thermal stabilities of Phanerochaete chrysosporium lignin peroxidase (LiP), a mesophilic fungal enzyme. A fungal ancestral LiP sequence was inferred using a phylogenetic tree comprising Basidiomycota and Ascomycota fungal peroxidase sequences. Eleven mutant enzymes containing ancestral residues were designed, heterologously expressed in Escherichia coli and purified. Several of these ancestral mutants showed higher thermal stabilities and increased specific activities and/or kcat/KM than those of wild-type LiP.

  5. Solar Photocatalytic Hydrogen Production from Water Using a Dual Bed Photosystem - Phase I Final Report and Phase II Proposal

    SciTech Connect

    Clovis A. Linkous; Darlene K. Slattery

    2000-09-11

    In this work we are attempting to perform the highly efficient storage of solar energy in the form of H{sub 2} via photocatalytic decomposition of water. While it has been demonstrated that H{sub 2} and O{sub 2} can be evolved from a single vessel containing a single suspended photocatalyst (Sayama 1994; 1997), we are attempting to perform net water-splitting by using two photocatalysts immobilized in separate containers, or beds. A schematic showing how the device would work is shown.

  6. Heat stress induces an inhibition of excitation energy transfer from phycobilisomes to photosystem II but not to photosystem I in a cyanobacterium Spirulina platensis.

    PubMed

    Wen, Xiaogang; Gong, Hongmei; Lu, Congming

    2005-04-01

    The effects of high temperature (30-52.5 degrees C) on excitation energy transfer from phycobilisomes (PBS) to photosystem I (PSI) and photosystem II (PSII) in a cyanobacterium Spirulina platensis grown at 30 degrees C were studied by measuring 77 K chlorophyll (Chl) fluorescence emission spectra. Heat stress had a significant effect on 77 K Chl fluorescence emission spectra excited either at 436 or 580 nm. In order to reveal what parts of the photosynthetic apparatus were responsible for the changes in the related Chl fluorescence emission peaks, we fitted the emission spectra by Gaussian components according to the assignments of emission bands to different components of the photosynthetic apparatus. The 643 and 664 nm emissions originate from C-phycocyanin (CPC) and allophycocyanin (APC), respectively. The 685 and 695 nm emissions originate mainly from the core antenna complexes of PSII, CP43 and CP47, respectively. The 725 and 751 nm band is most effectively produced by PSI. There was no significant change in F725 and F751 during heat stress, suggesting that heat stress had no effects on excitation energy transfer from PBS to PSI. On the other hand, heat stress induced an increase in the ratio of Chl fluorescence yield of PBS to PSII, indicating that heat stress inhibits excitation energy transfer from PBS to PSII. However, this inhibition was not associated with an inhibition of excitation energy transfer from CPC to APC since no significant changes in F643 occurred at high temperatures. A dramatic enhancement of F664 occurring at 52.5 degrees C indicates that excitation energy transfer from APC to the PSII core complexes is suppressed at this temperature, possibly due to the structural changes within the PBS core but not to a detachment of PBS from PSII, resulting in an inhibition of excitation energy transfer from APC to PSII core complexes (CP47 + CP43). A decrease in F685 and F695 in heat-stressed cells with excitation at 436 nm seems to suggest that heat

  7. A common ancestor for oxygenic and anoxygenic photosynthetic systems: a comparison based on the structural model of photosystem I.

    PubMed

    Schubert, W D; Klukas, O; Saenger, W; Witt, H T; Fromme, P; Krauss, N

    1998-07-10

    The 4 A structural model of photosystem I (PSI) has elucidated essential features of this protein complex. Inter alia, it demonstrates that the core proteins of PSI, PsaA and PsaB each consist of an N-terminal antenna-binding domain, and a C-terminal reaction center (RC)-domain. A comparison of the RC-domain of PSI and the photosynthetic RC of purple bacteria (PbRC), reveals significantly analogous structures. This provides the structural support for the hypothesis that the two RC-types (I and II) share a common evolutionary origin. Apart from a similar set of constituent cofactors of the electron transfer system, the analogous features include a comparable cofactor arrangement and a corresponding secondary structure motif of the RC-cores. Despite these analogies, significant differences are evident, particularly as regards the distances between and the orientation of individual cofactors, and the length and orientation of alpha-helices. Inferred roles of conserved amino acids are discussed for PSI, photosystem II (PSII), photosystem C (PSC, green sulfur bacteria) and photosystem H (PSH, heliobacteria). Significant sequence homology between the N-terminal, antenna-binding domains of the core proteins of type-I RCs, PsaA, PsaB, PscA and PshA (of PSI, PSC and PSH respectively) with the antenna-binding subunits CP43 and CP47 of PSII indicate that PSII has a modular structure comparable to that of PSI. PMID:9654453

  8. Mutation of Photosystem II D1 protein that empower efficient phenotypes of Chlamydomonas Reinhardtii under extreme environment in space

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oxygenic photosynthesis involves capture and conversion of light energy into chemical energy, a process fundamental to life including plant productivity on Earth. Photosynthetic electron transport is catalyzed by two photochemical reaction centres in series, photosystem II (PS II) and photosytem I (...

  9. Analysis of the photosystem II by modelling the fluorescence yield transients during 10 seconds after a 10 ns pulse

    NASA Astrophysics Data System (ADS)

    Belyaeva, Natalya E.; Schmitt, Franz-Josef; Paschenko, Vladimir Z.; Riznichenko, Galina Yu.; Rubin, Andrew B.

    2014-10-01

    The dynamics of the photosystem II (PS II) redox states is imitated over nine orders of magnitude in time. Our simulations focus on the information of the chlorophyll a fluorescence induced by a 10 ns laser flash. The PS II model analyzes differences in the PS II reaction between leaves (A. Thaliana, spinach) and thermophilic Chlorella cells.

  10. Predicting Light Acclimation in Cyanobacteria from Nonphotochemical Quenching of Photosystem II Fluorescence, Which Reflects State Transitions in These Organisms.

    PubMed Central

    Campbell, D.; Oquist, G.

    1996-01-01

    An important factor in photosynthetic ecophysiology is the light regime that a photobiont is acclimated to exploit. In a wide range of cyanobacteria and cyano-lichens, the easily measured fluorescence parameters, coefficient of nonphotochemical quenching of photosystem II variable fluorescence (qN) and nonphotochemical quenching, decline to a minimum near the acclimated growth light intensity. This characteristic pattern predicts the integrated light regime to which populations are acclimated, information that is particularly useful for cyanobacteria or cyano-lichens from habitats with highly variable light intensities. qN reflects processes that compete with photosystem II photochemistry for absorbed excitation energy. In cyanobacteria, we find no evidence for energy-dependent quenching mechanisms, which are the predominant components of qN in higher plants. Instead, in cyanobacteria, qN correlates closely with the excitation flow from the phycobilisome to photosystem I, indicating that qN reflects the state transition mechanism for equilibration of excitation from the phycobilisome to the two photosystems. PMID:12226362

  11. Photosystem II-inhibitors play a limited role in sweet corn response to 4-hydroxyphenyl pyruvate dioxygenase-inhibiting herbicides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Postemergence (POST) application of 4-hydroxyphenyl pyruvate dioxygenase (HPPD) inhibitors in combination with a photosystem II (PSII) inhibitor, such as atrazine, is common practice in sweet corn production. Given the sensitivity of sweet corn to HPPD-inhibiting herbicides, the objective of this wo...

  12. Artificial synthetic Mn(IV)Ca-oxido complexes mimic the oxygen-evolving complex in photosystem II.

    PubMed

    Chen, Changhui; Zhang, Chunxi; Dong, Hongxing; Zhao, Jingquan

    2015-03-14

    A novel family of heteronuclear Mn(IV)Ca-oxido complexes containing Mn(IV)Ca-oxido cuboidal moieties and reactive water molecules on Ca(2+) have been synthesized and characterized to mimic the oxygen-evolving complex (OEC) of photosystem II (PSII) in nature. PMID:25662151

  13. Light-Harvesting Complex Stress-Related Proteins Catalyze Excess Energy Dissipation in Both Photosystems of Physcomitrella patens.

    PubMed

    Pinnola, Alberta; Cazzaniga, Stefano; Alboresi, Alessandro; Nevo, Reinat; Levin-Zaidman, Smadar; Reich, Ziv; Bassi, Roberto

    2015-11-01

    Two LHC-like proteins, Photosystem II Subunit S (PSBS) and Light-Harvesting Complex Stress-Related (LHCSR), are essential for triggering excess energy dissipation in chloroplasts of vascular plants and green algae, respectively. The mechanism of quenching was studied in Physcomitrella patens, an early divergent streptophyta (including green algae and land plants) in which both proteins are active. PSBS was localized in grana together with photosystem II (PSII), but LHCSR was located mainly in stroma-exposed membranes together with photosystem I (PSI), and its distribution did not change upon high-light treatment. The quenched conformation can be preserved by rapidly freezing the high-light-treated tissues in liquid nitrogen. When using green fluorescent protein as an internal standard, 77K fluorescence emission spectra on isolated chloroplasts allowed for independent assessment of PSI and PSII fluorescence yield. Results showed that both photosystems underwent quenching upon high-light treatment in the wild type in contrast to mutants depleted of LHCSR, which lacked PSI quenching. Due to the contribution of LHCII, P. patens had a PSI antenna size twice as large with respect to higher plants. Thus, LHCII, which is highly abundant in stroma membranes, appears to be the target of quenching by LHCSR.

  14. Quality Control of Photosystem II: The Mechanisms for Avoidance and Tolerance of Light and Heat Stresses are Closely Linked to Membrane Fluidity of the Thylakoids

    PubMed Central

    Yamamoto, Yasusi

    2016-01-01

    When oxygenic photosynthetic organisms are exposed to excessive light and/or heat, Photosystem II is damaged and electron transport is blocked. In these events, reactive oxygen species, endogenous radicals and lipid peroxidation products generated by photochemical reaction and/or heat cause the damage. Regarding light stress, plants first dissipate excessive light energy captured by light-harvesting chlorophyll protein complexes as heat to avoid the hazards, but once light stress is unavoidable, they tolerate the stress by concentrating damage in a particular protein in photosystem II, i.e., the reaction-center binding D1 protein of Photosystem II. The damaged D1 is removed by specific proteases and replaced with a new copy produced through de novo synthesis (reversible photoinhibition). When light intensity becomes extremely high, irreversible aggregation of D1 occurs and thereby D1 turnover is prevented. Once the aggregated products accumulate in Photosystem II complexes, removal of them by proteases is difficult, and irreversible inhibition of Photosystem II takes place (irreversible photoinhibition). Important is that various aspects of both the reversible and irreversible photoinhibition are highly dependent on the membrane fluidity of the thylakoids. Heat stress-induced inactivation of photosystem II is an irreversible process, which may be also affected by the fluidity of the thylakoid membranes. Here I describe why the membrane fluidity is a key to regulate the avoidance and tolerance of Photosystem II on environmental stresses. PMID:27532009

  15. Quality Control of Photosystem II: The Mechanisms for Avoidance and Tolerance of Light and Heat Stresses are Closely Linked to Membrane Fluidity of the Thylakoids.

    PubMed

    Yamamoto, Yasusi

    2016-01-01

    When oxygenic photosynthetic organisms are exposed to excessive light and/or heat, Photosystem II is damaged and electron transport is blocked. In these events, reactive oxygen species, endogenous radicals and lipid peroxidation products generated by photochemical reaction and/or heat cause the damage. Regarding light stress, plants first dissipate excessive light energy captured by light-harvesting chlorophyll protein complexes as heat to avoid the hazards, but once light stress is unavoidable, they tolerate the stress by concentrating damage in a particular protein in photosystem II, i.e., the reaction-center binding D1 protein of Photosystem II. The damaged D1 is removed by specific proteases and replaced with a new copy produced through de novo synthesis (reversible photoinhibition). When light intensity becomes extremely high, irreversible aggregation of D1 occurs and thereby D1 turnover is prevented. Once the aggregated products accumulate in Photosystem II complexes, removal of them by proteases is difficult, and irreversible inhibition of Photosystem II takes place (irreversible photoinhibition). Important is that various aspects of both the reversible and irreversible photoinhibition are highly dependent on the membrane fluidity of the thylakoids. Heat stress-induced inactivation of photosystem II is an irreversible process, which may be also affected by the fluidity of the thylakoid membranes. Here I describe why the membrane fluidity is a key to regulate the avoidance and tolerance of Photosystem II on environmental stresses. PMID:27532009

  16. A chloroplast-targeted heat shock protein 70 (HSP70) contributes to the photoprotection and repair of photosystem II during and after photoinhibition.

    PubMed Central

    Schroda, M; Vallon, O; Wollman, F A; Beck, C F

    1999-01-01

    Dark-grown Chlamydomonas reinhardtii cultures that were illuminated at low fluence rates before exposure to high-light conditions exhibited a faster rate of recovery from photoinhibition than did dark-grown cells that were directly exposed to photoinhibitory conditions. This pretreatment has been shown to induce the expression of several nuclear heat shock protein 70 (HSP70) genes, including HSP70B, encoding a chloroplast-localized chaperone. To investigate a possible role of plastidic HSP70B in photoprotection and repair of photosystem II, which is the major target of photoinhibition, we have constructed strains overexpressing or underexpressing HSP70B. The effect of light stress on photosystem II in nuclear transformants harboring HSP70B in the sense or antisense orientation was monitored by measuring variable fluorescence, flash-induced charge separation, and relative amounts of various photosystem II polypeptides. Underexpression of HSP70B caused an increased light sensitivity of photosystem II, whereas overexpression of HSP70B had a protective effect. Furthermore, the reactivation of photosystem II after photoinhibition was enhanced in the HSP70B-overexpressing strain when compared with the wild type, both in the presence or absence of synthesis of chloroplast-encoded proteins. Therefore, HSP70B may participate in vivo both in the molecular protection of the photosystem II reaction centers during photoinhibition and in the process of photosystem II repair. PMID:10368186

  17. Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees.

    PubMed

    Groussin, Mathieu; Hobbs, Joanne K; Szöllősi, Gergely J; Gribaldo, Simonetta; Arcus, Vickery L; Gouy, Manolo

    2015-01-01

    The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in the inference of putative ancestors. We validate our in silico predictions using in vitro resurrection of the LeuB enzyme for the ancestor of the Firmicutes, a major and ancient bacterial phylum. With this particular protein, our experimental results demonstrate that information on the species phylogeny results in a biochemically more realistic and kinetically more stable ancestral protein. Additional resurrection experiments with different proteins are necessary to statistically quantify the impact of using species tree-aware gene trees on ancestral protein phenotypes. Nonetheless, our results suggest the need for incorporating both sequence and DTL information in future studies of protein resurrections to accurately define the genotype-phenotype space in which proteins diversify.

  18. Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees.

    PubMed

    Groussin, Mathieu; Hobbs, Joanne K; Szöllősi, Gergely J; Gribaldo, Simonetta; Arcus, Vickery L; Gouy, Manolo

    2015-01-01

    The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in the inference of putative ancestors. We validate our in silico predictions using in vitro resurrection of the LeuB enzyme for the ancestor of the Firmicutes, a major and ancient bacterial phylum. With this particular protein, our experimental results demonstrate that information on the species phylogeny results in a biochemically more realistic and kinetically more stable ancestral protein. Additional resurrection experiments with different proteins are necessary to statistically quantify the impact of using species tree-aware gene trees on ancestral protein phenotypes. Nonetheless, our results suggest the need for incorporating both sequence and DTL information in future studies of protein resurrections to accurately define the genotype-phenotype space in which proteins diversify. PMID:25371435

  19. Did warfare among ancestral hunter-gatherers affect the evolution of human social behaviors?

    PubMed

    Bowles, Samuel

    2009-06-01

    Since Darwin, intergroup hostilities have figured prominently in explanations of the evolution of human social behavior. Yet whether ancestral humans were largely "peaceful" or "warlike" remains controversial. I ask a more precise question: If more cooperative groups were more likely to prevail in conflicts with other groups, was the level of intergroup violence sufficient to influence the evolution of human social behavior? Using a model of the evolutionary impact of between-group competition and a new data set that combines archaeological evidence on causes of death during the Late Pleistocene and early Holocene with ethnographic and historical reports on hunter-gatherer populations, I find that the estimated level of mortality in intergroup conflicts would have had substantial effects, allowing the proliferation of group-beneficial behaviors that were quite costly to the individual altruist.

  20. The two sides of warfare: an extended model of altruistic behavior in ancestral human intergroup conflict.

    PubMed

    Rusch, Hannes

    2014-09-01

    Building on and partially refining previous theoretical work, this paper presents an extended simulation model of ancestral warfare. This model (1) disentangles attack and defense, (2) tries to differentiate more strictly between selfish and altruistic efforts during war, (3) incorporates risk aversion and deterrence, and (4) pays special attention to the role of brutality. Modeling refinements and simulation results yield a differentiated picture of possible evolutionary dynamics. The main observations are: (a) Altruism in this model is more likely to evolve for defenses than for attacks. (b) Risk aversion, deterrence, and the interplay of migration levels and brutality can change evolutionary dynamics substantially. (c) Unexpectedly, one occasional simulation outcome is a dynamically stable state of "tolerated intergroup theft," raising the question as to whether corresponding patterns also exist in real intergroup conflicts. Finally, possible implications for theories of the coevolution of bellicosity and altruism in humans are discussed.

  1. Ancestral monogamy shows kin selection is key to the evolution of eusociality.

    PubMed

    Hughes, William O H; Oldroyd, Benjamin P; Beekman, Madeleine; Ratnieks, Francis L W

    2008-05-30

    Close relatedness has long been considered crucial to the evolution of eusociality. However, it has recently been suggested that close relatedness may be a consequence, rather than a cause, of eusociality. We tested this idea with a comparative analysis of female mating frequencies in 267 species of eusocial bees, wasps, and ants. We found that mating with a single male, which maximizes relatedness, is ancestral for all eight independent eusocial lineages that we investigated. Mating with multiple males is always derived. Furthermore, we found that high polyandry (>2 effective mates) occurs only in lineages whose workers have lost reproductive totipotency. These results provide the first evidence that monogamy was critical in the evolution of eusociality, strongly supporting the prediction of inclusive fitness theory. PMID:18511689

  2. Ancestral network module regulating prdm1 expression in the lamprey neural plate border

    PubMed Central

    Nikitina, Natalya; Tong, Leslie; Bronner-Fraser, Marianne

    2012-01-01

    prdm1 is an important transcriptional regulator that plays diverse roles during development of a wide variety of vertebrate and invertebrate species. prdm1 is required for neural crest specification in zebrafish, but not in mouse embryos. The role of this gene in neural crest formation in other species has not been examined, and its regulation during embryonic development is poorly understood. Here, we investigate the expression pattern, function and the upstream regulatory inputs into prdm1 during lamprey neural crest development. prdm1 is strongly expressed in the lamprey neural plate border, suggesting a conserved ancestral role of this gene in the neural crest formation. We found that lamprey neural plate border expression of prdm1 is activated by Ap-2 and Msx, but is independent of Pax3/7 and Zic. PMID:21932309

  3. Origin of human chromosome 2: An ancestral telomere-telomere fusion

    SciTech Connect

    Ijdo, J.W.; Baldini, A.; Ward, D.C.; Reeders, S.T.; Wells, R.A. )

    1991-10-15

    The authors identified two allelic genomic cosmids from human chromosome 2, c8.1 and c29B, each containing two inverted arrays of the vertebrate telomeric repeat in a head-to-head arrangement, 5{prime}(TTAGGG){sub n}-(CCCTAA){sub m}3{prime}. Sequences flanking this telomeric repeat are characteristic of present-day human pretelomeres. BAL-31 nuclease experiments with yeast artificial chromosome clones of human telomeres and fluorescence in situ hybridization reveal that sequences flanking these inverted repeats hybridize both to band 2q13 and to different, but overlapping, subsets of human chromosome ends. They conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.

  4. Novel ancestral Dysferlin splicing mutation which migrated from the Iberian peninsula to South America.

    PubMed

    Vernengo, Luis; Oliveira, Jorge; Krahn, Martin; Vieira, Emilia; Santos, Rosário; Carrasco, Luisa; Negrão, Luís; Panuncio, Ana; Leturcq, France; Labelle, Veronique; Bronze-da-Rocha, Elsa; Mesa, Rosario; Pizzarossa, Carlos; Lévy, Nicolas; Rodriguez, Maria-Mirta

    2011-05-01

    Primary dysferlinopathies are a group of recessive heterogeneous muscular dystrophies. The most common clinical presentations are Miyoshi myopathy and LGMD2B. Additional presentations range from isolated hyperCKemia to severe functional disability. Symptomatology begins in the posterior muscle compartment of the calf and its clinical course progresses slowly in Miyoshi myopathy whereas LGMD2B involves predominantly the proximal muscles of the lower limbs. The age of onset ranges from 13 to 60years in Caucasians. We present five patients that carry a novel mutation in the exon12/intron12 boundary: c.1180_1180+7delAGTGCGTG (r.1054_1284del). We provide evidence of a founder effect due to a common ancestral origin of this mutation, detected in heterozygosity in four patients and in homozygosity in one patient.

  5. Category-specific attention for animals reflects ancestral priorities, not expertise

    PubMed Central

    New, Joshua; Cosmides, Leda; Tooby, John

    2007-01-01

    Visual attention mechanisms are known to select information to process based on current goals, personal relevance, and lower-level features. Here we present evidence that human visual attention also includes a high-level category-specialized system that monitors animals in an ongoing manner. Exposed to alternations between complex natural scenes and duplicates with a single change (a change-detection paradigm), subjects are substantially faster and more accurate at detecting changes in animals relative to changes in all tested categories of inanimate objects, even vehicles, which they have been trained for years to monitor for sudden life-or-death changes in trajectory. This animate monitoring bias could not be accounted for by differences in lower-level visual characteristics, how interesting the target objects were, experience, or expertise, implicating mechanisms that evolved to direct attention differentially to objects by virtue of their membership in ancestrally important categories, regardless of their current utility. PMID:17909181

  6. Divergent ancestral lineages of newfound hantaviruses harbored by phylogenetically related crocidurine shrew species in Korea

    PubMed Central

    Arai, Satoru; Gu, Se Hun; Baek, Luck Ju; Tabara, Kenji; Bennett, Shannon; Oh, Hong-Shik; Takada, Nobuhiro; Kang, Hae Ji; Tanaka-Taya, Keiko; Morikawa, Shigeru; Okabe, Nobuhiko; Yanagihara, Richard; Song, Jin-Won

    2012-01-01

    Spurred by the recent isolation of a novel hantavirus, named Imjin virus (MJNV), from the Ussuri white-toothed shrew (Crocidura lasiura), targeted trapping was conducted for the phylogenetically related Asian lesser white-toothed shrew (Crocidura shantungensis). Pair-wise alignment and comparison of the S, M and L segments of a newfound hantavirus, designated Jeju virus (JJUV), indicated remarkably low nucleotide and amino acid sequence similarity with MJNV. Phylogenetic analyses, using maximum likelihood and Bayesian methods, showed divergent ancestral lineages for JJUV and MJNV, despite the close phylogenetic relationship of their reservoir soricid hosts. Also, no evidence of host switching was apparent in tanglegrams, generated by TreeMap 2.0β. PMID:22230701

  7. Linkage-disequilibrium mapping of disease genes by reconstruction of ancestral haplotypes in founder populations.

    PubMed Central

    Service, S K; Lang, D W; Freimer, N B; Sandkuijl, L A

    1999-01-01

    Linkage disequilibrium (LD) mapping may be a powerful means for genome screening to identify susceptibility loci for common diseases. A new statistical approach for detection of LD around a disease gene is presented here. This method compares the distribution of haplotypes in affected individuals versus that expected for individuals descended from a common ancestor who carried a mutation of the disease gene. Simulations demonstrate that this method, which we term "ancestral haplotype reconstruction" (AHR), should be powerful for genome screening of phenotypes characterized by a high degree of etiologic heterogeneity, even with currently available marker maps. AHR is best suited to application in isolated populations where affected individuals are relatively recently descended (< approximately 25 generations) from a common disease mutation-bearing founder. PMID:10330361

  8. Energy metabolism of ancestral eukaryotes: a hypothesis based on the biochemistry of amitochondriate parasitic protists.

    PubMed

    Müller, M

    1992-01-01

    Parasitic amitochondriate protists, representatives of early branches of eukaryote evolution, differ considerably in their central, energy metabolism from mitochondrion-bearing cells. These differences are: significant metabolic functions of inorganic pyrophosphate, major role of iron-sulfur proteins in key metabolic steps and in hydrogenosome-bearing organisms the disposal of electrons by H2 formation. Cytochrome-mediated electron transport and electron transport-linked phosphorylation are absent. All proteins which have been sequenced so far were found to be homologous to isofunctional proteins from other organisms. A few reactions, however, are catabolized by proteins which are not homologous to enzymes performing similar reactions in other eukaryotes. Two significantly different types of metabolism of amitochondriate protists can be distinguished: (a) without compartmentation and (b) with cytosol/hydrogenosome compartmentation. It is likely that these metabolic types have conserved certain traits present in ancestral eukaryotes before mitochondria became established.

  9. Did warfare among ancestral hunter-gatherers affect the evolution of human social behaviors?

    PubMed

    Bowles, Samuel

    2009-06-01

    Since Darwin, intergroup hostilities have figured prominently in explanations of the evolution of human social behavior. Yet whether ancestral humans were largely "peaceful" or "warlike" remains controversial. I ask a more precise question: If more cooperative groups were more likely to prevail in conflicts with other groups, was the level of intergroup violence sufficient to influence the evolution of human social behavior? Using a model of the evolutionary impact of between-group competition and a new data set that combines archaeological evidence on causes of death during the Late Pleistocene and early Holocene with ethnographic and historical reports on hunter-gatherer populations, I find that the estimated level of mortality in intergroup conflicts would have had substantial effects, allowing the proliferation of group-beneficial behaviors that were quite costly to the individual altruist. PMID:19498163

  10. The two sides of warfare: an extended model of altruistic behavior in ancestral human intergroup conflict.

    PubMed

    Rusch, Hannes

    2014-09-01

    Building on and partially refining previous theoretical work, this paper presents an extended simulation model of ancestral warfare. This model (1) disentangles attack and defense, (2) tries to differentiate more strictly between selfish and altruistic efforts during war, (3) incorporates risk aversion and deterrence, and (4) pays special attention to the role of brutality. Modeling refinements and simulation results yield a differentiated picture of possible evolutionary dynamics. The main observations are: (a) Altruism in this model is more likely to evolve for defenses than for attacks. (b) Risk aversion, deterrence, and the interplay of migration levels and brutality can change evolutionary dynamics substantially. (c) Unexpectedly, one occasional simulation outcome is a dynamically stable state of "tolerated intergroup theft," raising the question as to whether corresponding patterns also exist in real intergroup conflicts. Finally, possible implications for theories of the coevolution of bellicosity and altruism in humans are discussed. PMID:24928285

  11. TEF30 Interacts with Photosystem II Monomers and Is Involved in the Repair of Photodamaged Photosystem II in Chlamydomonas reinhardtii1[OPEN

    PubMed Central

    Bujaldon, Sandrine; Geimer, Stefan

    2016-01-01

    The remarkable capability of photosystem II (PSII) to oxidize water comes along with its vulnerability to oxidative damage. Accordingly, organisms harboring PSII have developed strategies to protect PSII from oxidative damage and to repair damaged PSII. Here, we report on the characterization of the THYLAKOID ENRICHED FRACTION30 (TEF30) protein in Chlamydomonas reinhardtii, which is conserved in the green lineage and induced by high light. Fractionation studies revealed that TEF30 is associated with the stromal side of thylakoid membranes. By using blue native/Deriphat-polyacrylamide gel electrophoresis, sucrose density gradients, and isolated PSII particles, we found TEF30 to quantitatively interact with monomeric PSII complexes. Electron microscopy images revealed significantly reduced thylakoid membrane stacking in TEF30-underexpressing cells when compared with control cells. Biophysical and immunological data point to an impaired PSII repair cycle in TEF30-underexpressing cells and a reduced ability to form PSII supercomplexes after high-light exposure. Taken together, our data suggest potential roles for TEF30 in facilitating the incorporation of a new D1 protein and/or the reintegration of CP43 into repaired PSII monomers, protecting repaired PSII monomers from undergoing repeated repair cycles or facilitating the migration of repaired PSII monomers back to stacked regions for supercomplex reassembly. PMID:26644506

  12. Reversed-phase HPLC determination of chlorophyll a' and phylloquinone in Photosystem I of oxygenic photosynthetic organisms. Universal existence of one chlorophyll a' molecule in Photosystem I.

    PubMed

    Nakamura, Akimasa; Akai, Masahiko; Yoshida, Emi; Taki, Takashi; Watanabe, Tadashi

    2003-06-01

    Chlorophyll (Chl) a', the C132-epimer of Chl a, is a constituent of the primary electron donor (P700) of Photosystem (PS) I of a thermophilic cyanobacterium Synechococcus (Thermosynechococcus) elongatus, as was recently demonstrated by X-ray crystallography. To determine whether PS I of oxygenic photosynthetic organisms universally contains one molecule of Chl a', pigment compositions of thylakoid membranes and PS I complexes isolated from the cyanobacteria T. elongatus and Synechocystis sp. PCC 6803, the green alga Chlamydomonas reinhardtii, and the green plant spinach, were examined by simultaneous detection of phylloquinone (the secondary electron acceptor of PS I) and Chl a' by reversed-phase HPLC. The results were compared with the Chl a/P700 ratio determined spectrophotometrically. The Chl a'/PS I ratios of thylakoid membranes and PS I were about 1 for all the organisms examined, and one Chl a' molecule was found in PS I even after most of the peripheral subunits were removed. Chl a' showed a characteristic extraction behaviour significantly different from the bulk Chl a in acetone/methanol extraction upon varying the mixing ratio. These findings confirm that a single Chl a' molecule in P700 is the universal feature of PS I of the Chl a-based oxygenic photosynthetic organisms.

  13. Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees.

    PubMed

    Williams, Paul H; Byvaltsev, Alexandr M; Cederberg, Björn; Berezin, Mikhail V; Ødegaard, Frode; Rasmussen, Claus; Richardson, Leif L; Huang, Jiaxing; Sheffield, Cory S; Williams, Suzanne T

    2015-01-01

    Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs) using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC) models and Poisson-tree-process (PTP) models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and genetic groups show

  14. Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees

    PubMed Central

    Williams, Paul H.; Byvaltsev, Alexandr M.; Cederberg, Björn; Berezin, Mikhail V.; Ødegaard, Frode; Rasmussen, Claus; Richardson, Leif L.; Huang, Jiaxing; Sheffield, Cory S.; Williams, Suzanne T.

    2015-01-01

    Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs) using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC) models and Poisson-tree-process (PTP) models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and genetic groups show

  15. Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals.

    PubMed

    Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R

    2009-01-01

    Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of beta-casein occurred in the monotreme lineage, as opposed to more ancient duplications of alpha-casein in the eutherian lineage, while marsupials possess only single copies of alpha- and beta-caseins. Despite this variability, the close proximity of the main alpha- and beta-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages.

  16. Wiring a periscope--ocelli, retinula axons, visual neuropils and the ancestrality of sea spiders.

    PubMed

    Lehmann, Tobias; Hess, Martin; Melzer, Roland R

    2012-01-01

    The Pycnogonida or sea spiders are cryptic, eight-legged arthropods with four median ocelli in a 'periscope' or eye tubercle. In older attempts at reconstructing phylogeny they were Arthropoda incertae sedis, but recent molecular trees placed them as the sister group either to all other euchelicerates or even to all euarthropods. Thus, pycnogonids are among the oldest extant arthropods and hold a key position for the understanding of arthropod evolution. This has stimulated studies of new sets of characters conductive to cladistic analyses, e.g. of the chelifores and of the hox gene expression pattern. In contrast knowledge of the architecture of the visual system is cursory. A few studies have analysed the ocelli and the uncommon "pseudoinverted" retinula cells. Moreover, analyses of visual neuropils are still at the stage of Hanström's early comprehensive works. We have therefore used various techniques to analyse the visual fibre pathways and the structure of their interrelated neuropils in several species. We found that pycnogonid ocelli are innervated to first and second visual neuropils in close vicinity to an unpaired midline neuropil, i.e. possibly the arcuate body, in a way very similar to ancestral euarthropods like Euperipatoides rowelli (Onychophora) and Limulus polyphemus (Xiphosura). This supports the ancestrality of pycnogonids and sheds light on what eyes in the pycnogonid ground plan might have 'looked' like. Recently it was suggested that arthropod eyes originated from simple ocelli similar to larval eyes. Hence, pycnogonid eyes would be one of the early offshoots among the wealth of more sophisticated arthropod eyes. PMID:22279594

  17. Evolutionary History of Assassin Bugs (Insecta: Hemiptera: Reduviidae): Insights from Divergence Dating and Ancestral State Reconstruction

    PubMed Central

    Hwang, Wei Song; Weirauch, Christiane

    2012-01-01

    Assassin bugs are one of the most successful clades of predatory animals based on their species numbers (∼6,800 spp.) and wide distribution in terrestrial ecosystems. Various novel prey capture strategies and remarkable prey specializations contribute to their appeal as a model to study evolutionary pathways involved in predation. Here, we reconstruct the most comprehensive reduviid phylogeny (178 taxa, 18 subfamilies) to date based on molecular data (5 markers). This phylogeny tests current hypotheses on reduviid relationships emphasizing the polyphyletic Reduviinae and the blood-feeding, disease-vectoring Triatominae, and allows us, for the first time in assassin bugs, to reconstruct ancestral states of prey associations and microhabitats. Using a fossil-calibrated molecular tree, we estimated divergence times for key events in the evolutionary history of Reduviidae. Our results indicate that the polyphyletic Reduviinae fall into 11–14 separate clades. Triatominae are paraphyletic with respect to the reduviine genus Opisthacidius in the maximum likelihood analyses; this result is in contrast to prior hypotheses that found Triatominae to be monophyletic or polyphyletic and may be due to the more comprehensive taxon and character sampling in this study. The evolution of blood-feeding may thus have occurred once or twice independently among predatory assassin bugs. All prey specialists evolved from generalist ancestors, with multiple evolutionary origins of termite and ant specializations. A bark-associated life style on tree trunks is ancestral for most of the lineages of Higher Reduviidae; living on foliage has evolved at least six times independently. Reduviidae originated in the Middle Jurassic (178 Ma), but significant lineage diversification only began in the Late Cretaceous (97 Ma). The integration of molecular phylogenetics with fossil and life history data as presented in this paper provides insights into the evolutionary history of reduviids and clears

  18. Ancestral chromosomal blocks are triplicated in Brassiceae species with varying chromosome number and genome size.

    PubMed

    Lysak, Martin A; Cheung, Kwok; Kitschke, Michaela; Bures, Petr

    2007-10-01

    The paleopolyploid character of genomes of the economically important genus Brassica and closely related species (tribe Brassiceae) is still fairly controversial. Here, we report on the comparative painting analysis of block F of the crucifer Ancestral Karyotype (AK; n = 8), consisting of 24 conserved genomic blocks, in 10 species traditionally treated as members of the tribe Brassiceae. Three homeologous copies of block F were identified per haploid chromosome complement in Brassiceae species with 2n = 14, 18, 20, 32, and 36. In high-polyploid (n >or= 30) species Crambe maritima (2n = 60), Crambe cordifolia (2n = 120), and Vella pseudocytisus (2n = 68), six, 12, and six copies of the analyzed block have been revealed, respectively. Homeologous regions resembled the ancestral structure of block F within the AK or were altered by inversions and/or translocations. In two species of the subtribe Zillineae, two of the three homeologous regions were combined via a reciprocal translocation onto one chromosome. Altogether, these findings provide compelling evidence of an ancient hexaploidization event and corresponding whole-genome triplication shared by the tribe Brassiceae. No direct relationship between chromosome number and genome size variation (1.2-2.5 pg/2C) has been found in Brassiceae species with 2n = 14 to 36. Only two homeologous copies of block F suggest a whole-genome duplication but not the triplication event in Orychophragmus violaceus (2n = 24), and confirm a phylogenetic position of this species outside the tribe Brassiceae. Chromosome duplication detected in Orychophragmus as well as chromosome rearrangements shared by Zillineae species demonstrate the usefulness of comparative cytogenetics for elucidation of phylogenetic relationships.

  19. Magnetic Investigation of Ancestral Puebloan Rio Grande (New Mexico) Glaze Wares

    NASA Astrophysics Data System (ADS)

    Dyer, J. B.; Geissman, J. W.; Ramenofsky, A. F.

    2007-12-01

    In geologically heterogeneous regions, such as the Rio Grande, archaeologists typically rely on petrographic analyses to determine ceramic provenance and reconstruct prehistoric trade patterns. Even in these regions, other methods are useful for elucidating trade patterns and/or resolving ambiguities from the petrographic data. Magnetic properties of Ancestral central Rio Grande Puebloan ceramics are being acquired to assess their use in identifying provenance, trade patterns, composition, manufacturing techniques, and firing conditions of ceramics, before and during the early European contact period (ca. A.D. 1325-1700) in New Mexico. Similar to the study of Moskowitz et al. (1987), we use a combination of bulk susceptibility, NRM, ARM, and SIRM intensity, AF response by NRM, ARM, and SIRM, thermal demagnetization of NRM and SIRM, and coercivity of remanence, to study temporal change in Rio Grande glaze wares from four archaeological sites in the northern Rio Grande (approximately 90 sherds per site). Rio Grande glaze wares were widely traded among Ancestral Puebloan groups before and during the European contact period. The ceramics are from the two earliest Spanish administrative centers in New Mexico, San Gabriel del Yungue and Palace of the Governors, and two mission pueblos, Pecos Pueblo and San Marcos Pueblo. Magnetic property data are being compared with petrographic observations to test the effectiveness of several magnetic measurements to identify, among other things, ceramic provenance. A tentative observation in our study is that bulk susceptibility values correlate with different ceramic provenances. The mean bulk susceptibility values for Galisteo Basin ceramics, tempered with augite monzonite and hornblende latite, are significantly higher (5.56E-04 and 4.91E-04 SI mass, respectively) than those for Pajarito Plateau ceramics, tempered with glassy tuff, tuff rocks, and andesite, (1.79E-04, 2.53E-04, and 2.58E-04 SI mass, respectively). This study is

  20. Evolutionary history of assassin bugs (insecta: hemiptera: Reduviidae): insights from divergence dating and ancestral state reconstruction.

    PubMed

    Hwang, Wei Song; Weirauch, Christiane

    2012-01-01

    Assassin bugs are one of the most successful clades of predatory animals based on their species numbers (∼6,800 spp.) and wide distribution in terrestrial ecosystems. Various novel prey capture strategies and remarkable prey specializations contribute to their appeal as a model to study evolutionary pathways involved in predation. Here, we reconstruct the most comprehensive reduviid phylogeny (178 taxa, 18 subfamilies) to date based on molecular data (5 markers). This phylogeny tests current hypotheses on reduviid relationships emphasizing the polyphyletic Reduviinae and the blood-feeding, disease-vectoring Triatominae, and allows us, for the first time in assassin bugs, to reconstruct ancestral states of prey associations and microhabitats. Using a fossil-calibrated molecular tree, we estimated divergence times for key events in the evolutionary history of Reduviidae. Our results indicate that the polyphyletic Reduviinae fall into 11-14 separate clades. Triatominae are paraphyletic with respect to the reduviine genus Opisthacidius in the maximum likelihood analyses; this result is in contrast to prior hypotheses that found Triatominae to be monophyletic or polyphyletic and may be due to the more comprehensive taxon and character sampling in this study. The evolution of blood-feeding may thus have occurred once or twice independently among predatory assassin bugs. All prey specialists evolved from generalist ancestors, with multiple evolutionary origins of termite and ant specializations. A bark-associated life style on tree trunks is ancestral for most of the lineages of Higher Reduviidae; living on foliage has evolved at least six times independently. Reduviidae originated in the Middle Jurassic (178 Ma), but significant lineage diversification only began in the Late Cretaceous (97 Ma). The integration of molecular phylogenetics with fossil and life history data as presented in this paper provides insights into the evolutionary history of reduviids and clears

  1. Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms.

    PubMed

    Erkenbrack, Eric M; Ako-Asare, Kayla; Miller, Emily; Tekelenburg, Saira; Thompson, Jeffrey R; Romano, Laura

    2016-01-01

    Diverse sampling of organisms across the five major classes in the phylum Echinodermata is beginning to reveal much about the structure and function of gene regulatory networks (GRNs) in development and evolution. Sea urchins are the most studied clade within this phylum, and recent work suggests there has been dramatic rewiring at the top of the skeletogenic GRN along the lineage leading to extant members of the euechinoid sea urchins. Such rewiring likely accounts for some of the observed developmental differences between the two major subclasses of sea urchins-cidaroids and euechinoids. To address effects of topmost rewiring on downstream GRN events, we cloned four downstream regulatory genes within the skeletogenic GRN and surveyed their spatiotemporal expression patterns in the cidaroid Eucidaris tribuloides. We performed phylogenetic analyses with homologs from other non-vertebrate deuterostomes and characterized their spatiotemporal expression by quantitative polymerase chain reaction (qPCR) and whole-mount in situ hybridization (WMISH). Our data suggest the erg-hex-tgif subcircuit, a putative GRN kernel, exhibits a mesoderm-specific expression pattern early in Eucidaris development that is directly downstream of the initial mesodermal GRN circuitry. Comparative analysis of the expression of this subcircuit in four echinoderm taxa allowed robust ancestral state reconstruction, supporting hypotheses that its ancestral function was to stabilize the mesodermal regulatory state and that it has been co-opted and deployed as a unit in mesodermal subdomains in distantly diverged echinoderms. Importantly, our study supports the notion that GRN kernels exhibit structural and functional modularity, locking down and stabilizing clade-specific, embryonic regulatory states. PMID:26781941

  2. Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes

    PubMed Central

    Voss, Stephen R.; Kump, D. Kevin; Putta, Srikrishna; Pauly, Nathan; Reynolds, Anna; Henry, Rema J.; Basa, Saritha; Walker, John A.; Smith, Jeramiah J.

    2011-01-01

    Amphibian genomes differ greatly in DNA content and chromosome size, morphology, and number. Investigations of this diversity are needed to identify mechanisms that have shaped the evolution of vertebrate genomes. We used comparative mapping to investigate the organization of genes in the Mexican axolotl (Ambystoma mexicanum), a species that presents relatively few chromosomes (n = 14) and a gigantic genome (>20 pg/N). We show extensive conservation of synteny between Ambystoma, chicken, and human, and a positive correlation between the length of conserved segments and genome size. Ambystoma segments are estimated to be four to 51 times longer than homologous human and chicken segments. Strikingly, genes demarking the structures of 28 chicken chromosomes are ordered among linkage groups defining the Ambystoma genome, and we show that these same chromosomal segments are also conserved in a distantly related anuran amphibian (Xenopus tropicalis). Using linkage relationships from the amphibian maps, we predict that three chicken chromosomes originated by fusion, nine to 14 originated by fission, and 12–17 evolved directly from ancestral tetrapod chromosomes. We further show that some ancestral segments were fused prior to the divergence of salamanders and anurans, while others fused independently and randomly as chromosome numbers were reduced in lineages leading to Ambystoma and Xenopus. The maintenance of gene order relationships between chromosomal segments that have greatly expanded and contracted in salamander and chicken genomes, respectively, suggests selection to maintain synteny relationships and/or extremely low rates of chromosomal rearrangement. Overall, the results demonstrate the value of data from diverse, amphibian genomes in studies of vertebrate genome evolution. PMID:21482624

  3. Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals.

    PubMed

    Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R

    2009-01-01

    Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of beta-casein occurred in the monotreme lineage, as opposed to more ancient duplications of alpha-casein in the eutherian lineage, while marsupials possess only single copies of alpha- and beta-caseins. Despite this variability, the close proximity of the main alpha- and beta-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages. PMID:19874726

  4. Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees.

    PubMed

    Williams, Paul H; Byvaltsev, Alexandr M; Cederberg, Björn; Berezin, Mikhail V; Ødegaard, Frode; Rasmussen, Claus; Richardson, Leif L; Huang, Jiaxing; Sheffield, Cory S; Williams, Suzanne T

    2015-01-01

    Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs) using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC) models and Poisson-tree-process (PTP) models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and genetic groups show

  5. Magmatism and Epithermal Gold-Silver Deposits of the Southern Ancestral Cascade Arc, Western Nevada and Eastern California

    USGS Publications Warehouse

    John, David A.; du Bray, Edward A.; Henry, Christopher D.; Vikre, Peter

    2015-01-01

    Many epithermal gold-silver deposits are temporally and spatially associated with late Oligocene to Pliocene magmatism of the southern ancestral Cascade arc in western Nevada and eastern California. These deposits, which include both quartz-adularia (low- and intermediate-sulfidation; Comstock Lode, Tonopah, Bodie) and quartz-alunite (high-sulfidation; Goldfield, Paradise Peak) types, were major producers of gold and silver. Ancestral Cascade arc magmatism preceded that of the modern High Cascades arc and reflects subduction of the Farallon plate beneath North America. Ancestral arc magmatism began about 45 Ma, continued until about 3 Ma, and extended from near the Canada-United States border in Washington southward to about 250 km southeast of Reno, Nevada. The ancestral arc was split into northern and southern segments across an inferred tear in the subducting slab between Mount Shasta and Lassen Peak in northern California. The southern segment extends between 42°N in northern California and 37°N in western Nevada and was active from about 30 to 3 Ma. It is bounded on the east by the northeast edge of the Walker Lane. Ancestral arc volcanism represents an abrupt change in composition and style of magmatism relative to that in central Nevada. Large volume, caldera-forming, silicic ignimbrites associated with the 37 to 19 Ma ignimbrite flareup are dominant in central Nevada, whereas volcanic centers of the ancestral arc in western Nevada consist of andesitic stratovolcanoes and dacitic to rhyolitic lava domes that mostly formed between 25 and 4 Ma. Both ancestral arc and ignimbrite flareup magmatism resulted from rollback of the shallowly dipping slab that began about 45 Ma in northeast Nevada and migrated south-southwest with time. Most southern segment ancestral arc rocks have oxidized, high potassium, calc-alkaline compositions with silica contents ranging continuously from about 55 to 77 wt%. Most lavas are porphyritic and contain coarse plagioclase

  6. Photosystem II reconstitution into proteoliposomes and methodologies for structure-function characterization.

    PubMed

    Joly, David; Govindachary, Sridharan; Fragata, Mário

    2011-01-01

    This chapter discusses the photosystem II (PSII) reconstitution into proteoliposomes. In the first part of the chapter, protocols are outlined for the preparation of lipid bilayer vesicles (liposomes) constituted of individual thylakoid lipids or their mixtures, for the preparation of PSII particles, and for the incorporation of the PSII particles into the liposomes. In the second part of the chapter, methodologies are described for the structure-function characterization of the PSII-lipid complexes (proteoliposomes). This includes the sodium dodecylsulfate-polyacrylamide gel electrophoresis determination of the PSII proteins, the measurement of oxygen-evolving activity of PSII in the proteoliposomes, the study of structural changes of the PSII proteins upon their incorporation into the lipid bilayers by Fourier transform infrared (FT-IR) spectroscopy, and the characterization of the PSII activity by fluorescence induction.

  7. Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex.

    PubMed

    de Jong, Djurre H; Liguori, Nicoletta; van den Berg, Tom; Arnarez, Clement; Periole, Xavier; Marrink, Siewert J

    2015-06-25

    Electron transfers within and between protein complexes are core processes of the electron transport chains occurring in thylakoid (chloroplast), mitochondrial, and bacterial membranes. These electron transfers involve a number of cofactors. Here we describe the derivation of molecular mechanics parameters for the cofactors associated with the function of the photosystem II core complex: plastoquinone, plastoquinol, heme b, chlorophyll A, pheophytin, and β-carotene. Parameters were also obtained for ubiquinol and ubiquinone, related cofactors involved in the respiratory chain. Parameters were derived at both atomistic and coarse grain (CG) resolutions, compatible with the building blocks of the GROMOS united-atom and Martini CG force fields, respectively. Structural and thermodynamic properties of the cofactors were compared to experimental values when available. The topologies were further tested in molecular dynamics simulations of the cofactors in their physiological environment, e.g., either in a lipid membrane environment or in complex with the heme binding protein bacterioferritin.

  8. Molecular operation of metals into the function and state of photosystem II.

    PubMed

    Gaziyev, Arif; Aliyeva, Samira; Kurbanova, Inna; Ganiyeva, Rena; Bayramova, Sona; Gasanov, Ralphreed

    2011-12-01

    Action sites of different metals in the electron transport reactions of Photosystem II (PS II) evaluated by delayed fluorescence in the ms range (ms DF) and pigment-pigment, pigment-protein and protein-protein interaction states by electrophoretic measurements are presented. The main targets for the metals action were shown to be:(i) Cd(2+), Ni(2+), Co(2+)-Y(z) or CaMn(4)-cluster on the donor site with dependence on pH;(ii) Ni(2+), Co(2+), Zn(2+), Al(3+), Mn(2+) between Q(A) and Q(B) on the acceptor site; effect of Al(3+) and Mn(2+) is observed only in acidic pH. Investigated metals bring about monomerization of oligomeric and dimeric chlorophyll-protein complexes (CPC) and destabilization of protein-protein interactions. Molecular mechanisms of metals interference with the structure of PS II are discussed.

  9. Assembling and maintaining the Photosystem II complex in chloroplasts and cyanobacteria.

    PubMed

    Komenda, Josef; Sobotka, Roman; Nixon, Peter J

    2012-06-01

    Plants, algae and cyanobacteria grow because of their ability to use sunlight to extract electrons from water. This vital reaction is catalysed by the Photosystem II (PSII) complex, a large multi-subunit pigment-protein complex embedded in the thylakoid membrane. Recent results show that assembly of PSII occurs in a step-wise fashion in defined regions of the membrane system, involves conserved auxiliary factors and is closely coupled to chlorophyll biosynthesis. PSII is also repaired following damage by light. FtsH proteases play an important role in selectively removing damaged proteins from the complex, both in chloroplasts and cyanobacteria, whilst undamaged subunits and pigments are recycled. The chloroplastic Deg proteases play a supplementary role in PSII repair.

  10. Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model system.

    PubMed

    Kupitz, Christopher; Grotjohann, Ingo; Conrad, Chelsie E; Roy-Chowdhury, Shatabdi; Fromme, Raimund; Fromme, Petra

    2014-07-17

    Serial femtosecond crystallography (SFX) is a new emerging method, where X-ray diffraction data are collected from a fully hydrated stream of nano- or microcrystals of biomolecules in their mother liquor using high-energy, X-ray free-electron lasers. The success of SFX experiments strongly depends on the ability to grow large amounts of well-ordered nano/microcrystals of homogeneous size distribution. While methods to grow large single crystals have been extensively explored in the past, method developments to grow nano/microcrystals in sufficient amounts for SFX experiments are still in their infancy. Here, we describe and compare three methods (batch, free interface diffusion (FID) and FID centrifugation) for growth of nano/microcrystals for time-resolved SFX experiments using the large membrane protein complex photosystem II as a model system.

  11. Crystallization of the oxygen-evolving reaction centre of photosystem II in nine different detergent mixtures.

    PubMed

    Adir, N

    1999-04-01

    Oxygen-evolving photosystem II reaction centres (RCII) isolated from both spinach and pea have been crystallized. A single crystal form grew from RCII monomers in the presence of nine different three-component mixtures of non-ionic detergents and heptane-1,2, 3-triol. The crystals grew as hexagonal rods with dimensions of up to 1 x 0.3 x 0.3 mm. The crystals diffracted to a maximum resolution of 6.5 A and belong to a hexagonal space group with unit-cell parameters a = 495, b = 495, c = 115 A, alpha = beta = 90, gamma = 120 degrees. The growth of a single crystal form in the presence of such a large variety of detergents suggests a very limited range of crystal lattice formation sites in the RCII complex. PMID:10089326

  12. Structure, dynamics, and energetics of the primary photochemistry of photosystem II of oxygenic photosynthesis.

    PubMed

    Diner, Bruce A; Rappaport, Fabrice

    2002-01-01

    Recent progress in two-dimensional and three-dimensional electron and X-ray crystallography of Photosystem II (PSII) core complexes has led to major advances in the structural definition of this integral membrane protein complex. Despite the overall structural and kinetic similarity of the PSII reaction centers to their purple non-sulfur photosynthetic bacterial homologues, the different cofactors and subtle differences in their spatial arrangement result in significant differences in the energetics and mechanism of primary charge separation. In this review we discuss some of the recent spectroscopic, structural, and mutagenic work on the primary and secondary electron transfer reactions in PSII, stressing what is experimentally novel, what new insights have appeared, and where questions of interpretation remain.

  13. Methodology of Pulsed Photoacoustics and Its Application to Probe Photosystems and Receptors

    PubMed Central

    Hou, Harvey J.M.; Sakmar, Thomas P.

    2010-01-01

    We review recent advances in the methodology of pulsed time-resolved photoacoustics and its application to studies of photosynthetic reaction centers and membrane receptors such as the G protein-coupled receptor rhodopsin. The experimental parameters accessible to photoacoustics include molecular volume change and photoreaction enthalpy change. Light-driven volume change secondary to protein conformational changes or electrostriction is directly related to the photoreaction and thus can be a useful measurement of activity and function. The enthalpy changes of the photochemical reactions observed can be measured directly by photoacoustics. With the measurement of enthalpy change, the reaction entropy can also be calculated when free energy is known. Dissecting the free energy of a photoreaction into enthalpic and entropic components may provide critical information about photoactivation mechanisms of photosystems and photoreceptors. The potential limitations and future applications of time-resolved photoacoustics are also discussed. PMID:22219680

  14. Immobilization and orientation of Photosystem I reaction centers on solid surfaces. Final report

    SciTech Connect

    1998-01-20

    The overall objective of this project was to test the potential for immobilization and orientation of Photosystem I reaction center protein on solid surfaces. In order to maximize the resources available for this work, bleomycin complexes were used as a test substrate. The reaction of [(H{sub 2}O)(NH{sub 3}){sub 5}Ru{sup II}]{sup 2+} with bleomycin forms at least two stable products following oxidation to the Ru(III) analog. Spectroscopic and electrochemical measurements indicate monodentate binding of [(NH{sub 3}){sub 5}Ru{sup III}] to the imidazole and pyrimidine moieties, with coordination to the latter involving the exocyclic amine nitrogen. DNA cleavage studies show the complexes to be ineffective in DNA strand scission.

  15. Fast isolation of highly active photosystem II core complexes from spinach.

    PubMed

    Wang, Zhao-Gai; Xu, Tian-Hua; Liu, Cheng; Yang, Chun-Hong

    2010-09-01

    Purification of photosystem II (PSII) core complexes is a time-consuming and low-efficiency process. In order to isolate pure and active PSII core complexes in large amounts, we have developed a fast method to isolate highly active monomeric and dimeric PSII core complexes from spinach leaves by using sucrose gradient ultracentrifugation. By using a vertical rotor the process was completed significantly faster compared with a swing-out rotor. In order to keep the core complexes in high activity, the whole isolation procedure was performed in the presence of glycine betain and pH at 6.3. The isolated pigment-protein complexes were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, absorption spectroscopy, 77 K fluorescence spectroscopy and high performance liquid chromatography. Our results show that this method is a better choice for quick and efficient isolation of functionally active PSII core complexes. PMID:20738723

  16. Solar Photo Catalytic Hydrogen Production from water using a dual bed photosystem

    SciTech Connect

    Florida Solar Energy Center

    2003-03-30

    A body of work was performed in which the feasibility of photocatalytically decomposing water into its constituent elements using a dual bed, or modular photosystem, under solar radiation was investigated. The system envisioned consists of two modules, each consisting of a shallow, flat, sealed container, in which microscopic photocatalytic particles are immobilized. The photocatalysts absorb light, generating free electrons and lattice vacancy holes, which are capable of performing reductive and oxidative chemistry, respectively. The photocatalysts would be chosen as to whether they specifically promote H{sub 2} or O{sub 2} evolution in their respective containers. An aqueous solution containing a redox mediator is pumped between the two chambers in order to transfer electron equivalents from one reaction to the other.

  17. Molecular electronics of a single photosystem I reaction center: studies with scanning tunneling microscopy and spectroscopy.

    PubMed Central

    Lee, I; Lee, J W; Warmack, R J; Allison, D P; Greenbaum, E

    1995-01-01

    Thylakoids and photosystem I (PSI) reaction centers were imaged by scanning tunneling microscopy. The thylakoids were isolated from spinach chloroplasts, and PSI reaction centers were extracted from thylakoid membranes. Because thylakoids are relatively thick nonconductors, they were sputter-coated with Pd/Au before imaging. PSI photosynthetic centers and chemically platinized PSI were investigated without sputter-coating. They were mounted on flat gold substrates that had been treated with mercaptoacetic acid to help bind the proteins. With tunneling spectroscopy, the PSI centers displayed a semiconductor-like response with a band gap of 1.8 eV. Lightly platinized (platinized for 1 hr) centers displayed diode-like conduction that resulted in dramatic contrast changes between images taken with opposite bias voltages. The electronic properties of this system were stable under long-term storage. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:11607515

  18. Composition and structure of photosystem I in the moss Physcomitrella patens

    PubMed Central

    Busch, Andreas; Petersen, Jørgen; Webber-Birungi, Mariam T.; Powikrowska, Marta; Lassen, Lærke Marie Münter; Naumann-Busch, Bianca; Nielsen, Agnieszka Zygadlo; Ye, Juanying; Boekema, Egbert J.; Jensen, Ole Nørregaard; Lunde, Christina; Jensen, Poul Erik

    2013-01-01

    Recently, bryophytes, which diverged from the ancestor of seed plants more than 400 million years ago, came into focus in photosynthesis research as they can provide valuable insights into the evolution of photosynthetic complexes during the adaptation to terrestrial life. This study isolated intact photosystem I (PSI) with its associated light-harvesting complex (LHCI) from the moss Physcomitrella patens and characterized its structure, polypeptide composition, and light-harvesting function using electron microscopy, mass spectrometry, biochemical, and physiological methods. It became evident that Physcomitrella possesses a strikingly high number of isoforms for the different PSI core subunits as well as LHCI proteins. It was demonstrated that all these different subunit isoforms are expressed at the protein level and are incorporated into functional PSI–LHCI complexes. Furthermore, in contrast to previous reports, it was demonstrated that Physcomitrella assembles a light-harvesting complex consisting of four light-harvesting proteins forming a higher-plant-like PSI superstructure. PMID:23682117

  19. Temperature dependent steady state and picosecond kinetic fluorescence measurements of a photosystem I preparation from spinach

    SciTech Connect

    Mukerji, I.; Sauer, K.

    1988-08-01

    The fluorescence properties of a photosystem I (PSI) preparation from spinach containing approximately 200 chlorophyll (Chl) per reaction center were investigated. The preparation, characterized both spectroscopically and biochemically, contained the peripheral light harvesting antenna associated with PSI. In this study steady state fluorescence measurements were performed as a function of temperature. An emission maximum at 690 nm and a long wavelength shoulder from 710 to 740 nm were observed. The fluorescence yield at 690 nm is temperature independent, while the yield of the long wavelength shoulder increases dramatically with decreasing temperature. Additionally, kinetic measurements using the technique of single photon counting were done at room temperature and 77K. At 295K a four component fit was needed to describe the fluorescence decay; whereas at 77K, an additional 40-50 ps rise component indicative of fluorescence induction was necessary. 28 refs., 13 figs., 1 tab.

  20. Contribution of vitamin K1 to the electron spin polarization in spinach photosystem I

    SciTech Connect

    Rustandi, R.R.; Snyder, S.W.; Feezel, L.L.; Michalski, T.J.; Norris, J.R.; Thurnauer, M.C.; Biggins, J. )

    1990-09-04

    The electron spin polarized (ESP) electron paramagnetic resonance (EPR) signal observed in spinach photosystem I (PSI) particles was examined in preparations depleted of vitamin K1 by solvent extraction and following biological reconstitution by the quinone. The ESP EPR signal was not detected in the solvent-extracted PSI sample but was restored upon reconstitution with either protonated or deuterated vitamin K1 under conditions that also restored electron transfer to the terminal PSI acceptors. Reconstitution using deuterated vitamin K1 resulted in a line narrowing of the ESP EPR signal, supporting the conclusion that the ESP EPR signals in the reconstituted samples arise from a radical pair consisting of the oxidized PSI primary donor, P700+, and reduced vitamin K1.

  1. Composition and structure of photosystem I in the moss Physcomitrella patens.

    PubMed

    Busch, Andreas; Petersen, Jørgen; Webber-Birungi, Mariam T; Powikrowska, Marta; Lassen, Lærke Marie Münter; Naumann-Busch, Bianca; Nielsen, Agnieszka Zygadlo; Ye, Juanying; Boekema, Egbert J; Jensen, Ole Nørregaard; Lunde, Christina; Jensen, Poul Erik

    2013-07-01

    Recently, bryophytes, which diverged from the ancestor of seed plants more than 400 million years ago, came into focus in photosynthesis research as they can provide valuable insights into the evolution of photosynthetic complexes during the adaptation to terrestrial life. This study isolated intact photosystem I (PSI) with its associated light-harvesting complex (LHCI) from the moss Physcomitrella patens and characterized its structure, polypeptide composition, and light-harvesting function using electron microscopy, mass spectrometry, biochemical, and physiological methods. It became evident that Physcomitrella possesses a strikingly high number of isoforms for the different PSI core subunits as well as LHCI proteins. It was demonstrated that all these different subunit isoforms are expressed at the protein level and are incorporated into functional PSI-LHCI complexes. Furthermore, in contrast to previous reports, it was demonstrated that Physcomitrella assembles a light-harvesting complex consisting of four light-harvesting proteins forming a higher-plant-like PSI superstructure.

  2. Molecular design of the photosystem II light-harvesting antenna: photosynthesis and photoprotection.

    PubMed

    Horton, Peter; Ruban, Alexander

    2005-01-01

    The photosystem II (PSII) light-harvesting system carries out two essential functions, the efficient collection of light energy for photosynthesis, and the regulated dissipation of excitation energy in excess of that which can be used. This dual function requires structural and functional flexibility, in which light-harvesting proteins respond to an external signal, the thylakoid DeltapH, to induce feedback control. This process, referred to as non-photochemical quenching (NPQ) depends upon the xanthophyll cycle and the PsbS protein. In nature, NPQ is heterogeneous in terms of kinetics and capacity, and this adapts photosynthetic systems to the specific dynamic features of the light environment. The molecular features of the thylakoid membrane which may enable this flexibility and plasticity are discussed.

  3. Antenna ring around trimeric Photosystem I in chlorophyll b containing cyanobacterium Prochlorothrix hollandica.

    PubMed

    Bumba, Ladislav; Prasil, Ondrej; Vacha, Frantisek

    2005-06-01

    Prochlorothrix hollandica is one of the three known species of an unusual clade of cyanobacteria (formerly called "prochlorophytes") that contain chlorophyll a and b molecules bound to intrinsic light-harvesting antenna proteins. Here, we report the structural characterization of supramolecular complex consisting of Photosystem I (PSI) associated with the chlorophyll a/b-binding Pcb proteins. Electron microscopy and single particle image analysis of negatively stained preparations revealed that the Pcb-PSI supercomplex consists of a central trimeric PSI surrounded by a ring of 18 Pcb subunits. We conclude that the formation of the Pcb ring around trimeric PSI represents a mechanism for increasing the light-harvesting efficiency in chlorophyll b-containing cyanobacteria.

  4. Dynamics of Excitation Energy Transfer Between the Subunits of Photosystem II Dimer.

    PubMed

    Yoneda, Yusuke; Katayama, Tetsuro; Nagasawa, Yutaka; Miyasaka, Hiroshi; Umena, Yasufumi

    2016-09-14

    Energy transfer dynamics in monomer and dimer of the photosystem II core complex (PSII-CC) was investigated by means of femtosecond transient absorption (TA) spectroscopy. There is no profound difference between the TA dynamics of the monomer and the dimer in the weak excitation intensity condition (≤21 nJ). However, the fast recovery of the ground state bleach was pronounced at higher excitation intensities, and the excitation intensity dependence of the dimer was more significant than that of the monomer. This result indicates efficient exciton-exciton annihilation taking place in the dimer due to energy transfer between the two monomer units. The annihilation dynamics was reproduced by a simple model based on binomial theorem, which indicated that although PSII-CC dimer has two reaction centers, only one charge-separated state remained after annihilation. PMID:27541744

  5. Antisense inhibition of the photosystem I antenna protein Lhca4 in Arabidopsis thaliana.

    PubMed Central

    Zhang, H; Goodman, H M; Jansson, S

    1997-01-01

    The function of Lhca4, a gene encoding the photosystem 1 type IV chlorophyll a/b-binding protein complex in Arabidopsis, was investigated using antisense technology. Lhca4 protein was reduced in a number of mutant lines and abolished in one. The inhibition of protein was not correlated with the inhibition of mRNA. No depletion of Lhca1 was observed, but the low-temperature fluorescence emission spectrum was drastically altered in the mutants. The emission maximum was blue-shifted by 6 nm, showing that chlorophyll molecules bound to Lhca4 are responsible for most of the long-wavelength fluorescence emission. Some mutants also showed an unexplainable delay in flowering time and an increase in seed weight. PMID:9414561

  6. Variation potential propagation decreases heat-related damage of pea photosystem I by 2 different pathways

    PubMed Central

    Surova, Lyubov; Sherstneva, Oksana; Vodeneev, Vladimir; Sukhov, Vladimir

    2016-01-01

    ABSTRACT Local burning is known to generate and propagate variation potential (VP) in plants. VP affects different physiological processes, including reducing heat-related damage to photosystem I (PSI). We investigated mechanisms of the process. Photosynthesis parameters were measured with Dual-PAM-100 and GFS-3000. VP was induced by burning the first mature leaf and then waiting 5, 10, 15, or 20 min to initiate heating of the second mature leaf. Photosystems activities in the second leaf were investigated at 15 and 135 min after heating. In the absence of VP induction, when incubation in hot water (5 min) was used for heating the intact second leaf, PSI and PSII activities decreased after incubation at both exposure temperatures (45°C and 50°C). When local burning of the first leaf induced VP propagation into the second leaf, reduced photosynthesis (PSI) was observed. Arrival of VP in the second leaf prior to hot water incubation at 50°C decreased heating-induced suppression of PSI activity when measured 15 and 135 min later. Dependence of PSI activity on the time interval (5, 10, 15, or 20 min) between VP induction and heating of the second leaf was dissimilar at 15 and 135 min. Heat-induced suppression of PSII activity in the second leaf was stimulated after VP induction. In contrast, the effect of VP on PSI and PSII damage was weak when leaf 2 was heated at 45°C. VP-induced decrease of PSI activity suppression at 15 min after heating was correlated with stimulation of PSII activity suppression, but increase of PSI activity at 135 min after heating was not related to PSII activity. Thus, our results suggest the possibility of 2 different pathways of VP-induced decrease of heat-related PSI damage. PMID:26853242

  7. A Miniature Bioassay for Testing the Acute Phytotoxicity of Photosystem II Herbicides on Seagrass

    PubMed Central

    Wilkinson, Adam D.; Collier, Catherine J.; Flores, Florita; Mercurio, Phil; O’Brien, Jake; Ralph, Peter J.; Negri, Andrew P.

    2015-01-01

    Photosystem II (PSII) herbicides have been detected in nearshore tropical waters such as those of the Great Barrier Reef and may add to the pressure posed by runoff containing sediments and nutrients to threatened seagrass habitats. There is a growing number of studies into the potential effects of herbicides on seagrass, generally using large experimental setups with potted plants. Here we describe the successful development of an acute 12-well plate phytotoxicity assay for the PSII herbicide Diuron using isolated Halophila ovalis leaves. Fluorescence images demonstrated Diuron affected the entire leaf surface evenly and responses were not influenced by isolating leaves from the plant. The optimum exposure duration was 24 h, by which time the inhibition of effective quantum yield of PSII (∆F/Fm’) was highest and no deterioration of photosystems was evident in control leaves. The inhibition of ∆F/Fm’ by Diuron in isolated H. ovalis leaves was identical to both potted and hydroponically grown plants (with leaves remaining attached to rhizomes), indicating similar reductions in photosynthetic activity in these acute well-plate assays. The sensitivity of the assay was not influenced by irradiance (range tested 40 to 400 μmol photons m-2 s-1). High irradiance, however, caused photo-oxidative stress in H. ovalis and this generally impacted in an additive or sub-additive way with Diuron to damage PSII. The bioassay using isolated leaves is more rapid, uses far less biological material and does not rely on specialised aquarium facilities in comparison with assays using potted plants. The development and validation of this sensitive bioassay will be useful to reliably screen and monitor the phytotoxicity of existing and emerging PSII herbicides and contribute to risk assessments and water quality guideline development in the future. PMID:25674791

  8. Excess manganese differentially inhibits photosystem I versus II in Arabidopsis thaliana.

    PubMed

    Millaleo, R; Reyes-Díaz, M; Alberdi, M; Ivanov, A G; Krol, M; Hüner, N P A

    2013-01-01

    The effects of exposure to increasing manganese concentrations (50-1500 µM) from the start of the experiment on the functional performance of photosystem II (PSII) and photosystem I (PSI) and photosynthetic apparatus composition of Arabidopsis thaliana were compared. In agreement with earlier studies, excess Mn caused minimal changes in the PSII photochemical efficiency measured as F(v)/F(m), although the characteristic peak temperature of the S(2/3)Q(B) (-) charge recombinations was shifted to lower temperatures at the highest Mn concentration. SDS-PAGE and immunoblot analyses also did not exhibit any significant change in the relative abundance of PSII-associated polypeptides: PSII reaction centre protein D1, Lhcb1 (major light-harvesting protein of LHCII complex), and PsbO (OEC33, a 33 kDa protein of the oxygen-evolving complex). In addition, the abundance of Rubisco also did not change with Mn treatments. However, plants grown under excess Mn exhibited increased susceptibility to PSII photoinhibition. In contrast, in vivo measurements of the redox transients of PSI reaction centre (P700) showed a considerable gradual decrease in the extent of P700 photooxidation (P700(+)) under increased Mn concentrations compared to control. This was accompanied by a slower rate of P700(+) re-reduction indicating a downregulation of the PSI-dependent cyclic electron flow. The abundance of PSI reaction centre polypeptides (PsaA and PsaB) in plants under the highest Mn concentration was also significantly lower compared to the control. The results demonstrate for the first time that PSI is the major target of Mn toxicity within the photosynthetic apparatus of Arabidopsis plants. The possible involvement mechanisms of Mn toxicity targeting specifically PSI are discussed.

  9. Excess manganese differentially inhibits photosystem I versus II in Arabidopsis thaliana

    PubMed Central

    Alberdi, M.

    2013-01-01

    The effects of exposure to increasing manganese concentrations (50–1500 µM) from the start of the experiment on the functional performance of photosystem II (PSII) and photosystem I (PSI) and photosynthetic apparatus composition of Arabidopsis thaliana were compared. In agreement with earlier studies, excess Mn caused minimal changes in the PSII photochemical efficiency measured as Fv/Fm, although the characteristic peak temperature of the S2/3QB – charge recombinations was shifted to lower temperatures at the highest Mn concentration. SDS-PAGE and immunoblot analyses also did not exhibit any significant change in the relative abundance of PSII-associated polypeptides: PSII reaction centre protein D1, Lhcb1 (major light-harvesting protein of LHCII complex), and PsbO (OEC33, a 33kDa protein of the oxygen-evolving complex). In addition, the abundance of Rubisco also did not change with Mn treatments. However, plants grown under excess Mn exhibited increased susceptibility to PSII photoinhibition. In contrast, in vivo measurements of the redox transients of PSI reaction centre (P700) showed a considerable gradual decrease in the extent of P700 photooxidation (P700+) under increased Mn concentrations compared to control. This was accompanied by a slower rate of P700+ re-reduction indicating a downregulation of the PSI-dependent cyclic electron flow. The abundance of PSI reaction centre polypeptides (PsaA and PsaB) in plants under the highest Mn concentration was also significantly lower compared to the control. The results demonstrate for the first time that PSI is the major target of Mn toxicity within the photosynthetic apparatus of Arabidopsis plants. The possible involvement mechanisms of Mn toxicity targeting specifically PSI are discussed. PMID:23183256

  10. Photoinhibition of photosystem I in a pea mutant with altered LHCII organization.

    PubMed

    Ivanov, A G; Morgan-Kiss, R M; Krol, M; Allakhverdiev, S I; Zanev, Yu; Sane, P V; Huner, N P A

    2015-11-01

    Comparative analysis of in vivo chlorophyll fluorescence imaging revealed that photosystem II (PSII) photochemical efficiency (Fv/Fm) of leaves of the Costata 2/133 pea mutant with altered pigment composition and decreased level of oligomerization of the light harvesting chlorophyll a/b-protein complexes (LHCII) of PSII (Dobrikova et al., 2000; Ivanov et al., 2005) did not differ from that of WT. In contrast, photosystem I (PSI) activity of the Costata 2/133 mutant measured by the far-red (FR) light inducible P700 (P700(+)) signal exhibited 39% lower steady state level of P700(+), a 2.2-fold higher intersystem electron pool size (e(-)/P700) and higher rate of P700(+) re-reduction, which indicate an increased capacity for PSI cyclic electron transfer (CET) in the Costata 2/133 mutant than WT. The mutant also exhibited a limited capacity for state transitions. The lower level of oxidizable P700 (P700(+)) is consistent with a lower amount of PSI related chlorophyll protein complexes and lower abundance of the PsaA/PsaB heterodimer, PsaD and Lhca1 polypeptides in Costata 2/133 mutant. Exposure of WT and the Costata 2/133 mutant to high light stress resulted in a comparable photoinhibition of PSII measured in vivo, although the decrease of Fv/Fm was modestly higher in the mutant plants. However, under the same photoinhibitory conditions PSI photochemistry (P700(+)) measured as ΔA820-860 was inhibited to a greater extent (50%) in the Costata 2/133 mutant than in the WT (22%). This was accompanied by a 50% faster re-reduction rate of P700(+) in the dark indicating a higher capacity for CET around PSI in high light treated mutant leaves. The role of chloroplast thylakoid organization on the stability of the PSI complex and its susceptibility to high light stress is discussed.

  11. A miniature bioassay for testing the acute phytotoxicity of photosystem II herbicides on seagrass.

    PubMed

    Wilkinson, Adam D; Collier, Catherine J; Flores, Florita; Mercurio, Phil; O'Brien, Jake; Ralph, Peter J; Negri, Andrew P

    2015-01-01

    Photosystem II (PSII) herbicides have been detected in nearshore tropical waters such as those of the Great Barrier Reef and may add to the pressure posed by runoff containing sediments and nutrients to threatened seagrass habitats. There is a growing number of studies into the potential effects of herbicides on seagrass, generally using large experimental setups with potted plants. Here we describe the successful development of an acute 12-well plate phytotoxicity assay for the PSII herbicide Diuron using isolated Halophila ovalis leaves. Fluorescence images demonstrated Diuron affected the entire leaf surface evenly and responses were not influenced by isolating leaves from the plant. The optimum exposure duration was 24 h, by which time the inhibition of effective quantum yield of PSII (∆F/F(m)') was highest and no deterioration of photosystems was evident in control leaves. The inhibition of ∆F/F(m)' by Diuron in isolated H. ovalis leaves was identical to both potted and hydroponically grown plants (with leaves remaining attached to rhizomes), indicating similar reductions in photosynthetic activity in these acute well-plate assays. The sensitivity of the assay was not influenced by irradiance (range tested 40 to 400 μmol photons m(-2) s(-1)). High irradiance, however, caused photo-oxidative stress in H. ovalis and this generally impacted in an additive or sub-additive way with Diuron to damage PSII. The bioassay using isolated leaves is more rapid, uses far less biological material and does not rely on specialised aquarium facilities in comparison with assays using potted plants. The development and validation of this sensitive bioassay will be useful to reliably screen and monitor the phytotoxicity of existing and emerging PSII herbicides and contribute to risk assessments and water quality guideline development in the future. PMID:25674791

  12. Mechanism of Interaction of Al3+ with the Proteins Composition of Photosystem II

    PubMed Central

    Hasni, Imed; Yaakoubi, Hnia; Hamdani, Saber; Tajmir-Riahi, Heidar-Ali; Carpentier, Robert

    2015-01-01

    The inhibitory effect of Al3+on photosystem II (PSII) electron transport was investigated using several biophysical and biochemical techniques such as oxygen evolution, chlorophyll fluorescence induction and emission, SDS-polyacrylamide and native green gel electrophoresis, and FTIR spectroscopy. In order to understand the mechanism of its inhibitory action, we have analyzed the interaction of this toxic cation with proteins subunits of PSII submembrane fractions isolated from spinach. Our results show that Al 3+, especially above 3 mM, strongly inhibits oxygen evolution and affects the advancement of the S states of the Mn4O5Ca cluster. This inhibition was due to the release of the extrinsic polypeptides and the disorganization of the Mn4O5Ca cluster associated with the oxygen evolving complex (OEC) of PSII. This fact was accompanied by a significant decline of maximum quantum yield of PSII (Fv/Fm) together with a strong damping of the chlorophyll a fluorescence induction. The energy transfer from light harvesting antenna to reaction centers of PSII was impaired following the alteration of the light harvesting complex of photosystem II (LHCII). The latter result was revealed by the drop of chlorophyll fluorescence emission spectra at low temperature (77 K), increase of F0 and confirmed by the native green gel electrophoresis. FTIR measurements indicated that the interaction of Al 3+ with the intrinsic and extrinsic polypeptides of PSII induces major alterations of the protein secondary structure leading to conformational changes. This was reflected by a major reduction of α-helix with an increase of β-sheet and random coil structures in Al 3+-PSII complexes. These structural changes are closely related with the functional alteration of PSII activity revealed by the inhibition of the electron transport chain of PSII. PMID:25806795

  13. Photoinhibition of photosystem I in a pea mutant with altered LHCII organization.

    PubMed

    Ivanov, A G; Morgan-Kiss, R M; Krol, M; Allakhverdiev, S I; Zanev, Yu; Sane, P V; Huner, N P A

    2015-11-01

    Comparative analysis of in vivo chlorophyll fluorescence imaging revealed that photosystem II (PSII) photochemical efficiency (Fv/Fm) of leaves of the Costata 2/133 pea mutant with altered pigment composition and decreased level of oligomerization of the light harvesting chlorophyll a/b-protein complexes (LHCII) of PSII (Dobrikova et al., 2000; Ivanov et al., 2005) did not differ from that of WT. In contrast, photosystem I (PSI) activity of the Costata 2/133 mutant measured by the far-red (FR) light inducible P700 (P700(+)) signal exhibited 39% lower steady state level of P700(+), a 2.2-fold higher intersystem electron pool size (e(-)/P700) and higher rate of P700(+) re-reduction, which indicate an increased capacity for PSI cyclic electron transfer (CET) in the Costata 2/133 mutant than WT. The mutant also exhibited a limited capacity for state transitions. The lower level of oxidizable P700 (P700(+)) is consistent with a lower amount of PSI related chlorophyll protein complexes and lower abundance of the PsaA/PsaB heterodimer, PsaD and Lhca1 polypeptides in Costata 2/133 mutant. Exposure of WT and the Costata 2/133 mutant to high light stress resulted in a comparable photoinhibition of PSII measured in vivo, although the decrease of Fv/Fm was modestly higher in the mutant plants. However, under the same photoinhibitory conditions PSI photochemistry (P700(+)) measured as ΔA820-860 was inhibited to a greater extent (50%) in the Costata 2/133 mutant than in the WT (22%). This was accompanied by a 50% faster re-reduction rate of P700(+) in the dark indicating a higher capacity for CET around PSI in high light treated mutant leaves. The role of chloroplast thylakoid organization on the stability of the PSI complex and its susceptibility to high light stress is discussed. PMID:26321219

  14. Phylogenetic analyses of the core antenna domain: investigating the origin of photosystem I.

    PubMed

    Mix, Lucas J; Haig, David; Cavanaugh, Colleen M

    2005-02-01

    Phototrophy, the conversion of light to biochemical energy, occurs throughout the Bacteria and plants, however, debate continues over how different phototrophic mechanisms and the bacteria that contain them are related. There are two types of phototrophic mechanisms in the Bacteria: reaction center type 1 (RC1) has core and core antenna domains that are parts of a single polypeptide, whereas reaction center type 2 (RC2) is composed of short core proteins without antenna domains. In cyanobacteria, RC2 is associated with separate core antenna proteins that are homologous to the core antenna domains of RC1. We reconstructed evolutionary relationships among phototrophic mechanisms based on a phylogeny of core antenna domains/proteins. Core antenna domains of 46 polypeptides were aligned, including the RC1 core proteins of heliobacteria, green sulfur bacteria, and photosystem I (PSI) of cyanobacteria and plastids, plus core antenna proteins of photosystem II (PSII) from cyanobacteria and plastids. Maximum likelihood, parsimony, and neighbor joining methods all supported a single phylogeny in which PSII core antenna proteins (PsbC, PsbB) arose within the cyanobacteria from duplications of the RC1-associated core antenna domains and accessory antenna proteins (IsiA, PcbA, PcbC) arose from duplications of PsbB. The data indicate an evolutionary history of RC1 in which an initially homodimeric reaction center was vertically transmitted to green sulfur bacteria, heliobacteria, and an ancestor of cyanobacteria. A heterodimeric RC1 (=PSI) then arose within the cyanobacterial lineage. In this scenario, the current diversity of core antenna domains/proteins is explained without a need to invoke horizontal transfer.

  15. Synechocystis sp PCC 6803 strains lacking photosystem I and phycobilisome function.

    PubMed Central

    Shen, G; Boussiba, S; Vermaas, W F

    1993-01-01

    To design an in vivo system allowing detailed analysis of photosystem II (PSII) complexes without significant interference from other pigment complexes, part of the psaAB operon coding for the core proteins of photosystem I (PSI) and part of the apcE gene coding for the anchor protein linking the phycobilisome to the thylakoid membrane were deleted from the genome of the cyanobacterium Synechocystis sp strain PCC 6803. Upon transformation and segregation at low light intensity (5 microE m-2 sec-1), a PSI deletion strain was obtained that is light tolerant and grows reasonably well under photoheterotrophic conditions at 5 microE m-2 sec-1 (doubling time approximately 28 hr). Subsequent inactivation of apcE by an erythromycin resistance marker led to reduction of the phycobilin-to-chlorophyll ratio and to a further decrease in light sensitivity. The resulting PSI-less/apcE- strain grew photoheterotrophically at normal light intensity (50 microE m-2 sec-1) with a doubling time of 18 hr. Deletion of apcE in the wild type resulted in slow photoautotrophic growth. The remaining phycobilins in apcE- strains were inactive in transferring light energy to PSII. Cells of both the PSI-less and PSI-less/apcE- strains had an approximately sixfold enrichment of PSII on a chlorophyll basis and were as active in oxygen evolution (on a per PSII basis) as the wild type at saturating light intensity. Both PSI-less strains described here are highly appropriate both for detailed PSII studies and as background strains to analyze site- and region-directed PSII mutants in vivo. PMID:8305875

  16. δ-Conotoxin SuVIA suggests an evolutionary link between ancestral predator defence and the origin of fish-hunting behaviour in carnivorous cone snails

    PubMed Central

    Jin, Ai-Hua; Israel, Mathilde R.; Inserra, Marco C.; Smith, Jennifer J.; Lewis, Richard J.; Alewood, Paul F.; Vetter, Irina; Dutertre, Sébastien

    2015-01-01

    Some venomous cone snails feed on small fishes using an immobilizing combination of synergistic venom peptides that target Kv and Nav channels. As part of this envenomation strategy, δ-conotoxins are potent ichtyotoxins that enhance Nav channel function. δ-Conotoxins belong to an ancient and widely distributed gene superfamily, but any evolutionary link from ancestral worm-eating cone snails to modern piscivorous species has not been elucidated. Here, we report the discovery of SuVIA, a potent vertebrate-active δ-conotoxin characterized from a vermivorous cone snail (Conus suturatus). SuVIA is equipotent at hNaV1.3, hNaV1.4 and hNaV1.6 with EC50s in the low nanomolar range. SuVIA also increased peak hNaV1.7 current by approximately 75% and shifted the voltage-dependence of activation to more hyperpolarized potentials from –15 mV to –25 mV, with little effect on the voltage-dependence of inactivation. Interestingly, the proximal venom gland expression and pain-inducing effect of SuVIA in mammals suggest that δ-conotoxins in vermivorous cone snails play a defensive role against higher order vertebrates. We propose that δ-conotoxins originally evolved in ancestral vermivorous cones to defend against larger predators including fishes have been repurposed to facilitate a shift to piscivorous behaviour, suggesting an unexpected underlying mechanism for this remarkable evolutionary transition. PMID:26156767

  17. Exploring the diploid wheat ancestral A genome through sequence comparison at the High-Molecular-Weight glutenin locus region

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurate assembly of its genome. To explore the utility of ancestral diploid species o...

  18. Intersection of opposing pedagogical frameworks: Native Hawaiian ancestral stories and scientific inquiry in a high school science class

    NASA Astrophysics Data System (ADS)

    Kanahele-Mossman, Huihui

    Inquiry is defined as "an examination into facts and principles." In science education science inquiry is a process through which important discoveries are made by students through scientific methodology. The most important step in this process is forming the right question. The questions formed by students are usually the wrong questions which deem the remainder of the inquiry process impotent. This research will look at the pedagogy of ancestral stories for a solution. For the researcher, ancestral stories were a source of wonderment and learning not only from the lessons the stories revealed but mainly from the questions that still remained after the stories were told. Questions such as "why does the eel only swim near that part?", or "why does the story only talk about the uhu?" are examples of questions that remained after experiencing an ancestral narrative. The research questions were composed for the purpose of finding compatibility between the two pedagogies. The first research question which reads "how can Native Hawaiian ancestral stories encourage an increased level of student driven interactions at all levels of feedback from Native Hawaiian students in science classroom" focuses the research on the level of student feedback that initiate questions. Question two which reads "how can teachers of Native Hawaiian students facilitate the construction of science inquiry projects from ancestral stories" addresses the skill of the teacher and imbeds the concept of pedagogical knowledge into the literature. The last research question "how do analysis and discussion of the stories connect Native Hawaiian students to their ancestral intelligence" examines the role of identity and identity to ancestral intelligence. The method intended for this research was Grounded theory which allows the researcher to develop principles, concepts and theories based on the data presented. Another method utilized in this research is an undocumented but culturally imbedded method

  19. Higher plant photosystem II light-harvesting antenna, not the reaction center, determines the excited-state lifetime-both the maximum and the nonphotochemically quenched.

    PubMed

    Belgio, Erica; Johnson, Matthew P; Jurić, Snježana; Ruban, Alexander V

    2012-06-20

    The maximum chlorophyll fluorescence lifetime in isolated photosystem II (PSII) light-harvesting complex (LHCII) antenna is 4 ns; however, it is quenched to 2 ns in intact thylakoid membranes when PSII reaction centers (RCIIs) are closed (Fm). It has been proposed that the closed state of RCIIs is responsible for the quenching. We investigated this proposal using a new, to our knowledge, model system in which the concentration of RCIIs was highly reduced within the thylakoid membrane. The system was developed in Arabidopsis thaliana plants under long-term treatment with lincomycin, a chloroplast protein synthesis inhibitor. The treatment led to 1), a decreased concentration of RCIIs to 10% of the control level and, interestingly, an increased antenna component; 2), an average reduction in the yield of photochemistry to 0.2; and 3), an increased nonphotochemical chlorophyll fluorescence quenching (NPQ). Despite these changes, the average fluorescence lifetimes measured in Fm and Fm' (with NPQ) states were nearly identical to those obtained from the control. A 77 K fluorescence spectrum analysis of treated PSII membranes showed the typical features of preaggregation of LHCII, indicating that the state of LHCII antenna in the dark-adapted photosynthetic membrane is sufficient to determine the 2 ns Fm lifetime. Therefore, we conclude that the closed RCs do not cause quenching of excitation in the PSII antenna, and play no role in the formation of NPQ.

  20. Primary light harvesting system: the relationship of phycobilisomes to Photosystem I and II. Progress report, September 1983-May 1985. [Porphyridium cruentum

    SciTech Connect

    Gantt, E.

    1985-01-01

    The association of phycobilisomes, the primary photosynthetic antennae systems in red algae and cyanobacteria, with Photosystem II, previously expected from energy transfer measurements, has now been established. Photosystem-II-phycobilisome particles from the red alga Porphyridium cruentum were isolated. These particles lack photosystem I components, have high O/sub 2/-evolution rates, which are sensitive to DCMU and are abolished by 10 mM hydroxylamine. The phycobilisomes were functionally attached, since green light which is absorbed by phycoerythrin was most effective in driving O/sub 2/-evolution and 2,6-dichlorophenol indophenol reduction. The majority of the particles appear by electron microscopy to retain small membrane fragments at their base. Selective removal of the phycobilisome components results in the enrichment of a 50 kD polypeptide which is considered to be the putative photosystem II reaction center. 14 refs.

  1. In vivo photosystem I reduction in thermophilic and mesophilic cyanobacteria: The thermal resistance of the process is limited by factors other than the unfolding of the partners

    SciTech Connect

    Duran, Raul V.; Hervas, Manuel; Rosa, Miguel A. de la; Navarro, Jose A. . E-mail: jnavarro@ibvf.csic.es

    2005-08-19

    Photosystem I reduction by plastocyanin and cytochrome c {sub 6} in cyanobacteria has been extensively studied in vitro, but much less information is provided on this process inside the cell. Here, we report an analysis of the electron transfer from both plastocyanin and cytochrome c {sub 6} to photosystem I in intact cells of several cyanobacterial species, including a comparative study of the temperature effect in mesophilic and thermophilic organisms. Our data show that cytochrome c {sub 6} reduces photosystem I by following a reaction mechanism involving complex formation, whereas the copper-protein follows a simpler collisional mechanism. These results contrast with previous kinetic studies in vitro. The effect of temperature on photosystem I reduction leads us to conclude that the thermal resistance of this process is determined by factors other than the proper stability of the protein partners.

  2. Effect of photosystem I inactivation on chlorophyll a fluorescence induction in wheat leaves: Does activity of photosystem I play any role in OJIP rise?

    PubMed

    Zivcak, Marek; Brestic, Marian; Kunderlikova, Kristyna; Olsovska, Katarina; Allakhverdiev, Suleyman I

    2015-11-01

    Interpretation of the fast chlorophyll a fluorescence induction is still a subject of continuing discussion. One of the contentious issues is the influence of photosystem I (PSI) activity on the kinetics of the thermal JIP-phase of OJIP rise. To demonstrate this influence, we realized a series of measurements in wheat leaves subjected to PSI photoinactivation by the sequence of red saturation pulses (15,000 μmol photons m(-2) s(-1) for 0.3 s, every 10 s) applied in darkness. Such a treatment led to a moderate decrease of maximum quantum efficiency of PSII (by ~8%), but a strong decrease of the number of oxidizable PSI (by ~55%), which considerably limited linear electron transport and CO2 assimilation. Surprisingly, the PSI photoinactivation had low effects on OJIP kinetics of variable fluorescence. In particular, the amplitude of variable fluorescence of IP-step (ΔVIP), which has been considered to be a measure of PSI content, was not decreased, despite the low content of photooxidizable PSI. On the other hand, the slower relaxation of chlorophyll fluorescence after saturation pulse as well as the results of the double-hit method suggest that PSI inactivation treatment led to an increase of the fraction of QB-nonreducing PSII reaction centers. Our results somewhat challenge the mainstream interpretations of JIP-thermal phase, and at least suggest that the IP amplitude cannot serve to estimate reliably the PSI content or the PSI to PSII ratio. Moreover, these results recommend the use of the novel method of PSI inactivation, which might help clarify some important issues needed for the correct understanding of the OJIP fluorescence rise.

  3. Stoichiometry of Photosystem I, Photosystem II, and Phycobilisomes in the Red Alga Porphyridium cruentum as a Function of Growth Irradiance 1

    PubMed Central

    Cunningham, Francis X.; Dennenberg, Ronald J.; Mustardy, Laszlo; Jursinic, Paul A.; Gantt, Elisabeth

    1989-01-01

    Cells of the red alga Porphyridium cruentum (ATCC 50161) exposed to increasing growth irradiance exhibited up to a three-fold reduction in photosystems I and II (PSI and PSII) and phycobilisomes but little change in the relative numbers of these components. Batch cultures of P. cruentum were grown under four photon flux densities of continuous white light; 6 (low light, LL), 35 (medium light, ML), 180 (high light, HL), and 280 (very high light, VHL) microeinsteins per square meter per second and sampled in the exponential phase of growth. Ratios of PSII to PSI ranged between 0.43 and 0.54. About three PSII centers per phycobilisome were found, regardless of growth irradiance. The phycoerythrin content of phycobilisomes decreased by about 25% for HL and VHL compared to LL and ML cultures. The unit sizes of PSI (chlorophyll/P700) and PSII (chlorophyll/QA) decreased by about 20% with increase in photon flux density from 6 to 280 microeinsteins per square meter per second. A threefold reduction in cell content of chlorophyll at the higher photon flux densities was accompanied by a twofold reduction in β-carotene, and a drastic reduction in thylakoid membrane area. Cell content of zeaxanthin, the major carotenoid in P. cruentum, did not vary with growth irradiance, suggesting a role other than light-harvesting. HL cultures had a growth rate twice that of ML, eight times that of LL, and slightly greater than that of VHL cultures. Cell volume increased threefold from LL to VHL, but volume of the single chloroplast did not change. From this study it is evident that a relatively fixed stoichiometry of PSI, PSII, and phycobilisomes is maintained in the photosynthetic apparatus of this red alga over a wide range of growth irradiance. Images Figure 1 PMID:16667130

  4. Chromosome evolution in kangaroos (Marsupialia: Macropodidae): cross species chromosome painting between the tammar wallaby and rock wallaby spp. with the 2n = 22 ancestral macropodid karyotype.

    PubMed

    O'Neill, R J; Eldridge, M D; Toder, R; Ferguson-Smith, M A; O'Brien, P C; Graves, J A

    1999-06-01

    Marsupial mammals show extraordinary karyotype stability, with 2n = 14 considered ancestral. However, macropodid marsupials (kangaroos and wallabies) exhibit a considerable variety of karyotypes, with a hypothesised ancestral karyotype of 2n = 22. Speciation and karyotypic diversity in rock wallabies (Petrogale) is exceptional. We used cross species chromosome painting to examine the chromosome evolution between the tammar wallaby (2n = 16) and three 2n = 22 rock wallaby species groups with the putative ancestral karyotype. Hybridization of chromosome paints prepared from flow sorted chromosomes of the tammar wallaby to Petrogale spp., showed that this ancestral karyotype is largely conserved among 2n = 22 rock wallaby species, and confirmed the identity of ancestral chromosomes which fused to produce the bi-armed chromosomes of the 2n = 16 tammar wallaby. These results illustrate the fission-fusion process of karyotype evolution characteristic of the kangaroo group.

  5. Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction

    NASA Astrophysics Data System (ADS)

    Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Schneider, P.; Lieberman, D.; Holden, T.; Cheung, T.

    2013-09-01

    A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene

  6. Trans-Ancestral Studies Fine Map the SLE-Susceptibility Locus TNFSF4

    PubMed Central

    Manku, Harinder; Langefeld, Carl D.; Guerra, Sandra G.; Malik, Talat H.; Alarcon-Riquelme, Marta; Anaya, Juan-Manuel; Bae, Sang-Cheol; Boackle, Susan A.; Brown, Elizabeth E.; Criswell, Lindsey A.; Freedman, Barry I.; Gaffney, Patrick M.; Gregersen, Peter A.; Guthridge, Joel M.; Han, Sang-Hoon; Harley, John B.; Jacob, Chaim O.; James, Judith A.; Kamen, Diane L.; Kaufman, Kenneth M.; Kelly, Jennifer A.; Martin, Javier; Merrill, Joan T.; Moser, Kathy L.; Niewold, Timothy B.; Park, So-Yeon; Pons-Estel, Bernardo A.; Sawalha, Amr H.; Scofield, R. Hal; Shen, Nan; Stevens, Anne M.; Sun, Celi; Gilkeson, Gary S.; Edberg, Jeff C.; Kimberly, Robert P.; Nath, Swapan K.; Tsao, Betty P.; Vyse, Tim J.

    2013-01-01

    We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls), African-Americans (AA) (1529, 2048) and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122). The best evidence of association comes from two adjacent markers: rs2205960-T (P = 1.71×10−34, OR = 1.43[1.26–1.60]) and rs1234317-T (P = 1.16×10−28, OR = 1.38[1.24–1.54]). Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5′ region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3) imputation. Conditional regression analyses delineate the 5′ risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-κBp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-κB interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and

  7. Physico-chemical property of rare earths-effects on the energy regulation of photosystem II in Arabidopsis thaliana.

    PubMed

    Xiaoqing, Liu; Hao, Huang; Chao, Liu; Min, Zhou; Fashui, Hong

    2009-08-01

    Photosystem II (PSII) from Arabidopsis thaliana treated by lanthanum (La(3+)), cerium (Ce(3+)), and neodymium (Nd(3+)) were isolated to investigate the effects of 4f electron characteristics and alternation valence of rare earth elements (REEs) on PSII function regulation comparatively. Results showed that REE treatment could induce the generous expression of LhcII b in A. thaliana and increase the content of light-harvesting complex II and its trimer on the thylakoid membrane significantly. Meanwhile, the light absorption in the red and blue region and fluorescence quantum yield near 683 nm were obviously increased; oxygen evolution rate was greatly improved too, suggesting that REEs could enhance the efficiency of light absorption, regulate excitation energy distribution from photosystem I (PSI) to PSII, and thus increase the activity of photochemical reaction and oxygen evolution accordingly. The efficiency order of the four treatments was Ce(3+) > Nd(3+) > La(3+) > control.

  8. Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre

    NASA Astrophysics Data System (ADS)

    Zhang, Lu; Silva, Daniel-Adriano; Zhang, Houdao; Yue, Alexander; Yan, Yijing; Huang, Xuhui

    2014-06-01

    One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis.

  9. Photosystem II-phycobilisome preparation from the red alga, Porphyridium cruentum: oxygen evolution, ultrastructure, and polypeptide resolution

    SciTech Connect

    Clement-Metral, J.D.; Gantt, E.; Redlinger, T.

    1985-04-01

    The photosystem II-phycobilisome preparation, isolated by lauryldimethyl amine oxide treatment, had a greatly reduced chlorophyll content, with an average ratio of 90 chlorophyll a/phycobilisome as compared to approximately 1200 Chl/phycobilisome in unfractionated thylakoids. P700 was not detected in the particles. By electron microsopy the preparations were relatively homogeneous and were generally devoid of chloroplast membranes. In negatively stained preparations phycobilisome particles were seen often in clusters of two and three, probably due to retention of hydrophobic thylakoid fragments. The preparation was deficient in photosystem I chlorophyll complexes, but enriched in polypeptides of 85 to 92, approx. 43, and approx. 26 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The 43- and 26-kDa polypeptides are attributable to the PS II core and the oxygen-evolving complex, respectively. 27 references, 3 figures, 2 tables.

  10. Initial electron donor and acceptor in isolated Photosystem II reaction centers identified with femtosecond mid-IR spectroscopy

    PubMed Central

    Groot, Marie Louise; Pawlowicz, Natalia P.; van Wilderen, Luuk J. G. W.; Breton, Jacques; van Stokkum, Ivo H. M.; van Grondelle, Rienk

    2005-01-01

    Despite the apparent similarity between the plant Photosystem II reaction center (RC) and its purple bacterial counterpart, we show in this work that the mechanism of charge separation is very different for the two photosynthetic RCs. By using femtosecond visible-pump–mid-infrared probe spectroscopy in the region of the chlorophyll ester and keto modes, between 1,775 and 1,585 cm–1, with 150-fs time resolution, we show that the reduction of pheophytin occurs on a 0.6- to 0.8-ps time scale, whereas P+, the precursor state for water oxidation, is formed after ≈6 ps. We conclude therefore that in the Photosystem II RC the primary charge separation occurs between the “accessory chlorophyll” ChlD1 and the pheophytin on the so-called active branch. PMID:16135567

  11. Novel structural aspect of the diatom thylakoid membrane: lateral segregation of photosystem I under red-enhanced illumination

    PubMed Central

    Bína, David; Herbstová, Miroslava; Gardian, Zdenko; Vácha, František; Litvín, Radek

    2016-01-01

    Spatial segregation of photosystems in the thylakoid membrane (lateral heterogeneity) observed in plants and in the green algae is usually considered to be absent in photoautotrophs possessing secondary plastids, such as diatoms. Contrary to this assumption, here we show that thylakoid membranes in the chloroplast of a marine diatom, Phaeodactylum tricornutum, contain large areas occupied exclusively by a supercomplex of photosystem I (PSI) and its associated Lhcr antenna. These membrane areas, hundreds of nanometers in size, comprise hundreds of tightly packed PSI-antenna complexes while lacking other components of the photosynthetic electron transport chain. Analyses of the