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Sample records for proposed ancestral photosystem

  1. Photosystem II

    ScienceCinema

    James Barber

    2010-09-01

    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. DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications

    PubMed Central

    Ratan, Aakrosh; Raney, Brian J.; Suh, Bernard B.; Zhang, Louxin; Miller, Webb; Haussler, David

    2008-01-01

    Abstract Accurately reconstructing the large-scale gene order in an ancestral genome is a critical step to better understand genome evolution. In this paper, we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the ancestral orders by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to validate the algorithm. We also applied the method to reconstruct the ancestral chromosome X of placental mammals and the ancestral genomes of the ciliate Paramecium tetraurelia. PMID:18774902

  3. Analysis of cyanobacterial photosystem 2 genes by cloning and mutagenesis

    SciTech Connect

    Not Available

    1989-01-01

    The major goal of this current proposal was to isolate, clone, sequence and mutagenize specific proteins associated with the photosynthetic membrane and photosystem II in cyanobacteria. The analysis of photosystem II proteins led to investigate the growth of cyanobacteria under iron-deficient conditions and to detect a number of new proteins involved in the photosynthetic membrane. This work led to isolate proteins that are localized in the cytoplasmic membrane or in the cell wall membrane. 15 refs.

  4. Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods

    NASA Astrophysics Data System (ADS)

    Tannier, Eric

    In 2006, a debate has risen on the question of the efficiency of bioinformatics methods to reconstruct mammalian ancestral genomes. Three years later, Gordon et al. (PLoS Genetics, 5(5), 2009) chose not to use automatic methods to build up the genome of a 100 million year old Saccharomyces cerevisiae ancestor. Their manually constructed ancestor provides a reference genome to test whether automatic methods are indeed unable to approach confident reconstructions. Adapting several methodological frameworks to the same yeast gene order data, I discuss the possibilities, differences and similarities of the available algorithms for ancestral genome reconstructions. The methods can be classified into two types: local and global. Studying the properties of both helps to clarify what we can expect from their usage. Both methods propose contiguous ancestral regions that come very close (> 95% identity) to the manually predicted ancestral yeast chromosomes, with a good coverage of the extant genomes.

  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. Reconstruction of ancestral gene orders using intermediate genomes

    PubMed Central

    2015-01-01

    Background The problem of reconstructing ancestral genomes in a given phylogenetic tree arises in many different comparative genomics fields. Here, we focus on reconstructing the gene order of ancestral genomes, a problem that has been largely studied in the past 20 years, especially with the increasing availability of whole genome DNA sequences. There are two main approaches to this problem: event-based methods, that try to find the ancestral genomes that minimize the number of rearrangement events in the tree; and homology-based, that look for conserved structures, such as adjacent genes in the extant genomes, to build the ancestral genomes. Results We propose algorithms that use the concept of intermediate genomes, arising in optimal pairwise rearrangement scenarios. We show that intermediate genomes have combinatorial properties that make them easy to reconstruct, and develop fast algorithms with better reconstructed ancestral genomes than current event-based methods. The proposed framework is also designed to accept extra information, such as results from homology-based approaches, giving rise to combined algorithms with better results than the original methods. PMID:26451811

  7. 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,…

  8. Vibrational spectroscopy of photosystem I.

    PubMed

    Hastings, Gary

    2015-01-01

    Fourier transform infrared difference spectroscopy (FTIR DS) has been widely used to study the structural details of electron transfer cofactors (and their binding sites) in many types of photosynthetic protein complexes. This review focuses in particular on work that has been done to investigate the A₁cofactor in photosystem I photosynthetic reaction centers. A review of this subject area last appeared in 2006 [1], so only work undertaken since then will be covered here. Following light excitation of intact photosystem I particles the P700⁺A⁻(1) secondary radical pair state is formed within 100ps. This state decays within 300ns at room temperature, or 300μs at 77K. Given the short-lived nature of this state, it is not easily studied using "static" photo-accumulation FTIR difference techniques at either temperature. Time-resolved techniques are required. This article focuses on the use of time-resolved step-scan FTIR DS for the study of the P700⁺A⁻(1) state in intact photosystem I. Up until now, only our group has undertaken studies in this area. So, in this article, recent work undertaken in our lab is described, where we have used low-temperature (77K), microsecond time-resolved step-scan FTIR DS to study the P700⁺A⁻(1) state in photosystem I. In photosystem I a phylloquinone molecule occupies the A₁binding site. However, different quinones can be incorporated into the A1 binding site, and here work is described for photosystem I particles with plastoquinone-9, 2-phytyl naphthoquinone and 2-methyl naphthoquinone incorporated into the A₁binding site. Studies in which ¹⁸O isotope labeled phylloquinone has been incorporated into the A1 binding site are also discussed. To fully characterize PSI particles with different quinones incorporated into the A1 binding site nanosecond to millisecond visible absorption spectroscopy has been shown to be of considerable value, especially so when undertaken using identical samples under identical conditions

  9. Water oxidation chemistry of photosystem II.

    PubMed Central

    Vrettos, John S; Brudvig, Gary W

    2002-01-01

    The O(2)-evolving complex of photosystem II catalyses the light-driven four-electron oxidation of water to dioxygen in photosynthesis. In this article, the steps leading to photosynthetic O(2) evolution are discussed. Emphasis is given to the proton-coupled electron-transfer steps involved in oxidation of the manganese cluster by oxidized tyrosine Z (Y(*)(Z)), the function of Ca(2+) and the mechanism by which water is activated for formation of an O-O bond. Based on a consideration of the biophysical studies of photosystem II and inorganic manganese model chemistry, a mechanism for photosynthetic O(2) evolution is presented in which the O-O bond-forming step occurs via nucleophilic attack on an electron-deficient Mn(V)=O species by a calcium-bound water molecule. The proposed mechanism includes specific roles for the tetranuclear manganese cluster, calcium, chloride, Y(Z) and His190 of the D1 polypeptide. Recent studies of the ion selectivity of the calcium site in the O(2)-evolving complex and of a functional inorganic manganese model system that test key aspects of this mechanism are also discussed. PMID:12437878

  10. 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

  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. PMID:23653472

  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. 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.

  15. 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.

  16. Antenna complexes protect Photosystem I from Photoinhibition

    PubMed Central

    Alboresi, Alessandro; Ballottari, Matteo; Hienerwadel, Rainer; Giacometti, Giorgio M; Morosinotto, Tomas

    2009-01-01

    Background Photosystems are composed of two moieties, a reaction center and a peripheral antenna system. In photosynthetic eukaryotes the latter system is composed of proteins belonging to Lhc family. An increasing set of evidences demonstrated how these polypeptides play a relevant physiological function in both light harvesting and photoprotection. Despite the sequence similarity between antenna proteins associated with the two Photosystems, present knowledge on their physiological role is mostly limited to complexes associated to Photosystem II. Results In this work we analyzed the physiological role of Photosystem I antenna system in Arabidopsis thaliana both in vivo and in vitro. Plants depleted in individual antenna polypeptides showed a reduced capacity for photoprotection and an increased production of reactive oxygen species upon high light exposure. In vitro experiments on isolated complexes confirmed that depletion of antenna proteins reduced the resistance of isolated Photosystem I particles to high light and that the antenna is effective in photoprotection only upon the interaction with the core complex. Conclusion We show that antenna proteins play a dual role in Arabidopsis thaliana Photosystem I photoprotection: first, a Photosystem I with an intact antenna system is more resistant to high light because of a reduced production of reactive oxygen species and, second, antenna chlorophyll-proteins are the first target of high light damages. When photoprotection mechanisms become insufficient, the antenna chlorophyll proteins act as fuses: LHCI chlorophylls are degraded while the reaction center photochemical activity is maintained. Differences with respect to photoprotection strategy in Photosystem II, where the reaction center is the first target of photoinhibition, are discussed. PMID:19508723

  17. Balancing the two photosystems: photosynthetic electron transfer governs transcription of reaction centre genes in chloroplasts.

    PubMed Central

    Allen, J F; Pfannschmidt, T

    2000-01-01

    Chloroplasts are cytoplasmic organelles whose primary function is photosynthesis, but which also contain small, specialized and quasi-autonomous genetic systems. In photosynthesis, two energy converting photosystems are connected, electrochemically, in series. The connecting electron carriers are oxidized by photosystem I (PS I) and reduced by photosystem II (PS II). It has recently been shown that the oxidation reduction state of one connecting electron carrier, plastoquinone, controls transcription of chloroplast genes for reaction centre proteins of the two photosystems. The control counteracts the imbalance in electron transport that causes it: oxidized plastoquinone induces PS II and represses PS I; reduced plastoquinone induces PS I and represses PS II. This complementarity is observed both in vivo, using light favouring one or other photosystem, and in vitro, when site-specific electron transport inhibitors are added to transcriptionally and photosynthetically active chloroplasts. There is thus a transcriptional level of control that has a regulatory function similar to that of purely post-translational 'state transitions' in which the redistribution of absorbed excitation energy between photosystems is mediated by thylakoid membrane protein phosphorylation. The changes in rates of transcription that are induced by spectral changes in vivo can be detected even before the corresponding state transitions are complete, suggesting the operation of a branched pathway of redox signal transduction. These findings suggest a mechanism for adjustment of photosystem stoichiometry in which initial events involve a sensor of the redox state of plastoquinone, and may thus be the same as the initial events of state transitions. Redox control of chloroplast transcription is also consistent with the proposal that a direct regulatory coupling between electron transport and gene expression determines the function and composition of the chloroplast's extra-nuclear genetic

  18. Ancestral gene and "complementary" antibody dominate early ontogeny.

    PubMed

    Arend, Peter

    2013-05-01

    According to N.K. Jerne the somatic generation of immune recognition occurs in conjunction with germ cell evolution and precedes the formation of the zygote, i.e. operates before clonal selection. We propose that it is based on interspecies inherent, ancestral forces maintaining the lineage. Murine oogenesis may be offered as a model. So in C57BL/10BL sera an anti-A reactive, mercapto-ethanol sensitive glycoprotein of up to now unknown cellular origin, but exhibiting immunoglobulin M character, presents itself "complementary" to a syngeneic epitope, which encoded by histocompatibility gene A or meanwhile accepted ancestor of the ABO gene family, arises predominantly in ovarian tissue and was detected statistically significant exclusively in polar glycolipids. Reports either on loss, pronounced expressions or de novo appearances of A-type structures in various conditions of accelerated growth like germ cell evolution, wound healing, inflammation and tumor proliferation in man and ABO related animals might show the dynamics of ancestral functions guarantying stem cell fidelity in maturation and tissue renewal processes. Procedures vice versa generating pluripotent stem cells for therapeutical reasons may indicate, that any artificially started growth should somehow pass through the germ line from the beginning, where according to growing knowledge exclusively the oocyte's genome provides a completely channeling ancestral information. In predatory animals such as the modern-day sea anemone, ancestral proteins, particularly those of the p53 gene family govern the reproduction processes, and are active up to the current mammalian female germ line. Lectins, providing the dual function of growth promotion and defense in higher plants, are suggested to represent the evolutionary precursors of the mammalian immunoglobulin M molecules, or protein moiety implying the greatest functional diversity in nature. And apart from any established mammalian genetic tree, a common vetch

  19. 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

  20. Cu(2+) inhibits photosystem II activities but enhances photosystem I quantum yield of Microcystis aeruginosa.

    PubMed

    Deng, Chunnuan; Pan, Xiangliang; Wang, Shuzhi; Zhang, Daoyong

    2014-08-01

    Responses of photosystem I and II activities of Microcystis aeruginosa to various concentrations of Cu(2+) were simultaneously examined using a Dual-PAM-100 fluorometer. Cell growth and contents of chlorophyll a were significantly inhibited by Cu(2+). Photosystem II activity [Y(II)] and electron transport [rETRmax(II)] were significantly altered by Cu(2+). The quantum yield of photosystem II [Y(II)] decreased by 29 % at 100 μg L(-1) Cu(2+) compared to control. On the contrary, photosystem I was stable under Cu(2+) stress and showed an obvious increase of quantum yield [Y(I)] and electron transport [rETRmax(I)] due to activation of cyclic electron flow (CEF). Yield of cyclic electron flow [Y(CEF)] was enhanced by 17 % at 100 μg L(-1) Cu(2+) compared to control. The contribution of linear electron flow to photosystem I [Y(II)/Y(I)] decreased with increasing Cu(2+) concentration. Yield of cyclic electron flow [Y(CEF)] was negatively correlated with the maximal photosystem II photochemical efficiency (F v/F m). In summary, photosystem II was the major target sites of toxicity of Cu(2+), while photosystem I activity was enhanced under Cu(2+) stress. PMID:24920130

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships.

    PubMed

    Legarra, Andres; Christensen, Ole F; Vitezica, Zulma G; Aguilar, Ignacio; Misztal, Ignacy

    2015-06-01

    Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships. We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view which each population is considered as an infinite, unrelated pool. Several ancestral populations may be connected and therefore related. Each ancestral population can be represented as a "metafounder," a pseudo-individual included as founder of the pedigree and similar to an "unknown parent group." Metafounders have self- and across relationships according to a set of parameters, which measure ancestral relationships, i.e., homozygozities within populations and relationships across populations. These parameters can be estimated from existing pedigree and marker genotypes using maximum likelihood or a method based on summary statistics, for arbitrarily complex pedigrees. Equivalences of genetic variance and variance components between the classical and this new parameterization are shown. Segregation variance on crosses of populations is modeled. Efficient algorithms for computation of relationship matrices, their inverses, and inbreeding coefficients are presented. Use of metafounders leads to compatibility of genomic and pedigree relationship matrices and to simple computing algorithms. Examples and code are given. PMID:25873631

  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. Evidence for the involvement of cyclic electron transport in the protection of photosystem II against photoinhibition: influence of a new phenolic compound.

    PubMed

    Allakhverdiev, S I; Klimov, V V; Carpentier, R

    1997-04-01

    Organisms that perform oxygenic photosynthesis are subjected to inhibition of their photosynthetic functions when they are exposed to excessive illumination. Photoinhibition occurs mainly at the level of photosystem II, where a cyclic electron transport has often been proposed to be involved in photoprotection. However, a demonstration of direct protection by cyclic photosystem II against photoinhibitory damage has been lacking. In this report, we used the newly characterized compound 4-[methoxybis(trifluoromethyl)methyl]-2,6-dinitrophenylhydrazine methyl ketone (K-15), known to stimulate cyclic electron transport between the acceptor and donor sides of the photosystem [Klimov, V. V., Zharmukhamedov, S. K., Allakhverdiev, S. I., Kolobanova, L. P., & Baskakov, Y. A. (1993) Biol. Membr. 6, 715-732], to verify if photosystem II is significantly protected by cyclic electron transport against aerobic and anaerobic photoinhibitory damage. The photoinhibitory quenching of the maximal level of fluorescence and the decrease of the absorbance change at 685 nm related to pheophytin photoreduction observed during photoinhibitory illumination of untreated or Mn-depleted photosystem II submembrane fractions are significantly attenuated in the presence of K-15. The photodegradation of cytochrome b559 and the photobleaching of beta-carotene and chlorophyll-670 measured in Mn-depleted photosystem II preparations are also strongly retarded when K-15 is present. The detection, by photoacoustic spectroscopy, of the energy stored during the cyclic electron transport is also reported in Mn-depleted photosystem II submembrane fractions and in photosystem II reaction center complexes. This reaction is also gradually photoinhibited due to the progressive photodegradation of the required electron transport intermediates but is significantly more stable in the presence of K-15. It is deduced that cyclic electron transport around photosystem II constitutes an effective protective mechanism

  10. (Analysis of cyanobacterial photosystem II genes by cloning and mutagenesis): Progress report

    SciTech Connect

    Not Available

    1988-01-01

    The major goal of this current proposal was to isolate, clone, sequence and mutagenize specific proteins associated with the photosynthetic membrane and photosystem II (PSII) in cyanobacteria. We have made great progress toward most of our goals and we have also gone off in some important new directions. The analysis of photosystem II proteins led us to investigate the growth of cyanobacteria under iron-deficient conditions and to detect a number of new proteins involved in the photosynthetic membrane. In addition, this work led us to isolate proteins that are localized in the cytoplasmic membrane or in the cell wall membrane. These studies have tremendously enriched our knowledge of membrane structure and, at the same time, have enabled us to probe cyanobacterial membranes with increased precision. 11 refs.

  11. Physiological Functions of Cyclic Electron Transport Around Photosystem I in Sustaining Photosynthesis and Plant Growth.

    PubMed

    Yamori, Wataru; Shikanai, Toshiharu

    2016-04-29

    The light reactions in photosynthesis drive both linear and cyclic electron transport around photosystem I (PSI). Linear electron transport generates both ATP and NADPH, whereas PSI cyclic electron transport produces ATP without producing NADPH. PSI cyclic electron transport is thought to be essential for balancing the ATP/NADPH production ratio and for protecting both photosystems from damage caused by stromal overreduction. Two distinct pathways of cyclic electron transport have been proposed in angiosperms: a major pathway that depends on the PROTON GRADIENT REGULATION 5 (PGR5) and PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE 1 (PGRL1) proteins, which are the target site of antimycin A, and a minor pathway mediated by the chloroplast NADH dehydrogenase-like (NDH) complex. Recently, the regulation of PSI cyclic electron transport has been recognized as essential for photosynthesis and plant growth. In this review, we summarize the possible functions and importance of the two pathways of PSI cyclic electron transport. PMID:26927905

  12. ProCARs: Progressive Reconstruction of Ancestral Gene Orders

    PubMed Central

    2015-01-01

    Background In the context of ancestral gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs). Results In this paper, we present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. The method is based on detecting a set of potential ancestral adjacencies iteratively using the current set of CARs at each step, and constructing CARs progressively using a 2-phase assembling method. Conclusion We show the usefulness of the method through a reconstruction of the boreoeutherian ancestral gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program, written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/. PMID:26040958

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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. PMID:26069151

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    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)63-/Fe(CN)64-], 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.

  20. The initial steps of biogenesis of cyanobacterial photosystems occur in plasma membranes

    PubMed Central

    Zak, Elena; Norling, Birgitta; Maitra, Radhashree; Huang, Fang; Andersson, Bertil; Pakrasi, Himadri B.

    2001-01-01

    During oxygenic photosynthesis in cyanobacteria and chloroplasts of plants and eukaryotic algae, conversion of light energy to biologically useful chemical energy occurs in the specialized thylakoid membranes. Light-induced charge separation at the reaction centers of photosystems I and II, two multisubunit pigment-protein complexes in the thylakoid membranes, energetically drive sequential photosynthetic electron transfer reactions in this membrane system. In general, in the prokaryotic cyanobacterial cells, the thylakoid membrane is distinctly different from the plasma membrane. We have recently developed a two-dimensional separation procedure to purify thylakoid and plasma membranes from the genetically widely studied cyanobacterium Synechocystis sp. PCC 6803. Immunoblotting analysis demonstrated that the purified plasma membrane contained a number of protein components closely associated with the reaction centers of both photosystems. Moreover, these proteins were assembled in the plasma membrane as chlorophyll-containing multiprotein complexes, as evidenced from nondenaturing green gel and low-temperature fluorescence spectroscopy data. Furthermore, electron paramagnetic resonance spectroscopic analysis showed that in the partially assembled photosystem I core complex in the plasma membrane, the P700 reaction center was capable of undergoing light-induced charge separation. Based on these data, we propose that the plasma membrane, and not the thylakoid membrane, is the site for a number of the early steps of biogenesis of the photosynthetic reaction center complexes in these cyanobacterial cells. PMID:11687660

  1. Reconstruction of the ancestral marsupial karyotype from comparative gene maps

    PubMed Central

    2013-01-01

    Background The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. Results We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. Conclusions Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome. PMID:24261750

  2. 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

  3. Structural studies on photosystem II of cyanobacteria.

    PubMed

    Gabdulkhakov, A G; Dontsova, M V

    2013-12-01

    Photosynthesis is one of the most important chemical processes in the biosphere responsible for the maintenance of life on Earth. Light energy is converted into energy of chemical bonds in photoreaction centers, which, in particular, include photosystem II (PS II). PS II is a multisubunit pigment-protein complex located in the thylakoid membrane of cyanobacteria, algae and plants. PS II realizes the first stage of solar energy conversion that results in decomposition of water to molecular oxygen, protons, and bound electrons via a series of consecutive reactions. During recent years, considerable progress has been achieved in determination of the spatial structures of PS II from various cyanobacteria. In the present review, we outline the current state of crystallographic studies on PS II. PMID:24490738

  4. 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. PMID:26592144

  5. Water oxidation chemistry of photosystem II

    PubMed Central

    Brudvig, Gary W

    2007-01-01

    Photosystem II (PSII) uses light energy to split water into protons, electrons and O2. In this reaction, nature has solved the difficult chemical problem of efficient four-electron oxidation of water to yield O2 without significant amounts of reactive intermediate species such as superoxide, hydrogen peroxide and hydroxyl radicals. In order to use nature's solution for the design of artificial catalysts that split water, it is important to understand the mechanism of the reaction. The recently published X-ray crystal structures of cyanobacterial PSII complexes provide information on the structure of the Mn and Ca ions, the redox-active tyrosine called YZ and the surrounding amino acids that comprise the O2-evolving complex (OEC). The emerging structure of the OEC provides constraints on the different hypothesized mechanisms for O2 evolution. The water oxidation mechanism of PSII is discussed in the light of biophysical and computational studies, inorganic chemistry and X-ray crystallographic information. PMID:17954436

  6. 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

  7. Modeling electron transfer in photosystem I.

    PubMed

    Makita, Hiroki; Hastings, Gary

    2016-06-01

    Nanosecond to millisecond time-resolved absorption spectroscopy has been used to study electron transfer processes in photosystem I particles from Synechocystis sp. PCC 6803 with eight different quinones incorporated into the A1 binding site, at both 298 and 77K. A detailed kinetic model was constructed and solved within the context of Marcus electron transfer theory, and it was found that all of the data could be well described only if the in situ midpoint potentials of the quinones fell in a tightly defined range. For photosystem I with phylloquinone incorporated into the A1 binding site all of the time-resolved optical data is best modeled when the in situ midpoint potential of phylloquinone on the A/B branch is -635/-690 mV, respectively. With the midpoint potential of the F(X) iron sulfur cluster set at -680 mV, this indicates that forward electron transfer from A(1)(-) to F(X) is slightly endergonic/exergonic on the A/B branch, respectively. Additionally, for forward electron transfer from A(1)(-) to F(X), on both the A and B branches the reorganization energy is close to 0.7 eV. Reorganization energies of 0.4 or 1.0 eV are not possible. For the eight different quinones incorporated, the same kinetic model was used, allowing us to establish in situ redox potentials for all of the incorporated quinones on both branches. A linear correlation was found between the in situ and in vitro midpoint potentials of the quinones on both branches. PMID:26994812

  8. 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.

  9. 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

  10. Segregation of photosystems in thylakoid membranes as a critical phenomenon.

    PubMed

    Rojdestvenski, Igor; Ivanov, Alexander G; Cottam, M G; Borodich, Andrei; Huner, Norman P A; Oquist, Gunnar

    2002-04-01

    The distribution of the two photosystems, PSI and PSII, in grana and stroma lamellae of the chloroplast membranes is not uniform. PSII are mainly concentrated in grana and PSI in stroma thylakoids. The dynamics and factors controlling the spatial segregation of PSI and PSII are generally not well understood, and here we address the segregation of photosystems in thylakoid membranes by means of a molecular dynamics method. The lateral segregation of photosystems was studied assuming a model comprising a two-dimensional (in-plane), two-component, many-body system with periodic boundary conditions and competing interactions between the photosystems in the thylakoid membrane. PSI and PSII are represented by particles with different values of negative charge. The pair interactions between particles include a screened Coulomb repulsive part and an exponentially decaying attractive part. The modeling results suggest a complicated phase behavior of the system, including quasi-crystalline phase of randomly distributed complexes of PSII and PSI at low ionic screening, well defined clustered state of segregated complexes at high screening, and in addition, an intermediate agglomerate phase where the photosystems tend to aggregate together without segregation. The calculations demonstrated that the ordering of photosystems within the membrane was the result of interplay between electrostatic and lipid-mediated interactions. At some values of the model parameters the segregation can be represented visually as well as by analyzing the correlation functions of the configuration. PMID:11916833

  11. Segregation of photosystems in thylakoid membranes as a critical phenomenon.

    PubMed Central

    Rojdestvenski, Igor; Ivanov, Alexander G; Cottam, M G; Borodich, Andrei; Huner, Norman P A; Oquist, Gunnar

    2002-01-01

    The distribution of the two photosystems, PSI and PSII, in grana and stroma lamellae of the chloroplast membranes is not uniform. PSII are mainly concentrated in grana and PSI in stroma thylakoids. The dynamics and factors controlling the spatial segregation of PSI and PSII are generally not well understood, and here we address the segregation of photosystems in thylakoid membranes by means of a molecular dynamics method. The lateral segregation of photosystems was studied assuming a model comprising a two-dimensional (in-plane), two-component, many-body system with periodic boundary conditions and competing interactions between the photosystems in the thylakoid membrane. PSI and PSII are represented by particles with different values of negative charge. The pair interactions between particles include a screened Coulomb repulsive part and an exponentially decaying attractive part. The modeling results suggest a complicated phase behavior of the system, including quasi-crystalline phase of randomly distributed complexes of PSII and PSI at low ionic screening, well defined clustered state of segregated complexes at high screening, and in addition, an intermediate agglomerate phase where the photosystems tend to aggregate together without segregation. The calculations demonstrated that the ordering of photosystems within the membrane was the result of interplay between electrostatic and lipid-mediated interactions. At some values of the model parameters the segregation can be represented visually as well as by analyzing the correlation functions of the configuration. PMID:11916833

  12. Mechanism of Cd2+ toxicity: Cd2+ inhibits photoactivation of Photosystem II by competitive binding to the essential Ca2+ site.

    PubMed

    Faller, Peter; Kienzler, Katharina; Krieger-Liszkay, Anja

    2005-01-01

    Cadmium (Cd2+) is a well-known highly toxic element. The molecular mechanisms of the Cd2+ toxicity are not well understood. In photosynthetic organisms, toxic Cd2+ concentrations are often in the low-microM range. It has been proposed that low-microM Cd2+ concentrations affect photosynthesis at the level of Photosystem II by inhibiting oxygen evolution. However, in vitro studies on isolated, functional Photosystem II showed that much higher Cd2+ concentrations (mM range) were needed for inhibition. Here we show that Cd2+ in the low-microM range inhibited photoactivation (i.e., assembly of the water splitting complex) in Chlamydomonas reinhardtii and in isolated Photosystem II. Photoactivation is the last step in the assembly of Photosystem II before it becomes functional. The exact Cd2+ concentration necessary for inhibition depended on the concentration of calcium. It is proposed that Cd2+ binds competitively to the essential Ca2+ site in Photosystem II during photoactivation. The low Cd2+ concentration needed to inhibit photoactivation suggests that this event is also involved in the Cd2+-induced inhibition of photosynthesis in vivo. This mechanism is likely to be important for Cd2+ toxicity towards photosynthetic organisms in general, at least in unicellular like C. reinhardtii where Cd2+ has easy access to the photosynthetic apparatus. PMID:15620376

  13. The conditional ancestral selection graph with strong balancing selection.

    PubMed

    Wakeley, John; Sargsyan, Ori

    2009-06-01

    Using a heuristic separation-of-time-scales argument, we describe the behavior of the conditional ancestral selection graph with very strong balancing selection between a pair of alleles. In the limit as the strength of selection tends to infinity, we find that the ancestral process converges to a neutral structured coalescent, with two subpopulations representing the two alleles and mutation playing the role of migration. This agrees with a previous result of Kaplan et al., obtained using a different approach. We present the results of computer simulations to support our heuristic mathematical results. We also present a more rigorous demonstration that the neutral conditional ancestral process converges to the Kingman coalescent in the limit as the mutation rate tends to infinity. PMID:19371754

  14. 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

  15. Primate chromosome evolution: ancestral karyotypes, marker order and neocentromeres.

    PubMed

    Stanyon, R; Rocchi, M; Capozzi, O; Roberto, R; Misceo, D; Ventura, M; Cardone, M F; Bigoni, F; Archidiacono, N

    2008-01-01

    In 1992 the Japanese macaque was the first species for which the homology of the entire karyotype was established by cross-species chromosome painting. Today, there are chromosome painting data on more than 50 species of primates. Although chromosome painting is a rapid and economical method for tracking translocations, it has limited utility for revealing intrachromosomal rearrangements. Fortunately, the use of BAC-FISH in the last few years has allowed remarkable progress in determining marker order along primate chromosomes and there are now marker order data on an array of primate species for a good number of chromosomes. These data reveal inversions, but also show that centromeres of many orthologous chromosomes are embedded in different genomic contexts. Even if the mechanisms of neocentromere formation and progression are just beginning to be understood, it is clear that these phenomena had a significant impact on shaping the primate genome and are fundamental to our understanding of genome evolution. In this report we complete and integrate the dataset of BAC-FISH marker order for human syntenies 1, 2, 4, 5, 8, 12, 17, 18, 19, 21, 22 and the X. These results allowed us to develop hypotheses about the content, marker order and centromere position in ancestral karyotypes at five major branching points on the primate evolutionary tree: ancestral primate, ancestral anthropoid, ancestral platyrrhine, ancestral catarrhine and ancestral hominoid. Current models suggest that between-species structural rearrangements are often intimately related to speciation. Comparative primate cytogenetics has become an important tool for elucidating the phylogeny and the taxonomy of primates. It has become increasingly apparent that molecular cytogenetic data in the future can be fruitfully combined with whole-genome assemblies to advance our understanding of primate genome evolution as well as the mechanisms and processes that have led to the origin of the human genome. PMID

  16. β-Propeller Blades as Ancestral Peptides in Protein Evolution

    PubMed Central

    Kopec, Klaus O.; Lupas, Andrei N.

    2013-01-01

    Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. Despite the large size range of β-propellers, their blades frequently show sequence similarity indicative of a common ancestry and it has been proposed that the majority of β-propellers arose divergently by amplification and diversification of an ancestral blade. Given the structural versatility of β-propellers and the hypothesis that the first folded proteins evolved from a simpler set of peptides, we investigated whether this blade may have given rise to other folds as well. Using sequence comparisons, we identified proteins of four other folds as potential homologs of β-propellers: the luminal domain of inositol-requiring enzyme 1 (IRE1-LD), type II β-prisms, β-pinwheels, and WW domains. Because, with increasing evolutionary distance and decreasing sequence length, the statistical significance of sequence comparisons becomes progressively harder to distinguish from the background of convergent similarities, we complemented our analyses with a new method that evaluates possible homology based on the correlation between sequence and structure similarity. Our results indicate a homologous relationship of IRE1-LD and type II β-prisms with β-propellers, and an analogous one for β-pinwheels and WW domains. Whereas IRE1-LD most likely originated by fold-changing mutations from a fully formed PQQ motif β-propeller, type II β-prisms originated by amplification and differentiation of a single blade, possibly also of the PQQ type. We conclude that both β-propellers and type II β-prisms arose by independent amplification of a blade-sized fragment, which represents a remnant of an ancient peptide world. PMID:24143202

  17. 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

  18. 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.

  19. A comparison of ancestral state reconstruction methods for quantitative characters.

    PubMed

    Royer-Carenzi, Manuela; Didier, Gilles

    2016-09-01

    Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of seven of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares under Brownian, Brownian-with-trend and Ornstein-Uhlenbeck models, phylogenetic independent contrasts and squared parsimony methods. A review of the relations between these methods shows that the maximum likelihood, the restricted maximum likelihood and the generalized least squares under Brownian model infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide. The respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) directional or stabilizing selection. We give the general form of ancestral state distributions conditioned on leaf states under the simulation models. Ancestral distributions are used first, to give a theoretical lower bound of the expected reconstruction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states. Our simulations show that: (i) the distributions of the reconstruction uncertainty provided by the methods generally make sense (some more than others); (ii) it is essential to detect the presence of an evolutionary trend and to choose a reconstruction method accordingly; (iii) all the methods show good performances on characters under stabilizing selection; (iv) without trend or stabilizing selection, the maximum likelihood method is generally the most accurate. PMID:27234644

  20. 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

  1. 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…

  2. 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. PMID:21029545

  3. 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

  4. Structural changes in the S3 state of the oxygen evolving complex in photosystem II

    NASA Astrophysics Data System (ADS)

    Hatakeyama, Makoto; Ogata, Koji; Fujii, Katsushi; Yachandra, Vittal K.; Yano, Junko; Nakamura, Shinichiro

    2016-05-01

    The S3 state of the Mn4CaO5-cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S2 to S3 transition that becomes a substrate water, we examined if the water insertion is essential for the S3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S3 stage. The novel S3 state structure consisting of only short 2.7-2.8 Å Mnsbnd Mn distances was discussed.

  5. 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.

  6. 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

  7. Light-harvesting in photosystem I.

    PubMed

    Croce, Roberta; van Amerongen, Herbert

    2013-10-01

    This review focuses on the light-harvesting properties of photosystem I (PSI) and its LHCI outer antenna. LHCI consists of different chlorophyll a/b binding proteins called Lhca's, surrounding the core of PSI. In total, the PSI-LHCI complex of higher plants contains 173 chlorophyll molecules, most of which are there to harvest sunlight energy and to transfer the created excitation energy to the reaction center (RC) where it is used for charge separation. The efficiency of the complex is based on the capacity to deliver this energy to the RC as fast as possible, to minimize energy losses. The performance of PSI in this respect is remarkable: on average it takes around 50 ps for the excitation to reach the RC in plants, without being quenched in the meantime. This means that the internal quantum efficiency is close to 100% which makes PSI the most efficient energy converter in nature. In this review, we describe the light-harvesting properties of the complex in relation to protein and pigment organization/composition, and we discuss the important parameters that assure its very high quantum efficiency. Excitation energy transfer and trapping in the core and/or Lhcas, as well as in the supercomplexes PSI-LHCI and PSI-LHCI-LHCII are described in detail with the aim of giving an overview of the functional behavior of these complexes. PMID:23645376

  8. Charge recombination and thermoluminescence in photosystem II.

    PubMed

    Rappaport, Fabrice; Cuni, Aude; Xiong, Ling; Sayre, Richard; Lavergne, Jérôme

    2005-03-01

    In the recombination process of Photosystem II (S(2)Q(A)(-)-->S(1)Q(A)) the limiting step is the electron transfer from the reduced primary acceptor pheophytin Ph(-) to the oxidized primary donor P(+) and the rate depends on the equilibrium constant between states S(2)PPhQ(A)(-) and S(1)P(+)Ph(-)Q(A). Accordingly, mutations that affect the midpoint potential of Ph or of P result in a modified recombination rate. A strong correlation is observed between the effects on the recombination rate and on thermoluminescence (TL, the light emission from S(2)Q(A)(-) during a warming ramp): a slower recombination corresponds to a large enhancement and higher temperature of the TL peak. The current theory of TL does not account for these effects, because it is based on the assumption that the rate-limiting step coincides with the radiative process. When implementing the known fact that the radiative pathway represents a minor leak, the modified TL theory readily accounts qualitatively for the observed behavior. However, the peak temperature is still lower than predicted from the temperature-dependence of recombination. We argue that this reflects the heterogeneity of the recombination process combined with the enhanced sensitivity of TL to slower components. The recombination kinetics are accurately fitted as a sum of two exponentials and we show that this is not due to a progressive stabilization of the charge-separated state, but to a pre-existing conformational heterogeneity. PMID:15653722

  9. Photosystem I - based biohybrid photoelectrochemical cells.

    PubMed

    Ciesielski, Peter N; Hijazi, Frederick M; Scott, Amanda M; Faulkner, Christopher J; Beard, Lisa; Emmett, Kevin; Rosenthal, Sandra J; Cliffel, David; Kane Jennings, G

    2010-05-01

    Photosynthesis is the process by which Nature coordinates a tandem of protein complexes of impressive complexity that function to harness staggering amounts of solar energy on a global scale. Advances in biochemistry and nanotechnology have provided tools to isolate and manipulate the individual components of this process, thus opening a door to a new class of highly functional and vastly abundant biological resources. Here we show how one of these components, Photosystem I (PSI), is incorporated into an electrochemical system to yield a stand-alone biohybrid photoelectrochemical cell that converts light energy into electrical energy. The cells make use of a dense multilayer of PSI complexes assembled on the surface of the cathode to produce a photocatalytic effect that generates photocurrent densities of approximately 2 microA/cm(2) at moderate light intensities. We describe the relationship between the current and voltage production of the cells and the photoinduced interactions of PSI complexes with electrochemical mediators, and show that the performance of the present device is limited by diffusional transport of the electrochemical mediators through the electrolyte. These biohybrid devices display remarkable stability, as they remain active in ambient conditions for at least 280 days. Even at bench-scale production, the materials required to fabricate the cells described in this manuscript cost approximately 10 cents per cm(2) of active electrode area. PMID:20064713

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. Structure determination and improved model of plant photosystem I.

    PubMed

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

    2010-01-29

    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-A 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 beta-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

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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

  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. Inhibition of the water oxidizing complex of photosystem II and the reoxidation of the quinone acceptor QA- by Pb2+.

    PubMed

    Belatik, Ahmed; Hotchandani, Surat; Carpentier, Robert

    2013-01-01

    The action of the environmental toxic Pb(2+) 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 Pb(2+) 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 Pb(2+) 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 Pb(2+). This is proposed to be owing to a transmembrane modification of the acceptor side of the photosystem. PMID:23861859

  4. 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

  5. Defining the Far-red Limit of Photosystem I

    PubMed Central

    Mokvist, Fredrik; Mamedov, Fikret; Styring, Stenbjörn

    2014-01-01

    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. PMID:25023284

  6. 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

  7. Infant and juvenile growth in ancestral Pueblo Indians.

    PubMed

    Schillaci, Michael A; Nikitovic, Dejana; Akins, Nancy J; Tripp, Lianne; Palkovich, Ann M

    2011-06-01

    The present study examines patterns of infant and juvenile growth in a diachronic sample of ancestral Pueblo Indians (AD 1300-1680) from the American Southwest. An assessment of growth patterns is accompanied by an evaluation of pathological conditions often considered to be indicators of nutritional deficiencies and/or gastrointestinal infections. Growth patterns and the distribution of pathological conditions are interpreted relative to culturally relevant age categories defined by Puebloan rites of passage described in the ethnographic literature. A visual comparison of growth distance curves revealed that relative to a modern comparative group our sample of ancestral Pueblo infant and juveniles exhibited faltering growth beginning soon after birth to about 5 years of age. A comparison of curves describing growth relative to adult femoral length, however, indicated reduced growth occurring later, by around 2 years of age. Similar to previous studies, we observed a high proportion of nonsurvivors exhibiting porotic cranial lesions during the first 2 years of life. Contrary to expectations, infants and juveniles without evidence of porotic cranial lesions exhibited a higher degree of stunting. Our study is generally consistent with previous research reporting poor health and high mortality for ancestral Pueblo Indian infants and juveniles. Through use of a culturally relevant context defining childhood, we argue that the observed poor health and high mortality in our sample occur before the important transition from young to older child and the concomitant initial incorporation into tribal ritual organization. PMID:21469079

  8. 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. PMID:25831547

  9. 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

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

    PubMed Central

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

    2015-01-01

    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. PMID:25831547

  11. D1-protein dynamics in photosystem II: the lingering enigma

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The D1/D2 heterodimer core dominates the photosystem II reaction center. A characteristic feature of this heterodimer is the differentially rapid, light-dependent degradation of the D1 protein. The D1 protein is possibly the most researched photosynthetic polypeptide, with aspects of structure–funct...

  12. Biogenesis, assembly and turnover of photosystem II units.

    PubMed Central

    Baena-González, Elena; Aro, Eva-Mari

    2002-01-01

    Assembly of photosystem II, a multiprotein complex embedded in the thylakoid membrane, requires stoichiometric production of over 20 protein subunits. Since part of the protein subunits are encoded in the chloroplast genome and part in the nucleus, a signalling network operates between the two genetic compartments in order to prevent wasteful production of proteins. Coordinated synthesis of proteins also takes place among the chloroplast-encoded subunits, thus establishing a hierarchy in the protein components that allows a stepwise building of the complex. In addition to this dependence on assembly partners, other factors such as the developmental stage of the plastid and various photosynthesis-related parameters exert a strict control on the accumulation, membrane targeting and assembly of the PSII subunits. Here, we briefly review recent results on this field obtained with three major approaches: biogenesis of photosystem II during the development of chloroplasts from etioplasts, use of photosystem II-specific mutants and photosystem II turnover during its repair cycle. PMID:12437884

  13. 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…

  14. 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

  15. 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

  16. The ancestral carnivore karyotype (2n = 38) lives today in ringtails.

    PubMed

    Nash, William G; Menninger, Joan C; Padilla-Nash, Hesed M; Stone, Gary; Perelman, Polina L; O'Brien, Stephen J

    2008-01-01

    Chromosome painting was used to investigate the conservation of high-resolution longitudinal 4',6-diamidino-2-phenylindole (DAPI)/G bands in Carnivore chromosomes. Cat (Felis catus) and raccoon dog (Nyctereutes procyonoides) painting probes were hybridized to the ringtail (Bassaricus astutus), dwarf mongoose (Helogale parvula), and Malagasy civet (Fossa fossa) to identify homologous chromosome elements. The patterns of chromosome segment homology among Carnivore species allowed us to reconstruct and propose the disposition of a high-resolution banded ancestral carnivore karyotype (ACK). Three bi-armed chromosomes consistently found among Caniformia species are represented as 6 homologous acrocentric chromosomes among Feliformia species of Carnivora. However, reexamination of the most basal of Feliformia species, the African palm civet Nandinia, revealed the presence of the 3 heretofore Caniformia bi-armed chromosomes. Because these 3 bi-armed chromosomes are found in both Caniformia and Feliformia lineages, they are presumed ancestral for all Carnivora, suggesting that the ACK chromosome number would be 38, rather than the previously supposed 42. Banded chromosomes of the ACK are used to evaluate the consistency between recently determined molecular phylogenetic relationships and postulated cytogenetic dynamics in the same Carnivore species. PMID:18339652

  17. 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

  18. 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

  19. Photosystem I (PSI)/Photosystem II (PSII)-based photo-bioelectrochemical cells revealing directional generation of photocurrents.

    PubMed

    Yehezkeli, Omer; Tel-Vered, Ran; Michaeli, Dorit; Nechushtai, Rachel; Willner, Itamar

    2013-09-01

    Layered assemblies of photosystem I, PSI, and/or photosystem II, PSII, on ITO electrodes are constructed using a layer-by-layer deposition process, where poly N,N'-dibenzyl-4,4'-bipyridinium (poly-benzyl viologen, PBV(2+) ) is used as an inter-protein "glue". While the layered assembly of PSI generates an anodic photocurrent only in the presence of a sacrificial electron donor system, such as dichlorophenol indophenol (DCPIP)/ascorbate, the PSII-modified electrode leads, upon irradiation, to the formation of an anodic photocurrent (while evolving oxygen), in the absence of any sacrificial component. The photocurrent is generated by transferring the electrons from the PSII units to the PBV(2+) redox polymer. The charge-separated species allow, then, the injection of the electrons to the electrode, with the concomitant evolution of O2 . A layered assembly, consisting of a PSI layer attached to a layer of PSII by the redox polymer PBV(2+) , leads to an anodic photocurrent that is 2-fold higher, as compared to the anodic photocurrent generated by a PSII-modified electrode. This observation is attributed to an enhanced charge separation in the two-photosystem assembly. By the further nano-engineering of the two photosystems on the electrode using two different redox polymers, vectorial electron transfer to the electrode is demonstrated, resulting in a ca. 6-fold enhancement in the photocurrent. The reversed bi-layer assembly, consisting of a PSII layer linked to a layer of PSI by the PBV(2+) redox polymer, yields, upon irradiation, an inefficient cathodic current. This observation is attributed to a mixture of photoinduced electron transfer reactions of opposing effects on the photocurrent directions in the two-photosystem assembly. PMID:23606348

  20. Molecular basis of the heat denaturation of photosystem II.

    PubMed

    Thompson, L K; Blaylock, R; Sturtevant, J M; Brudvig, G W

    1989-08-01

    The thermal denaturation of the photosystem II (PSII) membrane protein complex is investigated by assigning the endothermic transitions observed by differential scanning calorimetry (DSC) to the denaturation of particular proteins of the PSII complex. In a prior DSC study of PSII membranes [Thompson, L. K., Sturtevant, J. M., & Brudvig, G. W. (1986) Biochemistry 25, 6161], five DSC peaks were observed in the 30-70 degrees C temperature range (A1, A2, B, C, and D). The A2 peak was assigned to denaturation of a component essential for water oxidation and the B peak to denaturation of a component critical to the remainder of the electron-transport chain. We have now extended these studies with thermal gel analysis and electron paramagnetic resonance (EPR) measurements. Thermal gel analysis, a technique which relies on a change in the solubility properties of a membrane protein upon denaturation, has been used to determine the temperatures of denaturation of all of the major membrane proteins of the PSII complex. EPR experiments have been used to monitor chlorophyll photooxidation and the stability of TyrD+. Peaks B, C, and D in the DSC denaturation profile are each assigned to the denaturation of several proteins, which provides information on the organization of the PSII complex into structural and functional units. Peak B corresponds to the denaturation of peripheral core proteins and closely associated antenna proteins, peak C to the PSII core, and peak D to the loosely associated antenna proteins. No membrane protein is observed to denature during the A2 peak. The A2 peak is altered by the presence of catalase, superoxide dismutase, low chloride, and high pH. These results suggest that the abnormally sharp A2 peak occurs when the highly oxidizing, sequestered Mn complex (the active site in water oxidation) becomes accessible to the aqueous phase, at elevated temperatures. We propose a mechanism for the reaction of the Mn complex with hydroxide ions, which involves

  1. 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

  2. Comparative paleogenomics of crucifers: ancestral genomic blocks revisited.

    PubMed

    Lysak, Martin A; Mandáková, Terezie; Schranz, M Eric

    2016-04-01

    A decade ago the concept of the Ancestral Crucifer Karyotype (ACK) and the definition of 24 conserved genomic blocks was presented. Subsequently, 35 cytogenetic reconstructions and/or draft genome sequences of crucifer species (members of the Brassicaceae family) have been analyzed in the context of this system; placing crucifers at the forefront of plant phylogenomics. In this review, we highlight how the ACK and genomic blocks have facilitated and guided genomic analysis of crucifers in the last 10 years and provide an update of this robust model. PMID:26945766

  3. Genomic evolution in domestic cattle: ancestral haplotypes and healthy beef.

    PubMed

    Williamson, Joseph F; Steele, Edward J; Lester, Susan; Kalai, Oscar; Millman, John A; Wolrige, Lindsay; Bayard, Dominic; McLure, Craig; Dawkins, Roger L

    2011-05-01

    We have identified numerous Ancestral Haplotypes encoding a 14-Mb region of Bota C19. Three are frequent in Simmental, Angus and Wagyu and have been conserved since common progenitor populations. Others are more relevant to the differences between these 3 breeds including fat content and distribution in muscle. SREBF1 and Growth Hormone, which have been implicated in the production of healthy beef, are included within these haplotypes. However, we conclude that alleles at these 2 loci are less important than other sequences within the haplotypes. Identification of breeds and hybrids is improved by using haplotypes rather than individual alleles. PMID:21338665

  4. 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

  5. Evolution and functional properties of photosystem II light harvesting complexes in eukaryotes.

    PubMed

    Ballottari, Matteo; Girardon, Julien; Dall'osto, Luca; Bassi, Roberto

    2012-01-01

    Photoautotrophic organisms, the major agent of inorganic carbon fixation into biomass, convert light energy into chemical energy. The first step of photosynthesis consists of the absorption of solar energy by pigments binding protein complexes named photosystems. Within photosystems, a family of proteins called Light Harvesting Complexes (LHC), responsible for light harvesting and energy transfer to reaction centers, has evolved along with eukaryotic organisms. Besides light absorption, these proteins catalyze photoprotective reactions which allowed functioning of oxygenic photosynthetic machinery in the increasingly oxidant environment. In this work we review current knowledge of LHC proteins serving Photosystem II. Balance between light harvesting and photoprotection is critical in Photosystem II, due to the lower quantum efficiency as compared to Photosystem I. In particular, we focus on the role of each antenna complex in light harvesting, energy transfer, scavenging of reactive oxygen species, chlorophyll triplet quenching and thermal dissipation of excess energy. This article is part of a Special Issue entitled: Photosystem II. PMID:21704018

  6. 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

  7. 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

  8. 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

  9. Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference

    PubMed Central

    Ni, Xumin; Yang, Xiong; Guo, Wei; Yuan, Kai; Zhou, Ying; Ma, Zhiming; Xu, Shuhua

    2016-01-01

    The length of ancestral tracks decays with the passing of generations which can be used to infer population admixture histories. Previous studies have shown the power in recovering the histories of admixed populations via the length distributions of ancestral tracks even under simple models. We believe that the deduction of length distributions under a general model will greatly elevate the power. Here we first deduced the length distributions under a general model and proposed general principles in parameter estimation and model selection with the deduced length distributions. Next, we focused on studying the length distributions and its applications under three typical special cases. Extensive simulations showed that the length distributions of ancestral tracks were well predicted by our theoretical framework. We further developed a new method, AdmixInfer, based on the length distributions and good performance was observed when it was applied to infer population histories under the three typical models. Notably, our method was insensitive to demographic history, sample size and threshold to discard short tracks. Finally, good performance was also observed when applied to some real datasets of African Americans, Mexicans and South Asian populations from the HapMap project and the Human Genome Diversity Project. PMID:26818889

  10. Integrated photosystem II-based photo-bioelectrochemical cells.

    PubMed

    Yehezkeli, Omer; Tel-Vered, Ran; Wasserman, Julian; Trifonov, Alexander; Michaeli, Dorit; Nechushtai, Rachel; Willner, Itamar

    2012-01-01

    Photosynthesis is a sustainable process that converts light energy into chemical energy. Substantial research efforts are directed towards the application of the photosynthetic reaction centres, photosystems I and II, as active components for the light-induced generation of electrical power or fuel products. Nonetheless, no integrated photo-bioelectrochemical device that produces electrical power, upon irradiation of an aqueous solution that includes two inter-connected electrodes is known. Here we report the assembly of photobiofuel cells that generate electricity upon irradiation of biomaterial-functionalized electrodes in aqueous solutions. The cells are composed of electrically contacted photosystem II-functionalized photoanodes and an electrically wired bilirubin oxidase/carbon nanotubes-modified cathode. Illumination of the photoanodes yields the oxidation of water to O(2) and the transfer of electrons through the external circuit to the cathode, where O(2) is re-reduced to water. PMID:22415833

  11. 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

  12. Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme.

    PubMed

    Say, Rafael F; Fuchs, Georg

    2010-04-15

    Most archaeal groups and deeply branching bacterial lineages harbour thermophilic organisms with a chemolithoautotrophic metabolism. They live at high temperatures in volcanic habitats at the expense of inorganic substances, often under anoxic conditions. These autotrophic organisms use diverse carbon dioxide fixation mechanisms generating acetyl-coenzyme A, from which gluconeogenesis must start. Here we show that virtually all archaeal groups as well as the deeply branching bacterial lineages contain a bifunctional fructose 1,6-bisphosphate (FBP) aldolase/phosphatase with both FBP aldolase and FBP phosphatase activity. This enzyme is missing in most other Bacteria and in Eukaryota, and is heat-stabile even in mesophilic marine Crenarchaeota. Its bifunctionality ensures that heat-labile triosephosphates are quickly removed and trapped in stabile fructose 6-phosphate, rendering gluconeogenesis unidirectional. We propose that this highly conserved, heat-stabile and bifunctional FBP aldolase/phosphatase represents the pace-making ancestral gluconeogenic enzyme, and that in evolution gluconeogenesis preceded glycolysis. PMID:20348906

  13. 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

  14. 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

  15. Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples

    NASA Astrophysics Data System (ADS)

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

    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.

  16. 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. PMID:26046591

  17. Photosystem II reaction centre quenching: mechanisms and physiological role.

    PubMed

    Ivanov, Alexander G; Sane, Prafullachandra V; Hurry, Vaughan; Oquist, Gunnar; Huner, Norman P A

    2008-01-01

    Dissipation of excess absorbed light energy in eukaryotic photoautotrophs through zeaxanthin- and DeltapH-dependent photosystem II antenna quenching is considered the major mechanism for non-photochemical quenching and photoprotection. However, there is mounting evidence of a zeaxanthin-independent pathway for dissipation of excess light energy based within the PSII reaction centre that may also play a significant role in photoprotection. We summarize recent reports which indicate that this enigma can be explained, in part, by the fact that PSII reaction centres can be reversibly interconverted from photochemical energy transducers that convert light into ATP and NADPH to efficient, non-photochemical energy quenchers that protect the photosynthetic apparatus from photodamage. In our opinion, reaction centre quenching complements photoprotection through antenna quenching, and dynamic regulation of photosystem II reaction centre represents a general response to any environmental condition that predisposes the accumulation of reduced Q(A) in the photosystem II reaction centres of prokaryotic and eukaryotic photoautotrophs. Since the evolution of reaction centres preceded the evolution of light harvesting systems, reaction centre quenching may represent the oldest photoprotective mechanism. PMID:18821028

  18. 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

  19. Effect of trehalose on oxygen evolution and electron transfer in photosystem 2 complexes.

    PubMed

    Mamedov, M D; Petrova, I O; Yanykin, D V; Zaspa, A A; Semenov, A Yu

    2015-01-01

    The pigment-protein complex of photosystem 2 (PS 2) catalyzes the light-driven oxidation of water molecule and the reduction of plastoquinone. In this work, we studied the effect of the disaccharide trehalose, which is unique in its physicochemical properties, on isolated PS 2 complex. It was found that trehalose significantly stimulated the steady-state rate of oxygen evolution. The study of single flash-induced fluorescence decay kinetics demonstrated that trehalose did not affect the rate of QA(-) oxidation, although it led to an increase in the relative fractions of PS 2 reaction centers capable of QA(-) oxidation. Trehalose also prevented PS 2 complexes from being inactivated on prolonged storage. We propose that in the presence of trehalose, which affects the extent of hydration, the protein can preferentially exist in a more optimal conformation for effective functioning. PMID:25754040

  20. The stoichiometry of the two photosystems in higher plants revisited.

    PubMed

    Fan, Da-Yong; Hope, Alexander B; Smith, Paul J; Jia, Husen; Pace, Ronald J; Anderson, Jan M; Chow, Wah Soon

    2007-08-01

    The stoichiometry of Photosystem II (PSII) to Photosystem I (PSI) reaction centres in spinach leaf segments was determined by two methods, each capable of being applied to monitor the presence of both photosystems in a given sample. One method was based on a fast electrochromic (EC) signal, which in the millisecond time scale represents a change in the delocalized electric potential difference across the thylakoid membrane resulting from charge separation in both photosystems. This method was applied to leaf segments, thus avoiding any potential artefacts associated with the isolation of thylakoid membranes. Two variations of this method, suppressing PSII activity by prior photoinactivation (in spinach and poplar leaf segments) or suppressing PSI by photo-oxidation of P700 (the chlorophyll dimer in PSI) with background far-red light (in spinach, poplar and cucumber leaf segments), each gave the separate contribution of each photosystem to the fast EC signal; the PSII/PSI stoichiometry obtained by this method was in the range 1.5-1.9 for the three plant species, and 1.5-1.8 for spinach in particular. A second method, based on electron paramagnetic resonance (EPR), gave values in a comparable range of 1.7-2.1 for spinach. A third method, which consisted of separately determining the content of functional PSII in leaf segments by the oxygen yield per single turnover-flash and that of PSI by photo-oxidation of P700 in thylakoids isolated from the corresponding leaves, gave a PSII/PSI stoichiometry (1.5-1.7) that was consistent with the above values. It is concluded that the ratio of PSII to PSI reaction centres is considerably higher than unity in typical higher plants, in contrast to a surprisingly low PSII/PSI ratio of 0.88, determined by EPR, that was reported for spinach grown in a cabinet under far-red-deficient light in Sweden [Danielsson et al. (2004) Biochim. Biophys. Acta 1608: 53-61]. We suggest that the low PSII/PSI ratio in the Swedish spinach, grown in far

  1. In Vivo Identification of Photosystem II Light Harvesting Complexes Interacting with PHOTOSYSTEM II SUBUNIT S1[OPEN

    PubMed Central

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

    2015-01-01

    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. PMID:26069151

  2. 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

  3. 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

  4. 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

  5. Female song is widespread and ancestral in songbirds.

    PubMed

    Odom, Karan J; Hall, Michelle L; Riebel, Katharina; Omland, Kevin E; Langmore, Naomi E

    2014-01-01

    Bird song has historically been considered an almost exclusively male trait, an observation fundamental to the formulation of Darwin's theory of sexual selection. Like other male ornaments, song is used by male songbirds to attract females and compete with rivals. Thus, bird song has become a textbook example of the power of sexual selection to lead to extreme neurological and behavioural sex differences. Here we present an extensive survey and ancestral state reconstruction of female song across songbirds showing that female song is present in 71% of surveyed species including 32 families, and that females sang in the common ancestor of modern songbirds. Our results reverse classical assumptions about the evolution of song and sex differences in birds. The challenge now is to identify whether sexual selection alone or broader processes, such as social or natural selection, best explain the evolution of elaborate traits in both sexes. PMID:24594930

  6. 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

  7. Ancestral reproductive structure in basal kelp Aureophycus aleuticus

    PubMed Central

    Kawai, Hiroshi; Hanyuda, Takeaki; Ridgway, L. Michelle; Holser, Karin

    2013-01-01

    Laminarialean species (so-called kelps) are the largest photosynthetic organisms in aquatic environments, constituting significant ecological components of coastal ecosystems. The largest kelps such as Macrocystis exhibit differentiation between stipe and blade, as well as buoyancy to maintain the distal portion at the water's surface for photosynthesis, while bearing reproductive structures only near the base on special blades (sporophylls). There is a considerable gap between basic kelps such as Chorda and derived kelps, and the evolution of kelp specialization remains unclear. Here we report novel reproductive adaptations in the recently discovered species Aureophycus aleuticus; unlike any known kelps, A. aleuticus forms zoidangia only on the expanded, disc-shaped holdfast. Molecular phylogeny suggests that A. aleuticus is most basal among derived kelps. Because Aureophycus lacks any of the elaborate anatomical structures found in other derived kelps, we suggest that it exhibits some of the most ancestral morphological features of kelps. PMID:23966101

  8. 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

  9. Ancestral European roots of Helicobacter pylori in India

    PubMed Central

    Devi, S Manjulata; Ahmed, Irshad; Francalacci, Paolo; Hussain, M Abid; Akhter, Yusuf; Alvi, Ayesha; Sechi, Leonardo A; Mégraud, Francis; Ahmed, Niyaz

    2007-01-01

    Background The human gastric pathogen Helicobacter pylori is co-evolved with its host and therefore, origins and expansion of multiple populations and sub populations of H. pylori mirror ancient human migrations. Ancestral origins of H. pylori in the vast Indian subcontinent are debatable. It is not clear how different waves of human migrations in South Asia shaped the population structure of H. pylori. We tried to address these issues through mapping genetic origins of present day H. pylori in India and their genomic comparison with hundreds of isolates from different geographic regions. Results We attempted to dissect genetic identity of strains by multilocus sequence typing (MLST) of the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC) and phylogeographic analysis of haplotypes using MEGA and NETWORK software while incorporating DNA sequences and genotyping data of whole cag pathogenicity-islands (cagPAI). The distribution of cagPAI genes within these strains was analyzed by using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined by gene sequencing. All the isolates analyzed revealed European ancestry and belonged to H. pylori sub-population, hpEurope. The cagPAI harbored by Indian strains revealed European features upon PCR based analysis and whole PAI sequencing. Conclusion These observations suggest that H. pylori strains in India share ancestral origins with their European counterparts. Further, non-existence of other sub-populations such as hpAfrica and hpEastAsia, at least in our collection of isolates, suggest that the hpEurope strains enjoyed a special fitness advantage in Indian stomachs to out-compete any endogenous strains. These results also might support hypotheses related to gene flow in India through Indo-Aryans and arrival of Neolithic practices and languages from the Fertile Crescent. PMID:17584914

  10. Increased air temperature during simulated autumn conditions impairs photosynthetic electron transport between photosystem II and photosystem I.

    PubMed

    Busch, Florian; Hüner, Norman P A; Ensminger, Ingo

    2008-05-01

    Changes in temperature and daylength trigger physiological and seasonal developmental processes that enable evergreen trees of the boreal forest to withstand severe winter conditions. Climate change is expected to increase the autumn air temperature in the northern latitudes, while the natural decreasing photoperiod remains unaffected. As shown previously, an increase in autumn air temperature inhibits CO2 assimilation, with a concomitant increased capacity for zeaxanthin-independent dissipation of energy exceeding the photochemical capacity in Pinus banksiana. In this study, we tested our previous model of antenna quenching and tested a limitation in intersystem electron transport in plants exposed to elevated autumn air temperatures. Using a factorial design, we dissected the effects of temperature and photoperiod on the function as well as the stoichiometry of the major components of the photosynthetic electron transport chain in P. banksiana. Natural summer conditions (16-h photoperiod/22 degrees C) and late autumn conditions (8-h photoperiod/7 degrees C) were compared with a treatment of autumn photoperiod with increased air temperature (SD/HT: 8-h photoperiod/22 degrees C) and a treatment with summer photoperiod and autumn temperature (16-h photoperiod/7 degrees C). Exposure to SD/HT resulted in an inhibition of the effective quantum yield associated with a decreased photosystem II/photosystem I stoichiometry coupled with decreased levels of Rubisco. Our data indicate that a greater capacity to keep the primary electron donor of photosystem I (P700) oxidized in plants exposed to SD/HT compared with the summer control may be attributed to a reduced rate of electron transport from the cytochrome b6f complex to photosystem I. Photoprotection under increased autumn air temperature conditions appears to be consistent with zeaxanthin-independent antenna quenching through light-harvesting complex II aggregation and a decreased efficiency in energy transfer from the

  11. Increased Air Temperature during Simulated Autumn Conditions Impairs Photosynthetic Electron Transport between Photosystem II and Photosystem I1[OA

    PubMed Central

    Busch, Florian; Hüner, Norman P.A.; Ensminger, Ingo

    2008-01-01

    Changes in temperature and daylength trigger physiological and seasonal developmental processes that enable evergreen trees of the boreal forest to withstand severe winter conditions. Climate change is expected to increase the autumn air temperature in the northern latitudes, while the natural decreasing photoperiod remains unaffected. As shown previously, an increase in autumn air temperature inhibits CO2 assimilation, with a concomitant increased capacity for zeaxanthin-independent dissipation of energy exceeding the photochemical capacity in Pinus banksiana. In this study, we tested our previous model of antenna quenching and tested a limitation in intersystem electron transport in plants exposed to elevated autumn air temperatures. Using a factorial design, we dissected the effects of temperature and photoperiod on the function as well as the stoichiometry of the major components of the photosynthetic electron transport chain in P. banksiana. Natural summer conditions (16-h photoperiod/22°C) and late autumn conditions (8-h photoperiod/7°C) were compared with a treatment of autumn photoperiod with increased air temperature (SD/HT: 8-h photoperiod/22°C) and a treatment with summer photoperiod and autumn temperature (16-h photoperiod/7°C). Exposure to SD/HT resulted in an inhibition of the effective quantum yield associated with a decreased photosystem II/photosystem I stoichiometry coupled with decreased levels of Rubisco. Our data indicate that a greater capacity to keep the primary electron donor of photosystem I (P700) oxidized in plants exposed to SD/HT compared with the summer control may be attributed to a reduced rate of electron transport from the cytochrome b6f complex to photosystem I. Photoprotection under increased autumn air temperature conditions appears to be consistent with zeaxanthin-independent antenna quenching through light-harvesting complex II aggregation and a decreased efficiency in energy transfer from the antenna to the photosystem

  12. 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

  13. Agnathan VIP, PACAP and Their Receptors: Ancestral Origins of Today's Highly Diversified Forms

    PubMed Central

    Ng, Stephanie Y. L.; Chow, Billy K. C.; Kasamatsu, Jun; Kasahara, Masanori; Lee, Leo T. O.

    2012-01-01

    VIP and PACAP are pleiotropic peptides belonging to the secretin superfamily of brain-gut peptides and interact specifically with three receptors (VPAC1, PAC1 and VPAC2) from the class II B G protein-coupled receptor family. There is immense interest regarding their molecular evolution which is often described closely alongside gene and/or genome duplications. Despite the wide array of information available in various vertebrates and one invertebrate the tunicate, their evolutionary origins remain unresolved. Through searches of genome databases and molecular cloning techniques, the first lamprey VIP/PACAP ligands and VPAC receptors are identified from the Japanese lamprey. In addition, two VPAC receptors (VPACa/b) are identified from inshore hagfish and ligands predicted for sea lamprey. Phylogenetic analyses group these molecules into their respective PHI/VIP, PRP/PACAP and VPAC receptor families and show they resemble ancestral forms. Japanese lamprey VIP/PACAP peptides synthesized were tested with the hagfish VPAC receptors. hfVPACa transduces signal via both adenylyl cylase and phospholipase C pathways, whilst hfVPACb was only able to transduce through the calcium pathway. In contrast to the widespread distribution of VIP/PACAP ligands and receptors in many species, the agnathan PACAP and VPAC receptors were found almost exclusively in the brain. In situ hybridisation further showed their abundance throughout the brain. The range of VIP/PACAP ligands and receptors found are highly useful, providing a glimpse into the evolutionary events both at the structural and functional levels. Though representative of ancestral forms, the VIP/PACAP ligands in particular have retained high sequence conservation indicating the importance of their functions even early in vertebrate evolution. During these nascent stages, only two VPAC receptors are likely responsible for eliciting functions before evolving later into specific subtypes post-Agnatha. We also propose VIP and

  14. 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

  15. Contrasting behavior of higher plant photosystem I and II antenna systems during acclimation.

    PubMed

    Ballottari, Matteo; Dall'Osto, Luca; Morosinotto, Tomas; Bassi, Roberto

    2007-03-23

    In this work we analyzed the photosynthetic apparatus in Arabidopsis thaliana plants acclimated to different light intensity and temperature conditions. Plants showed the ability to acclimate into different environments and avoid photoinhibition. When grown in high light, plants had a faster activation rate for energy dissipation (qE). This ability was correlated to higher accumulation levels of a specific photosystem II subunit, PsbS. The photosystem II antenna size was also regulated according to light exposure; smaller antenna size was observed in high light-acclimated plants with respect to low light plants. Different antenna polypeptides did not behave similarly, and Lhcb1, Lchb2, and Lhcb6 (CP24) are shown to undergo major levels of regulation, whereas Lhcb4 and Lhcb5 (CP29 and CP26) maintained their stoichiometry with respect to the reaction center in all growth conditions. The effect of acclimation on photosystem I antenna was different; in fact, the stoichiometry of any Lhca antenna proteins with respect to photosystem I core complex was not affected by growth conditions. Despite this stability in antenna stoichiometry, photosystem I light harvesting function was shown to be regulated through different mechanisms like the control of photosystem I to photosystem II ratio and the association or dissociation of Lhcb polypeptides to photosystem I. PMID:17229724

  16. Probing active electron transfer branch in photosystem I reaction center.

    NASA Astrophysics Data System (ADS)

    Savikhin, Sergei; Dashdorj, Naranbaatar; Xu, Wu; Martinsson, Peter; Chitnis, Parag

    2003-03-01

    Complimentary point mutations were introduced at the primary electron acceptor sites in A and B branches of the photosystem I (PS I) reaction center (RC) from Synechocystis sp. PCC 6803 and their effect on the kinetics of the electron transfer process was studied by means of ultrafast pump-probe spectroscopy. The results indicate that in these species the electron transfer occurs primarily along the A-branch. Previous optical experiments on PS I complexes from Chlorella sorokiniana demonstrated that both branches of RC are equally active. That suggests that the directionality of electron transfer in PS I is species dependent.

  17. Photosystem II: The Light-Driven Water: Plastoquinone Odixoreductase

    NASA Astrophysics Data System (ADS)

    Wydrzynski, Thomas J.; Satoh, Kimiyuki

    Dedicated to the memory of one of the early pioneers in this field of research, Professor Gerald T. Babcock, the 34 inclusive chapters of the present volume cover all major aspects of the molecular biology, biochemistry, biophysics and physiology of Photosystem II. The chapters were variously authored by a total of 75 scientific experts from leading research centers in Europe, North America, Asia and Australia, making the book a truly international effort. The book is divided into several parts which detail the protein constituents, functional sites, tertiary structure, molecular dynamics and mechanisms of subunit assembly and homeostasis.

  18. Electron transfer pathways in photosystem I reaction centers

    NASA Astrophysics Data System (ADS)

    Ivashin, Nikolaj; Larsson, Sven

    2003-07-01

    Electron transfer following charge separation in the photosystem I (PSI) reaction center of Synechococcus elongatus is studied using theoretical methods. The difference in rate between two almost symmetrical A- and B-branches is caused by a difference in a single residue (Trp B673 versus Gly A693), close to the F X iron-sulfur cluster. Partly due to its polar environment, Trp B673 acts as an electron acceptor in its π-system. The rate increases on the B-side due to shortened distances for electron transfer.

  19. 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. PMID:19169839

  20. Consistency of genome-wide associations across major ancestral groups.

    PubMed

    Ntzani, Evangelia E; Liberopoulos, George; Manolio, Teri A; Ioannidis, John P A

    2012-07-01

    It is not well known whether genetic markers identified through genome-wide association studies (GWAS) confer similar or different risks across people of different ancestry. We screened a regularly updated catalog of all published GWAS curated at the NHGRI website for GWAS-identified associations that had reached genome-wide significance (p ≤ 5 × 10(-8)) in at least one major ancestry group (European, Asian, African) and for which replication data were available for comparison in at least two different major ancestry groups. These groups were compared for the correlation between and differences in risk allele frequencies and genetic effects' estimates. Data on 108 eligible GWAS-identified associations with a total of 900 datasets (European, n = 624; Asian, n = 217; African, n = 60) were analyzed. Risk-allele frequencies were modestly correlated between ancestry groups, with >10% absolute differences in 75-89% of the three pairwise comparisons of ancestry groups. Genetic effect (odds ratio) point estimates between ancestry groups correlated modestly (pairwise comparisons' correlation coefficients: 0.20-0.33) and point estimates of risks were opposite in direction or differed more than twofold in 57%, 79%, and 89% of the European versus Asian, European versus African, and Asian versus African comparisons, respectively. The modest correlations, differing risk estimates, and considerable between-association heterogeneity suggest that differential ancestral effects can be anticipated and genomic risk markers may need separate further evaluation in different ancestry groups. PMID:22183176

  1. 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

  2. Female rule in lemurs is ancestral and hormonally mediated.

    PubMed

    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

  3. 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

  4. 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

  5. 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. PMID:27104872

  6. 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

  7. 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.

  8. 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. PMID:25747397

  9. 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.

  10. 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

  11. 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.

  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. Lateral Heterogeneity of Photosystems in Thylakoid Membranes Studied by Brownian Dynamics Simulations

    PubMed Central

    Borodich, Andrei; Rojdestvenski, Igor; Cottam, Michael

    2003-01-01

    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. PMID:12885627

  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. PMID:12885627

  15. Loss of phylloquinone in Chlamydomonas affects plastoquinone pool size and photosystem II synthesis.

    PubMed

    Lefebvre-Legendre, Linnka; Rappaport, Fabrice; Finazzi, Giovanni; Ceol, Mauro; Grivet, Chantal; Hopfgartner, Gérard; Rochaix, Jean-David

    2007-05-01

    Phylloquinone functions as the electron transfer cofactor at the A(1) site of photosystem I. We have isolated and characterized a mutant of Chlamydomonas reinhardtii, menD1, that is deficient in MenD, which encodes 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase, an enzyme that catalyzes the first specific step of the phylloquinone biosynthetic pathway. The mutant is photosynthetically active but light-sensitive. Analysis of total pigments by mass spectrometry reveals that phylloquinone is absent in menD1, but plastoquinone levels are not affected. This is further confirmed by the rescue of menD1 by addition of phylloquinone to the growth medium. Analysis of electron transfer by absorption spectroscopy indicates that plastoquinone replaces phylloquinone in photosystem I and that electron transfer from A(1) to the iron-sulfur centers is slowed down at least 40-fold. Consistent with a replacement of phylloquinone by plastoquinone, the size of the free plastoquinone pool of menD1 is reduced by 20-30%. In contrast to cyanobacterial MenD-deficient mutants, photosystem I accumulates normally in menD1, whereas the level of photosystem II declines. This decrease is because of reduced synthesis of the photosystem II core subunits. The relationship between plastoquinone occupancy of the A(1) site in photosystem I and the reduced accumulation of photosystem II is discussed. PMID:17339322

  16. 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

  17. 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.

  18. 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

  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. Wiring photosystem I for direct solar hydrogen production.

    PubMed

    Lubner, Carolyn E; Grimme, Rebecca; Bryant, Donald A; Golbeck, John H

    2010-01-26

    The generation of H(2) by the use of solar energy is a promising way to supply humankind's energy needs while simultaneously mitigating environmental concerns that arise due to climate change. The challenge is to find a way to connect a photochemical module that harnesses the sun's energy to a catalytic module that generates H(2) with high quantum yields and rates. In this review, we describe a technology that employs a "molecular wire" to connect a terminal [4Fe-4S] cluster of Photosystem I directly to a catalyst, which can be either a Pt nanoparticle or the distal [4Fe-4S] cluster of an [FeFe]- or [NiFe]-hydrogenase enzyme. The keys to connecting these two moieties are surface-located cysteine residues, which serve as ligands to Fe-S clusters and which can be changed through site-specific mutagenesis to glycine residues, and the use of a molecular wire terminated in sulfhydryl groups to connect the two modules. The sulfhydryl groups at the end of the molecular wire form a direct chemical linkage to a suitable catalyst or can chemically rescue a [4Fe-4S] cluster, thereby generating a strong coordination bond. Specifically, the molecular wire can connect the F(B) iron-sulfur cluster of Photosystem I either to a Pt nanoparticle or, by using the same type of genetic modification, to the differentiated iron atom of the distal [4Fe-4S].(Cys)(3)(Gly) cluster of hydrogenase. When electrons are supplied by a sacrificial donor, this technology forms the cathode of a photochemical half-cell that evolves H(2) when illuminated. If such a device were connected to the anode of a photochemical half-cell that oxidizes water, an in vitro solar energy converter could be realized that generates only O(2) and H(2) in the light. A similar methodology can be used to connect Photosystem I to other redox proteins that have surface-located [4Fe-4S] clusters. The controlled light-driven production of strong reductants by such systems can be used to produce other biofuels or to provide

  1. 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.

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    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.

  4. Photoinhibition of photosystem I under high light in the shade-established tropical tree species Psychotria rubra

    PubMed Central

    Huang, Wei; Zhang, Shi-Bao; Zhang, Jiao-Lin; Hu, Hong

    2015-01-01

    The photosynthetic sensitivity to high light differs among understory plants of shade- and sun- established tree species. Shade-established tree species are sensitive to high light but the underlying photosynthetic mechanism has not been fully resolved. In the present study, we examined the responses of photosystem I (PSI) and photosystem II (PSII) to high light in shade leaves of a shade-established tree species Psychotria rubra and a sun-established tree species Pometia tomentosa. After exposure to 2000 μmol photons m–2 s–1 for 2 h, the maximum photo-oxidizable P700 (Pm) decreased by 40 and 9% in P. rubra and P. tomentosa, respectively. These results indicate that the shade-established species P. rubra is incapable of protecting PSI under high light. Strong photoinhibition of PSII under high light led to large depression of electron transfer from PSII to PSI and then prevented further photodamage to PSI. During the high light treatment of 2000 μmol photons m–2 s–1, PSI photoinhibition in P. rubra was accompanied with high levels of cyclic electron flow (CEF) and P700 oxidation ratio. Therefore, we propose that PSI photoinhibition under high light in P. rubra is dependent on electron transfer from PSII to PSI, and CEF is unlikely to play a major role in photoprotection for PSI in P. rubra. These findings suggest that photoinhibition of PSI is another important mechanism underlying why shade-established species cannot survive under high light. PMID:26483816

  5. 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

  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. PMID:26697050

  7. 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

  8. 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

  9. 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

  10. Structure of plant photosystem I revealed by theoretical modeling.

    PubMed

    Jolley, Craig; Ben-Shem, Adam; Nelson, Nathan; Fromme, Petra

    2005-09-30

    Photosystem (PS) I is a large membrane protein complex vital for oxygenic photosynthesis, one of the most important biological processes on the planet. We present an "atomic" model of higher plant PSI, based on theoretical modeling using the recent 4.4 angstroms x-ray crystal structure of PSI from pea. Because of the lack of information on the amino acid side chains in the x-ray structural model and the high cofactor content in this system, novel modeling techniques were developed. Our model reveals some important structural features of plant PSI that were not visible in the crystal structure, and our model sheds light on the evolutionary relationship between plant and cyanobacterial PSI. PMID:15955818

  11. Polarization-dependent single-molecule spectroscopy on photosystem I

    NASA Astrophysics Data System (ADS)

    Skandary, S.; Konrad, A.; Hussels, M.; Meixner, A. J.; Brecht, M.

    2015-08-01

    Single-molecule spectroscopy (SMS) at low temperature was used to study the spectral properties, heterogeneities and spectral dynamics of the chlorophyll a (Chl a) molecules responsible for the fluorescence emission of photosystem I (PS I). The fluorescence spectra of single PS I complexes are dominated by several red-shifted Chl a molecules categorized into red pools called C708 and C719. By polarization dependent measurements we demonstrate spectrally separate emissions corresponding to C708 and C719 in single PS I monomers and trimers. Moreover, we compared the results of SMS polarization dependent between monomeric and trimeric PS I complexes and give an estimation for the orientation between these red pools. As a consequence, we get new insight into the energy transfer towards and between the red Chl a molecules in PS I complexes.

  12. 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

  13. Pathogenesis of autoimmune diseases associated with 8.1 ancestral haplotype: effect of multiple gene interactions.

    PubMed

    Candore, Giuseppina; Lio, Domenico; Colonna Romano, Giuseppina; Caruso, Calogero

    2002-02-01

    Genetic studies have shown that individuals with certain HLA alleles have a higher risk of specific autoimmune disease than those without these alleles. Particularly, the association in all Caucasian populations of an impressive number of autoimmune diseases with genes from the HLA-B8,DR3 haplotype that is part of the ancestral haplotype (AH) 8.1 HLA-A1, Cw7, B8, TNFAB*a2b3, TNFN*S, C2*C, Bf*s, C4A*Q0, C4B*1, DRB1*0301, DRB3*0101, DQA1*0501, DQB1*0201 has been reported by different research groups. This haplotype, the more common one in northern Europe, is also associated in healthy subjects with a number of immune system dysfunctions. It has been proposed that a small number of genes within the 8.1 AH modify immune responsiveness and hence affect multiple immunopathological diseases. In this paper, the characteristic features of this haplotype that might give rise to these diverse conditions are reviewed, focusing on the role of multiple gene interactions in disease susceptibility of 8.1 AH. PMID:12849055

  14. 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

  15. 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

  16. Excitation energy transfer and charge separation in photosystem II membranes revisited.

    PubMed

    Broess, Koen; Trinkunas, Gediminas; van der Weij-de Wit, Chantal D; Dekker, Jan P; van Hoek, Arie; van Amerongen, Herbert

    2006-11-15

    We have performed time-resolved fluorescence measurements on photosystem II (PSII) containing membranes (BBY particles) from spinach with open reaction centers. The decay kinetics can be fitted with two main decay components with an average decay time of 150 ps. Comparison with recent kinetic exciton annihilation data on the major light-harvesting complex of PSII (LHCII) suggests that excitation diffusion within the antenna contributes significantly to the overall charge separation time in PSII, which disagrees with previously proposed trap-limited models. To establish to which extent excitation diffusion contributes to the overall charge separation time, we propose a simple coarse-grained method, based on the supramolecular organization of PSII and LHCII in grana membranes, to model the energy migration and charge separation processes in PSII simultaneously in a transparent way. All simulations have in common that the charge separation is fast and nearly irreversible, corresponding to a significant drop in free energy upon primary charge separation, and that in PSII membranes energy migration imposes a larger kinetic barrier for the overall process than primary charge separation. PMID:16861268

  17. Phytotoxicity of Four Photosystem II Herbicides to Tropical Seagrasses

    PubMed Central

    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/Fm′), 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

  18. 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

  19. Mechanism of proton-coupled quinone reduction in Photosystem II

    PubMed Central

    Saito, Keisuke; Rutherford, A. William; Ishikita, Hiroshi

    2013-01-01

    Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, QA and QB, working in series. QA is a one-electron carrier, whereas QB undergoes sequential reduction and protonation to form QBH2. QBH2 exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to QB•– occurs from the protonated, D1-His252 to QB•– via D1-Ser264. The second PT is likely to occur from D1-His215 to QBH− via an H-bond with an energy profile with a single well, resulting in the formation of QBH2 and the D1-His215 anion. The pathway for reprotonation of D1-His215– may involve bicarbonate, D1-Tyr246 and water in the QB site. Formate ligation to Fe2+ did not significantly affect the protonation of reduced QB, suggesting that formate inhibits QBH2 release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe3+ state in the presence of QB•–, a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for QB reduction is presented. PMID:23277574

  20. Mechanism of proton-coupled quinone reduction in Photosystem II.

    PubMed

    Saito, Keisuke; Rutherford, A William; Ishikita, Hiroshi

    2013-01-15

    Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, Q(A) and Q(B), working in series. Q(A) is a one-electron carrier, whereas Q(B) undergoes sequential reduction and protonation to form Q(B)H(2). Q(B)H(2) exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to Q(B)(•-) occurs from the protonated, D1-His252 to Q(B)(•)(-) via D1-Ser264. The second PT is likely to occur from D1-His215 to Q(B)H(-) via an H-bond with an energy profile with a single well, resulting in the formation of Q(B)H(2) and the D1-His215 anion. The pathway for reprotonation of D1-His215(-) may involve bicarbonate, D1-Tyr246 and water in the Q(B) site. Formate ligation to Fe(2+) did not significantly affect the protonation of reduced Q(B), suggesting that formate inhibits Q(B)H(2) release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe(3+) state in the presence of Q(B)(•-), a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for Q(B) reduction is presented. PMID:23277574

  1. Differential Roles of Carotenes and Xanthophylls in Photosystem I Photoprotection.

    PubMed

    Cazzaniga, Stefano; Bressan, Mauro; Carbonera, Donatella; Agostini, Alessandro; Dall'Osto, Luca

    2016-07-01

    Carotenes and their oxygenated derivatives, xanthophylls, are structural elements of the photosynthetic apparatus and contribute to increasing both the light-harvesting and photoprotective capacity of the photosystems. β-Carotene is present in both the core complexes and light-harvesting system (LHCI) of Photosystem (PS) I, while xanthophylls lutein and violaxanthin bind exclusively to its antenna moiety; another xanthophyll, zeaxanthin, which protects chloroplasts against photooxidative damage, binds to the LHCI complexes under conditions of excess light. We functionally dissected various components of the xanthophyll- and carotene-dependent photoprotection mechanism of PSI by analyzing two Arabidopsis mutants: szl1 plants, with a carotene content lower than that of the wild type, and npq1, with suppressed zeaxanthin formation. When exposed to excess light, the szl1 genotype displayed PSI photoinhibition stronger than that of wild-type plants, while removing zeaxanthin had no such effect. The PSI-LHCI complex purified from szl1 was more photosensitive than the corresponding wild-type and npq1 complexes, as is evident from its faster photobleaching and increased rate of singlet oxygen release, suggesting that β-carotene is crucial in controlling chlorophyll triplet formation. Accordingly, fluorescence-detected magnetic resonance analysis showed an increase in the amplitude of signals assigned to chlorophyll triplets in β-carotene-depleted complexes. When PSI was fractioned into its functional moieties, it was revealed that the boost in the rate of singlet oxygen release caused by β-carotene depletion was greater in LHCI than in the core complex. We conclude that PSI-LHCI complex-bound β-carotene elicits a protective response, consisting of a reduction in the yield of harmful triplet excited states, while accumulation of zeaxanthin plays a minor role in restoring phototolerance. PMID:27290879

  2. 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.

  3. 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

  4. Limited photosynthetic electron flow but no CO2 fixation in Chlamydomonas mutants lacking photosystem I.

    PubMed

    Cournac, L; Redding, K; Bennoun, P; Peltier, G

    1997-10-13

    By measuring O2 and CO2 exchange in mutants of the green alga Chlamydomonas reinhardtii in which genes encoding the reaction center of photosystem I (psaA or psaB) have been deleted, we found that a photosystem II-dependent electron flow using O2 as the final acceptor can be sustained in the light. However, in contrast with recent reports using other Chlamydomonas mutants (B4 and F8), we show here that CO2 fixation does not occur in the absence of photosystem I. By deleting the psaA gene in both B4 and F8 strains, we conclude that the ability of these mutants to fix CO2 in the light is due to the presence of residual amounts of photosystem I. PMID:9369234

  5. 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

  6. 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.

  7. 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.

  8. Effects of Light, Food Availability and Temperature Stress on the Function of Photosystem II and Photosystem I of Coral Symbionts

    PubMed Central

    Hoogenboom, Mia O.; Campbell, Douglas A.; Beraud, Eric; DeZeeuw, Katrina; Ferrier-Pagès, Christine

    2012-01-01

    Background Reef corals are heterotrophic coelenterates that achieve high productivity through their photosynthetic dinoflagellate symbionts. Excessive seawater temperature destabilises this symbiosis and causes corals to “bleach,” lowering their photosynthetic capacity. Bleaching poses a serious threat to the persistence of coral reefs on a global scale. Despite expanding research on the causes of bleaching, the mechanisms remain a subject of debate. Methodology/Principal Findings This study determined how light and food availability modulate the effects of temperature stress on photosynthesis in two reef coral species. We quantified the activities of Photosystem II, Photosystem I and whole chain electron transport under combinations of normal and stressful growth temperatures, moderate and high light levels and the presence or absence of feeding of the coral hosts. Our results show that PS1 function is comparatively robust against temperature stress in both species, whereas PS2 and whole chain electron transport are susceptible to temperature stress. In the symbiotic dinoflagellates of Stylophora pistillata the contents of chlorophyll and major photosynthetic complexes were primarily affected by food availability. In Turbinaria reniformis growth temperature was the dominant influence on the contents of the photosynthetic complexes. In both species feeding the host significantly protected photosynthetic function from high temperature stress. Conclusions/Significance Our findings support the photoinhibition model of coral bleaching and demonstrate that PS1 is not a major site for thermal damage during bleaching events. Feeding mitigates bleaching in two scleractinian corals, so that reef responses to temperature stresses will likely be influenced by the coinciding availabilities of prey for the host. PMID:22253915

  9. 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

  10. 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

  11. Hierarchical coarse-graining model for photosystem II including electron and excitation-energy transfer processes.

    PubMed

    Matsuoka, Takeshi; Tanaka, Shigenori; Ebina, Kuniyoshi

    2014-03-01

    We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achieve a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics. PMID:24418347

  12. 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

  13. Structural characterization of a plant photosystem I and NAD(P)H dehydrogenase supercomplex.

    PubMed

    Kouřil, Roman; Strouhal, Ondřej; Nosek, Lukáš; Lenobel, René; Chamrád, Ivo; Boekema, Egbert J; Šebela, Marek; Ilík, Petr

    2014-02-01

    Cyclic electron transport (CET) around photosystem I (PSI) plays an important role in balancing the ATP/NADPH ratio and the photoprotection of plants. The NAD(P)H dehydrogenase complex (NDH) has a key function in one of the CET pathways. Current knowledge indicates that, in order to fulfill its role in CET, the NDH complex needs to be associated with PSI; however, until now there has been no direct structural information about such a supercomplex. Here we present structural data obtained for a plant PSI-NDH supercomplex. Electron microscopy analysis revealed that in this supercomplex two copies of PSI are attached to one NDH complex. A constructed pseudo-atomic model indicates asymmetric binding of two PSI complexes to NDH and suggests that the low-abundant Lhca5 and Lhca6 subunits mediate the binding of one of the PSI complexes to NDH. On the basis of our structural data, we propose a model of electron transport in the PSI-NDH supercomplex in which the association of PSI to NDH seems to be important for efficient trapping of reduced ferredoxin by NDH. PMID:24313886

  14. Spatial distribution of the electric potential from photosystem I reaction centers in lipid vesicles.

    PubMed

    Pennisi, C P; Greenbaum, E; Yoshida, K

    2008-06-01

    Photosynthetic reaction centers are integral membrane complexes that produce a net transmembrane charge separation in response to light. The Photosystem I (PSI) complex is a thoroughly studied reaction center that has been proposed as a nanoscale photovoltaic structure in diverse applications, including activation of excitable cells by triggering of voltage-gated ion channels. An electrostatic model of a spherical lipid vesicle embedded with PSI and suspended in an aqueous medium is presented. The distribution of the electric potential is obtained by solving the nonlinear Poisson-Boltzmann equation with the finite-element method. The model predicts a maximum potential difference of 1.3 V between charges. This value depends mostly on the intrinsic dielectric constants of the reaction center and distance between charges. However, the potential distribution near the reaction center depends on the ionic strength of the aqueous medium. When the ionic strength is zero, the vesicle develops a transmembrane potential that increases linearly with the density of reaction centers. When the ionic strength increases, this potential difference approaches to zero. The main results of the simulations are consistent with previously reported experimental data. Based on the presented results, the potential application of PSI to light activation of voltage-gated ion channels is discussed. PMID:18556264

  15. 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

  16. Inactivation of the clpC1 gene encoding a chloroplast Hsp100 molecular chaperone causes growth retardation, leaf chlorosis, lower photosynthetic activity, and a specific reduction in photosystem content.

    PubMed

    Sjögren, Lars L E; MacDonald, Tara M; Sutinen, Sirkka; Clarke, Adrian K

    2004-12-01

    ClpC is a molecular chaperone of the Hsp100 family. In higher plants there are two chloroplast-localized paralogs (ClpC1 and ClpC2) that are approximately 93% similar in primary sequence. In this study, we have characterized two independent Arabidopsis (Arabidopsis thaliana) clpC1 T-DNA insertion mutants lacking on average 65% of total ClpC content. Both mutants display a retarded-growth phenotype, leaves with a homogenous chlorotic appearance throughout all developmental stages, and more perpendicular secondary influorescences. Photosynthetic performance was also impaired in both knockout lines, with relatively fewer photosystem I and photosystem II complexes, but no changes in ATPase and Rubisco content. However, despite the specific drop in photosystem I and photosystem II content, no changes in leaf cell anatomy or chloroplast ultrastructure were observed in the mutants compared to the wild type. Previously proposed functions for envelope-associated ClpC in chloroplast protein import and degradation of mistargeted precursors were examined and shown not to be significantly impaired in the clpC1 mutants. In the stroma, where the majority of ClpC protein is localized, marked increases of all ClpP paralogs were observed in the clpC1 mutants but less variation for the ClpR paralogs and a corresponding decrease in the other chloroplast-localized Hsp100 protein, ClpD. Increased amounts of other stromal molecular chaperones (Cpn60, Hsp70, and Hsp90) and several RNA-binding proteins were also observed. Our data suggest that overall ClpC as a stromal molecular chaperone plays a vital role in chloroplast function and leaf development and is likely involved in photosystem biogenesis. PMID:15563614

  17. Direct Measurement of the Effective Rate Constant for Primary Charge Separation in Isolated Photosystem II Reaction Centers

    SciTech Connect

    Greenfield, S. R.; Seibert, M.; Govindjee; Wasielewski, M. R.

    1997-03-27

    Transient absorption measurements of the pheophytin a anion band and Qx band bleach region using preferential excitation of P680 are performed on isolated photosystem II reaction centers to determine the effective rate constant for charge separtion. A novel analysis of the Qx band bleach region explicity takes the changing background into account in order to directly measure the rate of growth of the bleach. Both spectral regions reveal biphasic kinetics, with a ca. (8 ps)-1 rate constant for the faster component, and a ca. (50 ps)-1 rate constant for the slower component. We propose that the fster component corresponds to the effective rate constant for charge separation from within the equilibrated reaction center core and provides a lower limit for the intrinsic rate constant for charge separation. The slower component corresponds to charge separation that is limited by slow energy transfer from a long-wavelength accessory chlorophyll a.

  18. 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

  19. Social capital and health: evidence that ancestral trust promotes health among children of immigrants.

    PubMed

    Ljunge, Martin

    2014-12-01

    This paper presents evidence that generalized trust promotes health. Children of immigrants in a broad set of European countries with ancestry from across the world are studied. Individuals are examined within country of residence using variation in trust across countries of ancestry. The approach addresses reverse causality and concerns that the trust measure picks up institutional factors in the individual's contextual setting. There is a significant positive estimate of ancestral trust in explaining self-assessed health. The finding is robust to accounting for individual, parental, and extensive ancestral country characteristics. Individuals with higher ancestral trust are also less likely to be hampered by health problems in their daily life, providing evidence of trust influencing real life outcomes. Individuals with high trust feel and act healthier, enabling a more productive life. PMID:25464341

  20. Experimental evidence needed to demonstrate inter- and trans-generational effects of ancestral experiences in mammals

    PubMed Central

    Dias, Brian G.; Ressler, Kerry J.

    2015-01-01

    Environmental factors routinely influence an organism’s biology. The inheritance or transmission of such influences to descendant generations would be an efficient mode of information transfer across generations. The developmental stage at which a specific environment is encountered by the ancestral generation, and the number of generations over which information about that environment is registered, determines an inter- vs. trans-generational effect of ancestral influence. This commentary will outline the distinction between these influences. While seductive in principle, inter- and trans-generational inheritance in mammals is a hotly debated area of research inquiry. We present constructive criticism of such inheritance, and suggest potential experimental avenues for reconciliation. Finally, epigenetic mechanisms present an avenue for gene regulation that is dynamic. We briefly discuss how such malleability affords the potential for a reversal of any detrimental environmental influences that might have adversely impacted ancestral or descendant generations. PMID:25154497

  1. 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

  2. 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.

  3. Photoassembly of the Water-Oxidizing Complex in Photosystem II

    PubMed Central

    Dasgupta, Jyotishman; Ananyev, Gennady M; Dismukes, G. Charles

    2008-01-01

    The light-driven steps in the biogenesis and repair of the inorganic core comprising the O2-evolving center of oxygenic photosynthesis (photosystem II water-oxidation complex, PSII-WOC) are reviewed. These steps, known collectively as photoactivation, involve the photoassembly of the free inorganic cofactors to the cofactor-depleted PSII-(apo-WOC) driven by light and produce the active O2-evolving core comprised of Mn4CaOxCly. We focus on the functional role of the inorganic components as seen through the competition with non-native cofactors (“inorganic mutants”) on water oxidation activity, the rate of the photoassembly reaction, and on structural insights gained from EPR spectroscopy of trapped intermediates formed in the initial steps of the assembly reaction. A chemical mechanism for the initial steps in photoactivation is given that is based on these data. Photoactivation experiments offer the powerful insights gained from replacement of the native cofactors, which together with the recent X-ray structural data for the resting holoenzyme provide a deeper understanding of the chemistry of water oxidation. We also review some new directions in research that photoactivation studies have inspired that look at the evolutionary history of this remarkable catalyst. PMID:19190725

  4. Dissipative pathways in the photosystem-II antenna in plants.

    PubMed

    Duffy, Christopher D P; Ruban, Alexander V

    2015-11-01

    The antenna of photosystem II in plants possesses a remarkable functional flexibility, allowing for the photoprotective regulation of light-harvesting in the face of rapid fluctuations in light intensity. Central to this adaptability is the reversible formation of dissipative energy transfer pathways within the antenna that protect the reaction centres from a potentially damaging excess of excitation energy. The exact molecular nature of these pathways and the mechanism by which they form are still open questions within the field of photosynthesis research. We present a review of current knowledge on the subject. We discuss the multi-scale nature of these pathways, how intrinsic structural and electronic changes within individual antenna proteins are coupled to large scale changes in the structure and energetic connectivity of the membrane as a whole. We review the physical properties and likely validity of current competing models of the dissipation mechanism before discussing a recently studied general property of the dissipative pathways--the slow and economic nature of the NPQ quencher. This property reflects the finely-tuned nature of the quenching pathway, i.e., its ability to offer protection to the photosynthetic machinery without compromising normal photosynthetic function. PMID:26404506

  5. 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

  6. 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

  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. Water in Photosystem II: structural, functional and mechanistic considerations.

    PubMed

    Linke, Katrin; Ho, Felix M

    2014-01-01

    Water is clearly important for the functioning of Photosystem II (PSII). Apart from being the very substrate that needs to be transported in this water oxidation enzyme, water is also vital for the transport of protons to and from the catalytic center as well as other important co-factors and key residues in the enzyme. The latest crystal structural data of PSII have enabled detailed analyses of the location and possible function of water molecules in the enzyme. Significant progress has also been made recently in the investigation of channels and pathways through the protein complex. Through these studies, the mechanistic significance of water for PSII is becoming increasingly clear. An overview and discussion of key aspects of the current research on water in PSII is presented here. The role of water in three other systems (aquaporin, bacteriorhodopsin and cytochrome P450) is also outlined to illustrate further points concerning the central significance that water can have, and potential applications of these ideas for continued research on PSII. It is advocated that water be seen as an integral part of the protein and far from a mere solvent. PMID:23978393

  9. Redox potentials of chlorophylls in the photosystem II reaction center.

    PubMed

    Ishikita, Hiroshi; Loll, Bernhard; Biesiadka, Jacek; Saenger, Wolfram; Knapp, Ernst-Walter

    2005-03-15

    Water oxidation generating atmospheric oxygen occurs in photosystem II (PSII), a large protein-pigment complex located in the thylakoid membrane. The recent crystal structures at 3.2 and 3.5 A resolutions provide novel details on amino acid side chains, especially in the D1/D2 subunits. We calculated the redox potentials for one-electron oxidation of the chlorophyll a (Chla) molecules in PSII, considering the protein environment in atomic detail. The calculated redox potentials for the dimer Chla (P(D1/D2)) and accessory Chla (Chl(D1/D2)) were 1.11-1.30 V relative to the normal hydrogen electrode at pH 7, which is high enough for water oxidation. The D1/D2 proteins and their cofactors contribute approximately 390 mV to the enormous upshift of 470 mV compared to the redox potential of monomeric Chla in dimethylformamide. The other subunits are responsible for the remaining 80 mV. The high redox potentials of the two accessory Chla Chl(D1/D2) suggests that they also participate in the charge separation process. PMID:15751989

  10. Deformation of chlorin rings in the Photosystem II crystal structure.

    PubMed

    Saito, Keisuke; Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren; Kamiya, Nobuo; Ishikita, Hiroshi

    2012-05-29

    The crystal structure of Photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed deformations of chlorin rings in the chlorophylls for the first time. We investigated the degrees of chlorin ring deformation and factors that contributed to them in the PSII crystal structure, using a normal-coordinate structural decomposition procedure. The out-of-plane distortion of the P(D1) chlorin ring can be described predominantly by a large "doming mode" arising from the axial ligand, D1-His198, as well as the chlorophyll side chains and PSII protein environment. In contrast, the deformation of P(D2) was caused by a "saddling mode" arising from the D2-Trp191 ring and the doming mode arising from D2-His197. Large ruffling modes, which were reported to lower the redox potential in heme proteins, were observed in P(D1) and Chl(D1), but not in P(D2) and Chl(D2). Furthermore, as P(D1) possessed the largest doming mode among the reaction center chlorophylls, the corresponding bacteriochlorophyll P(L) possessed the largest doming mode in bacterial photosynthetic reaction centers. However, the majority of the redox potential shift in the protein environment was determined by the electrostatic environment. The difference in the chlorin ring deformation appears to directly refer to the difference in "the local steric protein environment" rather than the redox potential value in PSII. PMID:22568617

  11. Function of redox-active tyrosine in photosystem II.

    PubMed

    Ishikita, Hiroshi; Knapp, Ernst-Walter

    2006-06-01

    Water oxidation at photosystem II Mn-cluster is mediated by the redox-active tyrosine Y(Z). We calculated the redox potential (E(m)) of Y(Z) and its symmetrical counterpart Y(D), by solving the linearized Poisson-Boltzmann equation. The calculated E(m)(Y( )/Y(-)) were +926 mV/+694 mV for Y(Z)/Y(D) with the Mn-cluster in S2 state. Together with the asymmetric position of the Mn-cluster relative to Y(Z/D), differences in H-bond network between Y(Z) (Y(Z)/D1-His(190)/D1-Asn(298)) and Y(D) (Y(D)/D2-His(189)/D2-Arg(294)/CP47-Glu(364)) are crucial for E(m)(Y(Z/D)). When D1-His(190) is protonated, corresponding to a thermally activated state, the calculated E(m)(Y(Z)) was +1216 mV, which is as high as the E(m) for P(D1/D2). We observed deprotonation at CP43-Arg(357) upon S-state transition, which may suggest its involvement in the proton exit pathway. E(m)(Y(D)) was affected by formation of P(D2)(+) (but not P(D1)(+)) and sensitive to the protonation state of D2-Arg(180). This points to an electrostatic link between Y(D) and P(D2). PMID:16513785

  12. 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

  13. Structure/Function/Dynamics of Photosystem II Plastoquinone Binding Sites

    PubMed Central

    Lambreva, Maya D.; Russo, Daniela; Polticelli, Fabio; Scognamiglio, Viviana; Antonacci, Amina; Zobnina, Veranika; Campi, Gaetano; Rea, Giuseppina

    2014-01-01

    Photosystem II (PSII) continuously attracts the attention of researchers aiming to unravel the riddle of its functioning and efficiency fundamental for all life on Earth. Besides, an increasing number of biotechnological applications have been envisaged exploiting and mimicking the unique properties of this macromolecular pigment-protein complex. The PSII organization and working principles have inspired the design of electrochemical water splitting schemes and charge separating triads in energy storage systems as well as biochips and sensors for environmental, agricultural and industrial screening of toxic compounds. An intriguing opportunity is the development of sensor devices, exploiting native or manipulated PSII complexes or ad hoc synthesized polypeptides mimicking the PSII reaction centre proteins as bio-sensing elements. This review offers a concise overview of the recent improvements in the understanding of structure and function of PSII donor side, with focus on the interactions of the plastoquinone cofactors with the surrounding environment and operational features. Furthermore, studies focused on photosynthetic proteins structure/function/dynamics and computational analyses aimed at rational design of high-quality bio-recognition elements in biosensor devices are discussed. PMID:24678671

  14. 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. PMID:25897076

  15. 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

  16. (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.

  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. Does body posture influence hand preference in an ancestral primate model?

    PubMed Central

    2011-01-01

    Background The origin of human handedness and its evolution in primates is presently under debate. Current hypotheses suggest that body posture (postural origin hypothesis and bipedalism hypothesis) have an important impact on the evolution of handedness in primates. To gain insight into the origin of manual lateralization in primates, we studied gray mouse lemurs, suggested to represent the most ancestral primate condition. First, we investigated hand preference in a simple food grasping task to explore the importance of hand usage in a natural foraging situation. Second, we explored the influence of body posture by applying a forced food grasping task with varying postural demands (sit, biped, cling, triped). Results The tested mouse lemur population did not prefer to use their hands alone to grasp for food items. Instead, they preferred to pick them up using a mouth-hand combination or the mouth alone. If mouth usage was inhibited, they showed an individual but no population level handedness for all four postural forced food grasping tasks. Additionally, we found no influence of body posture on hand preference in gray mouse lemurs. Conclusion Our results do not support the current theories of primate handedness. Rather, they propose that ecological adaptation indicated by postural habit and body size of a given species has an important impact on hand preference in primates. Our findings suggest that small-bodied, quadrupedal primates, adapted to the fine branch niche of dense forests, prefer mouth retrieval of food and are less manually lateralized than large-bodied species which consume food in a more upright, and less stable body posture. PMID:21356048

  19. 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

  20. Hypercontrols in Genotype-Phenotype Analysis Reveal Ancestral Haplotypes Associated With Essential Hypertension

    PubMed Central

    Balam-Ortiz, Eros; Esquivel-Villarreal, Adolfo; Huerta-Hernandez, David; Fernandez-Lopez, Juan Carlos; Alfaro-Ruiz, Luis; Muñoz-Monroy, Omar; Gutierrez, Ruth; Figueroa-Genis, Enrique; Carrillo, Karol; Elizalde, Adela; Hidalgo, Alfredo; Rodriguez, Mauricio; Urushihara, Maki; Kobori, Hiroyuki; Jimenez-Sanchez, Gerardo

    2012-01-01

    The angiotensinogen gene locus has been associated with essential hypertension in most populations analyzed to date. Increased plasma angiotensinogen levels have been proposed as an underlying cause of essential hypertension in whites; however, differences in the genetic regulation of plasma angiotensinogen levels have also been reported for other populations. The aim of this study was to analyze the relationship between angiotensinogen gene polymorphisms and haplotypes with plasma angiotensinogen levels and the risk of essential hypertension in the Mexican population. We genotyped 9 angiotensinogen gene polymorphisms in 706 individuals. Four polymorphisms, A-6, C4072, C6309, and G12775, were associated with increased risk, and the strongest association was found for the C6309 allele (χ2 = 23.9; P = 0.0000009), which resulted in an odds ratio of 3.0 (95% CI: 1.8–4.9; P = 0.000006) in the recessive model. Two polymorphisms, A-20C (P = 0.003) and C3389T (P = 0.0001), were associated with increased plasma angiotensinogen levels but did not show association with essential hypertension. The haplotypes H1 (χ2 = 8.1; P = 0.004) and H5 (χ2 = 5.1; P = 0.02) were associated with essential hypertension. Using phylogenetic analysis, we found that haplotypes 1 and 5 are the human ancestral haplotypes. Our results suggest that the positive association between angiotensinogen gene polymorphisms and haplotypes with essential hypertension is not simply explained by an increase in plasma angiotensinogen concentration. Complex interactions between risk alleles suggest that these haplotypes act as “superalleles.” PMID:22371359

  1. Hypercontrols in genotype-phenotype analysis reveal ancestral haplotypes associated with essential hypertension.

    PubMed

    Balam-Ortiz, Eros; Esquivel-Villarreal, Adolfo; Huerta-Hernandez, David; Fernandez-Lopez, Juan Carlos; Alfaro-Ruiz, Luis; Muñoz-Monroy, Omar; Gutierrez, Ruth; Figueroa-Genis, Enrique; Carrillo, Karol; Elizalde, Adela; Hidalgo, Alfredo; Rodriguez, Mauricio; Urushihara, Maki; Kobori, Hiroyuki; Jimenez-Sanchez, Gerardo

    2012-04-01

    The angiotensinogen gene locus has been associated with essential hypertension in most populations analyzed to date. Increased plasma angiotensinogen levels have been proposed as an underlying cause of essential hypertension in whites; however, differences in the genetic regulation of plasma angiotensinogen levels have also been reported for other populations. The aim of this study was to analyze the relationship between angiotensinogen gene polymorphisms and haplotypes with plasma angiotensinogen levels and the risk of essential hypertension in the Mexican population. We genotyped 9 angiotensinogen gene polymorphisms in 706 individuals. Four polymorphisms, A-6, C4072, C6309, and G12775, were associated with increased risk, and the strongest association was found for the C6309 allele (χ(2)=23.9; P=0.0000009), which resulted in an odds ratio of 3.0 (95% CI: 1.8-4.9; P=0.000006) in the recessive model. Two polymorphisms, A-20C (P=0.003) and C3389T (P=0.0001), were associated with increased plasma angiotensinogen levels but did not show association with essential hypertension. The haplotypes H1 (χ(2)=8.1; P=0.004) and H5 (χ(2)=5.1; P=0.02) were associated with essential hypertension. Using phylogenetic analysis, we found that haplotypes 1 and 5 are the human ancestral haplotypes. Our results suggest that the positive association between angiotensinogen gene polymorphisms and haplotypes with essential hypertension is not simply explained by an increase in plasma angiotensinogen concentration. Complex interactions between risk alleles suggest that these haplotypes act as "superalleles." PMID:22371359

  2. 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

  3. Topological studies of spinach 22 kDa protein of Photosystem II.

    PubMed

    Kim, S; Pichersky, E; Yocum, C F

    1994-12-30

    An intrinsic 22 kDa polypeptide is associated with the O2-evolving Photosystem II core complex in a variety of green plants, although it does not appear to be required for O2 evolution. Digestion of thylakoid membranes and isolated Photosystem II preparations with trypsin, followed by immunoblotting using spinach anti-22 kDa antibodies, leads to two observations: (1) the domain between the 2nd and 3rd transmembrane helices of the 22 kDa protein is stromally exposed, and (2) only in a reaction center complex preparation, lacking the chlorophyll a/b-light harvesting complex II, is there extensive proteolytic cleavage of the 22 kDa protein. We also found that after, but not prior to, selective extraction of the 22 and 10 kDa proteins from Photosystem II membranes, the chlorophyll a/b-light harvesting complex II can be separated from the Photosystem II reaction center core by precipitation with MgCl2. This result suggests that the 22 kDa polypeptide is located between the Photosystem II reaction center polypeptides and light-harvesting complex II; it is possible that the protein serves as a link between the two protein complexes. The presence of the 22 kDa protein in several species was also examined by immunoblotting with polyclonal spinach anti-22 kDa antibodies. PMID:7803450

  4. TEF30 Interacts with Photosystem II Monomers and Is Involved in the Repair of Photodamaged Photosystem II in Chlamydomonas reinhardtii.

    PubMed

    Muranaka, Ligia Segatto; Rütgers, Mark; Bujaldon, Sandrine; Heublein, Anja; Geimer, Stefan; Wollman, Francis-André; Schroda, Michael

    2016-02-01

    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

  5. 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

  6. Consequences of Decreased Light Harvesting Capability on Photosystem II Function in Synechocystis sp. PCC 6803

    PubMed Central

    Nagarajan, Aparna; Page, Lawrence E.; Liberton, Michelle; Pakrasi, Himadri B.

    2014-01-01

    Cyanobacteria use large pigment-protein complexes called phycobilisomes to harvest light energy primarily for photosystem II (PSII). We used a series of mutants with partial to complete reduction of phycobilisomes to examine the effects of antenna truncation on photosystem function in Synechocystis sp. PCC 6803. The antenna mutants CB, CK, and PAL expressed increasing levels of functional PSII centers to compensate for the loss of phycobilisomes, with a concomitant decrease in photosystem I (PSI). This increased PSII titer led to progressively higher oxygen evolution rates on a per chlorophyll basis. The mutants also exhibited impaired S-state transition profiles for oxygen evolution. Additionally, P700+ re-reduction rates were impacted by antenna reduction. Thus, a decrease in antenna size resulted in overall physiological changes in light harvesting and delivery to PSII as well as changes in downstream electron transfer to PSI. PMID:25513759

  7. 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.

  8. NMR analysis of the transient complex between membrane photosystem I and soluble cytochrome c6.

    PubMed

    Díaz-Moreno, Irene; Díaz-Quintana, Antonio; Molina-Heredia, Fernando P; Nieto, Pedro M; Hansson, Orjan; De la Rosa, Miguel A; Karlsson, B Göran

    2005-03-01

    A structural analysis of the surface areas of cytochrome c(6), responsible for the transient interaction with photosystem I, was performed by NMR transverse relaxation-optimized spectroscopy. The hemeprotein was titrated by adding increasing amounts of the chlorophyllic photosystem, and the NMR spectra of the free and bound protein were analyzed in a comparative way. The NMR signals of cytochrome c(6) residues located at the hydrophobic and electrostatic patches, which both surround the heme cleft, were specifically modified by binding. The backbones of internal residues close to the hydrophobic patch of cytochrome c(6) were also affected, a fact that is ascribed to the conformational changes taking place inside the hemeprotein when interacting with photosystem I. To the best of our knowledge, this is the first structural analysis by NMR spectroscopy of a transient complex between soluble and membrane proteins. PMID:15611120

  9. Computer simulation of interaction of photosystem 1 with plastocyanin and ferredoxin.

    PubMed

    Kovalenko, Ilya B; Abaturova, Anna M; Riznichenko, Galina Yu; Rubin, Andrei B

    2011-02-01

    We designed 3D multiparticle computer models to simulate diffusion and interactions of spinach plastocyanin and ferredoxin with plant photosystem 1 in a solution. Using these models we studied kinetic characteristics of plastocyanin-photosystem 1 and ferredoxin-photosystem 1 complex formation at a variety of ionic strength values. The computer multiparticle models demonstrate non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Our calculations show that the decrease in the association second-order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in "wrong" orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer. PMID:20934483

  10. Polypeptide composition of the purified photosystem II pigment-protein complex from spinach.

    PubMed

    Satoh, K

    1979-04-11

    The Photosystem II pigment-protein complex, the chlorophyll alpha-protein comprising the reaction center of Photosystem II, was prepared from EDTA-treated spinach chloroplasts by digitonin extraction, sucrose-gradient centrifugation, DEAE-cellulose column chromatography, and isoelectrofocussing on Ampholine. The dissociated pigment-protein complex exhibits two polypeptide subunits that migrate in SDS-polyacrylamide gel with electrophoretic mobilities corresponding to molecular weights of approximately 43,000 and 27,000. the chlorophyll was always found in the free pigment zone at the completion of the electrophoresis. Heat-treatment of the sample (100 degrees C, 90 s) for electrophoresis caused association of the two polypeptides into large aggregates. It is concluded that these two polypeptides, 43,000 and 27,000, are valid structural or functional components of Photosystem II pigment-protein complex. PMID:444494

  11. Three-dimensional structure of cyanobacterial photosystem I at 2.5Å resolution

    NASA Astrophysics Data System (ADS)

    Jordan, Patrick; Fromme, Petra; Witt, Horst Tobias; Klukas, Olaf; Saenger, Wolfram; Krauß, Norbert

    2001-06-01

    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.

  12. 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

  13. 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

  14. Hydrogen Production in Chlamydomonas: Photosystem II-Dependent and -Independent Pathways Differ in Their Requirement for Starch Metabolism1[W

    PubMed Central

    Chochois, Vincent; Dauvillée, David; Beyly, Audrey; Tolleter, Dimitri; Cuiné, Stéphan; Timpano, Hélène; Ball, Steven; Cournac, Laurent; Peltier, Gilles

    2009-01-01

    Under sulfur deprivation conditions, the green alga Chlamydomonas reinhardtii produces hydrogen in the light in a sustainable manner thanks to the contribution of two pathways, direct and indirect. In the direct pathway, photosystem II (PSII) supplies electrons to hydrogenase through the photosynthetic electron transport chain, while in the indirect pathway, hydrogen is produced in the absence of PSII through a photosystem I-dependent process. Starch metabolism has been proposed to contribute to both pathways by feeding respiration and maintaining anoxia during the direct pathway and by supplying reductants to the plastoquinone pool during the indirect pathway. At variance with this scheme, we report that a mutant lacking starch (defective for sta6) produces similar hydrogen amounts as the parental strain in conditions of sulfur deprivation. However, when PSII is inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea, conditions where hydrogen is produced by the indirect pathway, hydrogen production is strongly reduced in the starch-deficient mutant. We conclude that starch breakdown contributes to the indirect pathway by feeding electrons to the plastoquinone pool but is dispensable for operation of the direct pathway that prevails in the absence of DCMU. While hydrogenase induction was strongly impaired in the starch-deficient mutant under dark anaerobic conditions, wild-type-like induction was observed in the light. Because this light-driven hydrogenase induction is DCMU insensitive and strongly inhibited by carbonyl cyanide-p-trifluoromethoxyphenylhydrazone or 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, we conclude that this process is regulated by the proton gradient generated by cyclic electron flow around PSI. PMID:19700559

  15. 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. PMID:26275856

  16. 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. PMID:24461774

  17. Ancestral TCDD exposure promotes epigenetic transgenerational inheritance of imprinted gene Igf2: Methylation status and DNMTs.

    PubMed

    Ma, Jing; Chen, Xi; Liu, Yanan; Xie, Qunhui; Sun, Yawen; Chen, Jingshan; Leng, Ling; Yan, Huan; Zhao, Bin; Tang, Naijun

    2015-12-01

    Ancestral TCDD exposure could induce epigenetic transgenerational phenotypes, which may be mediated in part by imprinted gene inheritance. The aim of our study was to evaluate the transgenerational effects of ancestral TCDD exposure on the imprinted gene insulin-like growth factor-2 (Igf2) in rat somatic tissue. TCDD was administered daily by oral gavage to groups of F0 pregnant SD rats at dose levels of 0 (control), 200 or 800 ng/kg bw during gestation day 8-14. Animal transgenerational model of ancestral exposure to TCDD was carefully built, avoiding sibling inbreeding. Hepatic Igf2 expression of the TCDD male progeny was decreased concomitantly with hepatic damage and increased activities of serum hepatic enzymes both in the F1 and F3 generation. Imprinted Control Region (ICR) of Igf2 manifested a hypermethylated pattern, whereas methylation status in the Differentially Methylated Region 2 (DMR2) showed a hypomethylated manner in the F1 generation. These epigenetic alterations in these two regions maintained similar trends in the F3 generation. Meanwhile, the expressions of DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) changed in a non-monotonic manner both in the F1 and F3 generation. This study provides evidence that ancestral TCDD exposure may promote epigenetic transgenerational alterations of imprinted gene Igf2 in adult somatic tissue. PMID:26455773

  18. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell

    PubMed Central

    Makarova, Kira S.; Wolf, Yuri I.; Mekhedov, Sergey L.; Mirkin, Boris G.; Koonin, Eugene V.

    2005-01-01

    Gene duplication is a crucial mechanism of evolutionary innovation. A substantial fraction of eukaryotic genomes consists of paralogous gene families. We assess the extent of ancestral paralogy, which dates back to the last common ancestor of all eukaryotes, and examine the origins of the ancestral paralogs and their potential roles in the emergence of the eukaryotic cell complexity. A parsimonious reconstruction of ancestral gene repertoires shows that 4137 orthologous gene sets in the last eukaryotic common ancestor (LECA) map back to 2150 orthologous sets in the hypothetical first eukaryotic common ancestor (FECA) [paralogy quotient (PQ) of 1.92]. Analogous reconstructions show significantly lower levels of paralogy in prokaryotes, 1.19 for archaea and 1.25 for bacteria. The only functional class of eukaryotic proteins with a significant excess of paralogous clusters over the mean includes molecular chaperones and proteins with related functions. Almost all genes in this category underwent multiple duplications during early eukaryotic evolution. In structural terms, the most prominent sets of paralogs are superstructure-forming proteins with repetitive domains, such as WD-40 and TPR. In addition to the true ancestral paralogs which evolved via duplication at the onset of eukaryotic evolution, numerous pseudoparalogs were detected, i.e. homologous genes that apparently were acquired by early eukaryotes via different routes, including horizontal gene transfer (HGT) from diverse bacteria. The results of this study demonstrate a major increase in the level of gene paralogy as a hallmark of the early evolution of eukaryotes. PMID:16106042

  19. Loss of ancestral N-glycosylation sites in conserved proteins during human evolution.

    PubMed

    Kim, Dong Seon; Choi, Dongjin; Hahn, Yoonsoo

    2015-12-01

    N-linked protein glycosylation is involved in various biological processes, such as protein quality control and adhesion or signaling among cells. The loss of ancestrally conserved N-glycosylation sites may result in the evolution of protein structure and function. In the present study, a mouse glycoproteome dataset and mammalian proteome data were assessed to identify 40 ancestral N-glycosylation sites in 37 proteins that disappeared during human evolution since the last common ancestor of the Euarchonta (primates and treeshrews). The results showed that each of the human proteins, CELSR1, ST3GAL5 and VSIG10, lost an ancestrally conserved N-glycosylation site following human-chimpanzee divergence. Notably, CELSR1 and ST3GAL5 are crucial for normal development and function of the mammalian nervous system, suggesting an association with the evolution of human cognitive function. Thus, the lost ancestrally conserved N-glycosylation sites identified in the present study may be useful targets for functional analyses to identify molecular changes linked with the evolution of human phenotypes. PMID:26458842

  20. Language Shift and Maintenance in Multilingual Mauritius: The Case of Indian Ancestral Languages

    ERIC Educational Resources Information Center

    Bissoonauth, Anu

    2011-01-01

    This paper reports on a research study conducted in Mauritius between June and July 2009. The aim of this research was to investigate the use of Indian ancestral languages in the domestic domain by the younger generations. The data were collected in the field by means of a questionnaire and interviews from a quota sample of secondary school…

  1. Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast

    PubMed Central

    van Welsem, Tibor; Friedman, Nir; Rando, Oliver J.; van Leeuwen, Fred

    2011-01-01

    Replicating chromatin involves disruption of histone-DNA contacts and subsequent reassembly of maternal histones on the new daughter genomes. In bulk, maternal histones are randomly segregated to the two daughters, but little is known about the fine details of this process: do maternal histones re-assemble at preferred locations or close to their original loci? Here, we use a recently developed method for swapping epitope tags to measure the disposition of ancestral histone H3 across the yeast genome over six generations. We find that ancestral H3 is preferentially retained at the 5′ ends of most genes, with strongest retention at long, poorly transcribed genes. We recapitulate these observations with a quantitative model in which the majority of maternal histones are reincorporated within 400 bp of their pre-replication locus during replication, with replication-independent replacement and transcription-related retrograde nucleosome movement shaping the resulting distributions of ancestral histones. We find a key role for Topoisomerase I in retrograde histone movement during transcription, and we find that loss of Chromatin Assembly Factor-1 affects replication-independent turnover. Together, these results show that specific loci are enriched for histone proteins first synthesized several generations beforehand, and that maternal histones re-associate close to their original locations on daughter genomes after replication. Our findings further suggest that accumulation of ancestral histones could play a role in shaping histone modification patterns. PMID:21666805

  2. Structural elements and organization of the ancestral translational machinery

    NASA Technical Reports Server (NTRS)

    Rein, R.; Srinivasan, S.; Mcdonald, J.; Raghunathan, G.; Shibata, M.

    1987-01-01

    The molecular mechanisms of the primitive translational apparatus are discussed in the framework of present-day protein biosynthesis. The structural necessities of an early adaptor and the multipoint recognition properties of such an adaptor are investigated on the basis of structure/function relationships found in a contemporary system and a molecular model of the contemporary transpeptidation complex. A model of the tRNA(Tyr)-tyrosyl tRNA synthetase complex including the positioning of the disordered region is proposed; the model is used to illustrate the required recognition properties of the ancestor aminoacyl synthetase.

  3. Photochemical reactions of photosystem II in ethylene glycol.

    PubMed

    Hillier, W; Lukins, P; Seibert, M; Wydrzynski, T

    1997-01-01

    The behavior of photosystem II (PSII) reactions was investigated under conditions of decreasing water content by the addition of increasing concentrations of ethylene glycol (EG). The photosynthetic activities were measured for PSII samples either directly in aqueous solutions of EG or in the standard buffer medium following EG treatment. Several effects on PSII arise upon exposure to EG. Below 50% EG there are no significant irreversible changes, although there is a slowing of the QA-reoxidation kinetics in the presence of EG. At concentrations of 50-70% EG, protein structural changes occur that include the release of the 16, 23, and 33 kDa extrinsic proteins and two of the catalytic Mn ions. For these samples, the capacity for O2 evolution is considerably reduced and the formation of donor side H2O2 is enhanced. In 60% EG, the nanosecond components in the rate of P680+ reduction are converted entirely to microsecond kinetics which upon return of the sample to the standard buffer medium are partially restored, indicating that EG has a reversible, solvent effect on the PSII donor side. At concentrations of EG > 70% chlorophyll fluorescence measurements reveal reversible increases in the FO level concomitant with the generation and disappearance of a 5 microseconds decay component in the P680+ reduction kinetics. This result may indicate a solvent-induced uncoupling of the light harvesting pigment bed from the reaction center complex. As the EG concentration is increased to 80-100%, there is an irreversible loss of the primary charge separation. The use of EG as a cryoprotectant and as a water-miscible organic solvent for PSII is discussed. PMID:8993320

  4. Overwintering Periwinkle (Vinca minor L.) Exhibits Increased Photosystem I Activity 1

    PubMed Central

    Huner, N. P. A.; Krol, M.; Williams, J. P.; Maissan, E.

    1988-01-01

    The effects of natural, overwintering conditions on photosystem I and photosystem II activity were examined in isolated thylakoids of periwinkle (Vinca minor L.), an endemic, cold-tolerant, herbaceous evergreen. DCMU-Insensitive photosystem I activity (ascorbate/dichlorophenolindophenol → methylviologen) exhibited a twofold increase in light-saturated rates upon exposure to low temperature and freezing stress with no effect on the apparent quantum yield of this reaction. DCMU-Sensitive photosystem II activity (H2O → dichlorlophenolindophenol) exhibited only minor fluctuations in light-saturated rates but a 50% decrease in the apparent quantum yield of this reaction upon exposure to overwintering conditions. This was correlated with a decrease in the 77°K fluorescence emission at 694 nanometers. These functional changes occurred with no detectable changes in the relative chlorophyll contents of the chlorophyll-protein complexes or the chlorophyll-thylakoid protein. The chlorophyll a/b varied less than 10% during any single growth year. Analyses of total leaf extracts indicated that all lipid classes exhibited increased levels of linoleic and linolenic acid. Neither the trans-Δ3-hexadecenoic acid level nor the ratio of oligomeric:monomeric light harvesting of photosystem II was affected by exposure to winter stress. The content of the major chloroplast lipids monogalactosyldiacylglycerol, digalactosyldiacylglycerol, phosphatidyl-diacyl-glycerol, and sulfoquinovosyldiacylglycerol exhibited minor fluctuations, whereas phosphatidylcholine and phosphatidylethanolamine content doubled on a mole percent or chlorophyll basis. We conclude that the previously reported increase in photosystem I activity during controlled, low temperature growth is observed during exposure to natural overwintering conditions. This appears to occur with minimal changes in the structure and composition of the photosynthetic apparatus of periwinkle. PMID:16666214

  5. 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

  6. An Ancestral Recombination Graph for Diploid Populations with Skewed Offspring Distribution

    PubMed Central

    Birkner, Matthias; Blath, Jochen; Eldon, Bjarki

    2013-01-01

    A large offspring-number diploid biparental multilocus population model of Moran type is our object of study. At each time step, a pair of diploid individuals drawn uniformly at random contributes offspring to the population. The number of offspring can be large relative to the total population size. Similar “heavily skewed” reproduction mechanisms have been recently considered by various authors (cf. e.g., Eldon and Wakeley 2006, 2008) and reviewed by Hedgecock and Pudovkin (2011). Each diploid parental individual contributes exactly one chromosome to each diploid offspring, and hence ancestral lineages can coalesce only when in distinct individuals. A separation-of-timescales phenomenon is thus observed. A result of Möhle (1998) is extended to obtain convergence of the ancestral process to an ancestral recombination graph necessarily admitting simultaneous multiple mergers of ancestral lineages. The usual ancestral recombination graph is obtained as a special case of our model when the parents contribute only one offspring to the population each time. Due to diploidy and large offspring numbers, novel effects appear. For example, the marginal genealogy at each locus admits simultaneous multiple mergers in up to four groups, and different loci remain substantially correlated even as the recombination rate grows large. Thus, genealogies for loci far apart on the same chromosome remain correlated. Correlation in coalescence times for two loci is derived and shown to be a function of the coalescence parameters of our model. Extending the observations by Eldon and Wakeley (2008), predictions of linkage disequilibrium are shown to be functions of the reproduction parameters of our model, in addition to the recombination rate. Correlations in ratios of coalescence times between loci can be high, even when the recombination rate is high and sample size is large, in large offspring-number populations, as suggested by simulations, hinting at how to distinguish between

  7. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.

    PubMed

    Rannala, Bruce; Yang, Ziheng

    2003-08-01

    The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be approximately 20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models. PMID:12930768

  8. Frequency of carriers of 8.1 ancestral haplotype and its fragments in two Caucasian populations.

    PubMed

    Kiszel, Petra; Kovács, Margit; Szalai, Csaba; Yang, Yan; Pozsonyi, Eva; Blaskó, Bernadett; Laki, Judit; Prohászka, Zoltán; Fazakas, Adám; Pánczél, Pál; Hosszúfalusi, Nóra; Rajczy, Katalin; Wu, Yee-Ling; Chung, Erwin K; Zhou, Bi; Blanchong, Carol A; Vatay, Agnes; Yu, C Yung; Füst, G

    2007-01-01

    Within the human MHC region larger stretches of conserved DNA, called conserved ancestral haplotypes exist. However, many MHC haplotypes contain only fragments of an ancestral haplotype. Little is known, however, on relative distribution of the ancestral haplotypes to their fragments. Therefore we determined the frequency of carriers of the whole ancestral haplotype 8.1 (AH8.1) and its fragments in 127 healthy Hungarian people, 101 healthy Ohioian females, and in nine Hungarian families. The HLA-DQ2, HLA-DR3(17), RAGE -429C allele, the mono-S-C4B genotype, the HSP70-2 1267G allele and the TNF -308A (TNF2) allele were used as markers of the AH8.1. Frequency of carriers of the whole AH8.1 and its fragments was similar in the both populations. 18% of the subjects carried the whole AH8.1 in at least one chromosome, while 17-20%, 36-39%, and 24-29%, respectively carried two or three constituents of the haplotype, only one constituent or none of them. Similar results were obtained in the family study. In addition, marked differences were found in the relationship of the constituents' alleles to the whole AH8.1. In both populations, 29%, 50-59%, 52-56% and 76-96%, respectively of the carriers of HSP70-2 1267G, RAGE-429C, TNF2, and mono-S carriers carried the whole 8.1 haplotype. These findings may have important implications for studies of the disease associations with different MHC ancestral haplotypes. PMID:17558713

  9. Photosystem II repair in plant chloroplasts--Regulation, assisting proteins and shared components with photosystem II biogenesis.

    PubMed

    Järvi, Sari; Suorsa, Marjaana; Aro, Eva-Mari

    2015-09-01

    Photosystem (PS) II is a multisubunit thylakoid membrane pigment-protein complex responsible for light-driven oxidation of water and reduction of plastoquinone. Currently more than 40 proteins are known to associate with PSII, either stably or transiently. The inherent feature of the PSII complex is its vulnerability in light, with the damage mainly targeted to one of its core proteins, the D1 protein. The repair of the damaged D1 protein, i.e. the repair cycle of PSII, initiates in the grana stacks where the damage generally takes place, but subsequently continues in non-appressed thylakoid domains, where many steps are common for both the repair and de novo assembly of PSII. The sequence of the (re)assembly steps of genuine PSII subunits is relatively well-characterized in higher plants. A number of novel findings have shed light into the regulation mechanisms of lateral migration of PSII subcomplexes and the repair as well as the (re)assembly of the complex. Besides the utmost importance of the PSII repair cycle for the maintenance of PSII functionality, recent research has pointed out that the maintenance of PSI is closely dependent on regulation of the PSII repair cycle. This review focuses on the current knowledge of regulation of the repair cycle of PSII in higher plant chloroplasts. Particular emphasis is paid on sequential assembly steps of PSII and the function of the number of PSII auxiliary proteins involved both in the biogenesis and repair of PSII. This article is part of a Special Issue entitled: Chloroplast Biogenesis. PMID:25615587

  10. 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.