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Sample records for proposed ancestral photosystem

  1. Photosystem II

    ScienceCinema

    James Barber

    2016-07-12

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

  2. Are palaeoscolecids ancestral ecdysozoans?

    PubMed

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

    2010-01-01

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

  3. Photoinhibition of Photosystem II.

    PubMed

    Tyystjärvi, Esa

    2013-01-01

    Photoinhibition of Photosystem II (PSII) is the light-induced loss of PSII electron-transfer activity. Although photoinhibition has been studied for a long time, there is no consensus about its mechanism. On one hand, production of singlet oxygen ((1)O(2)) by PSII has promoted models in which this reactive oxygen species (ROS) is considered to act as the agent of photoinhibitory damage. These chemistry-based models have often not taken into account the photophysical features of photoinhibition-like light response and action spectrum. On the other hand, models that reproduce these basic photophysical features of the reaction have not considered the importance of data about ROS. In this chapter, it is shown that the evidence behind the chemistry-based models and the photophysically oriented models can be brought together to build a mechanism that confirms with all types of experimental data. A working hypothesis is proposed, starting with inhibition of the manganese complex by light. Inability of the manganese complex to reduce the primary donor promotes recombination between the oxidized primary donor and Q(A), the first stable quinone acceptor of PSII. (1)O(2) production due to this recombination may inhibit protein synthesis or spread the photoinhibitory damage to another PSII center. The production of (1)O(2) is transient because loss of activity of the oxygen-evolving complex induces an increase in the redox potential of Q(A), which lowers (1)O(2) production. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Ancestral hierarchy and conflict.

    PubMed

    Boehm, Christopher

    2012-05-18

    Ancestral Pan, the shared predecessor of humans, bonobos, and chimpanzees, lived in social dominance hierarchies that created conflict through individual and coalitional competition. This ancestor had male and female mediators, but individuals often reconciled independently. An evolutionary trajectory is traced from this ancestor to extant hunter-gatherers, whose coalitional behavior results in suppressed dominance and competition, except in mate competition. A territorial ancestral Pan would not have engaged in intensive warfare if we consider bonobo behavior, but modern human foragers have the potential for full-scale war. Although hunter-gatherers are able to resolve conflicts preemptively, they also use mechanisms, such as truces and peace pacts, to mitigate conflict when the costs become too high. Today, humans retain the genetic underpinnings of both conflict and conflict management; thus, we retain the potential for both war and peace.

  5. 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.

  6. Structural and functional dynamics of plant photosystem II.

    PubMed Central

    Anderson, Jan M; Chow, W S

    2002-01-01

    Given the unique problem of the extremely high potential of the oxidant P(+)(680) that is required to oxidize water to oxygen, the photoinactivation of photosystem II in vivo is inevitable, despite many photoprotective strategies. There is, however, a robustness of photosystem II, which depends partly on the highly dynamic compositional and structural heterogeneity of the cycle between functional and non-functional photosystem II complexes in response to light level. This coordinated regulation involves photon usage (energy utilization in photochemistry) and excess energy dissipation as heat, photoprotection by many molecular strategies, photoinactivation followed by photon damage and ultimately the D1 protein dynamics involved in the photosystem II repair cycle. Compelling, though indirect evidence suggests that the radical pair P(+)(680)Pheo(-) in functional PSII should be protected from oxygen. By analogy to the tentative oxygen channel of cytochrome c oxidase, oxygen may be liberated from the two water molecules bound to the catalytic site of the Mn cluster, via a specific pathway to the membrane surface. The function of the proposed oxygen pathway is to prevent O(2) from having direct access to P(+)(680)Pheo(-) and prevent the generation of singlet oxygen via the triplet-P(680) state in functional photosytem IIs. Only when the, as yet unidentified, potential trigger with a fateful first oxidative step destroys oxygen evolution, will the ensuing cascade of structural perturbations of photosystem II destroy the proposed oxygen, water and proton pathways. Then oxygen has direct access to P(+)(680)Pheo(-), singlet oxygen will be produced and may successively oxidize specific amino acids of the phosphorylated D1 protein of photosystem II dimers that are confined to appressed granal domains, thereby targeting D1 protein for eventual degradation and replacement in non-appressed thylakoid domains. PMID:12437881

  7. Dichromate effect on energy dissipation of photosystem II and photosystem I in Chlamydomonas reinhardtii.

    PubMed

    Perreault, François; Ait Ali, Nadia; Saison, Cyril; Popovic, Radovan; Juneau, Philippe

    2009-07-17

    In this study, we investigated the energy dissipation processes via photosystem II and photosystem I activity in green alga Chlamydomonas reinhardtii exposed to dichromate inhibitory effect. Quantum yield of photosystem II and also photosystem I were highly decreased by dichromate effect. Such inhibition by dichromate induced strong quenching effect on rapid OJIP fluorescence transients, indicating deterioration of photosystem II electron transport via plastoquinone pool toward photosystem I. The decrease of energy dissipation dependent on electron transport of photosystem II and photosystem I by dichromate effect was associated with strong increase of non-photochemical energy dissipation processes. By showing strong effect of dichromate on acceptor side of photosystem I, we indicated that dichromate inhibitory effect was not associated only with PSII electron transport. Here, we found that energy dissipation via photosystem I was limited by its electron acceptor side. By the analysis of P700 oxido-reduction state with methylviolagen as an exogenous PSI electron transport mediator, we showed that PSI electron transport discrepancy induced by dichromate effect was also caused by inhibitory effect located beyond photosystem I. Therefore, these results demonstrated that dichromate has different sites of inhibition which are associated with photosystem II, photosystem I and electron transport sink beyond photosystems.

  8. Bicarbonate accelerates assembly of the inorganic core of the water-oxidizing complex in manganese-depleted photosystem II: a proposed biogeochemical role for atmospheric carbon dioxide in oxygenic photosynthesis.

    PubMed

    Baranov, S V; Ananyev, G M; Klimov, V V; Dismukes, G C

    2000-05-23

    The proposed role for bicarbonate (HCO(3)(-)) as an intrinsic cofactor within the water-oxidizing complex (WOC) of photosystem II (PSII) [Klimov et al. (1997) Biochemistry 36, 16277-16281] was tested by investigation of its influence on the kinetics and yield of photoactivation, the light-induced assembly of the functional inorganic core (Mn(4)O(y)Ca(1)Cl(x)) starting from the cofactor-depleted apo-WOC-PSII center and free Mn(2+), Ca(2+), and Cl(-). Two binding sites for bicarbonate were found that stimulate photoactivation by accelerating the formation and suppressing the decay, respectively, of the first light-induced assembly intermediate, IM(1) [apo-WOC-Mn(OH)(2)(+)]. A high-affinity bicarbonate site (K(D)

  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. Yeast ancestral genome reconstructions: the possibilities of computational methods II.

    PubMed

    Chauve, Cedric; Gavranovic, Haris; Ouangraoua, Aida; Tannier, Eric

    2010-09-01

    Since the availability of assembled eukaryotic genomes, the first one being a budding yeast, many computational methods for the reconstruction of ancestral karyotypes and gene orders have been developed. The difficulty has always been to assess their reliability, since we often miss a good knowledge of the true ancestral genomes to compare their results to, as well as a good knowledge of the evolutionary mechanisms to test them on realistic simulated data. In this study, we propose some measures of reliability of several kinds of methods, and apply them to infer and analyse the architectures of two ancestral yeast genomes, based on the sequence of seven assembled extant ones. The pre-duplication common ancestor of S. cerevisiae and C. glabrata has been inferred manually by Gordon et al. (Plos Genet. 2009). We show why, in this case, a good convergence of the methods is explained by some properties of the data, and why results are reliable. In another study, Jean et al. (J. Comput Biol. 2009) proposed an ancestral architecture of the last common ancestor of S. kluyveri, K. thermotolerans, K. lactis, A. gossypii, and Z. rouxii inferred by a computational method. In this case, we show that the dataset does not seem to contain enough information to infer a reliable architecture, and we construct a higher resolution dataset which gives a good reliability on a new ancestral configuration.

  11. Ancestral polyploidy in seed plants and angiosperms.

    PubMed

    Jiao, Yuannian; Wickett, Norman J; Ayyampalayam, Saravanaraj; Chanderbali, André S; Landherr, Lena; Ralph, Paula E; Tomsho, Lynn P; Hu, Yi; Liang, Haiying; Soltis, Pamela S; Soltis, Douglas E; Clifton, Sandra W; Schlarbaum, Scott E; Schuster, Stephan C; Ma, Hong; Leebens-Mack, Jim; dePamphilis, Claude W

    2011-05-05

    Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications-one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.

  12. Stress Tolerance of Photosystem II in Vivo

    PubMed Central

    Havaux, Michel

    1992-01-01

    The in vivo photochemical activity of photosystem II was inferred from modulated chlorophyll fluorescence and photoacoustic measurements in intact leaves of several plant species (Lycopersicon esculentum Mill., Solanum tuberosum L., Solanum nigrum L.) exposed to various environmental stresses (drought, heat, strong light) applied separately or in combination. Photosystem II was shown to be highly drought-resistant: even a drastic desiccation in air of detached leaf samples only marginally affected the quantum yield for photochemistry in photosystem II. However, water stress markedly modified the responses of photosystem II to superimposed constraints. The stability of photosystem II to heat was observed to increase strongly in leaves exposed to water stress conditions: heat treatments (e.g. 42°C in the dark), which caused a complete and irreversible inhibition of photosystem II in well-watered (tomato) leaves, resulted in a small and fully reversible reduction of the photochemical efficiency of photosystem II in drought-stressed leaves. In vivo photoacoustic data indicated that photosystem I was highly resistant to both heat and water stresses. When leaves were illuminated with intense white light at 25°C, photoinhibition damage of photosystem II was more pronounced in water-stressed leaves than in undesiccated controls. However, in nondehydrated leaves, photoinhibition of photosystem II was strongly temperature dependent, being drastically stimulated at high temperatures above 38 to 40°C. As a consequence, when exposed to strong light at high temperature, photosystem II photochemistry was significantly less inhibited in dehydrated leaves than in control well-hydrated leaves. Our results demonstrate the existence of a marked antagonism between physicochemical stresses, with water stress enhancing the resistance of photosystem II to constraints (heat, strong light at high temperature) that are usually associated with drought in the field. PMID:16652979

  13. The ancestral flower of angiosperms and its early diversification

    PubMed Central

    Sauquet, Hervé; von Balthazar, Maria; Magallón, Susana; Doyle, James A.; Endress, Peter K.; Bailes, Emily J.; Barroso de Morais, Erica; Bull-Hereñu, Kester; Carrive, Laetitia; Chartier, Marion; Chomicki, Guillaume; Coiro, Mario; Cornette, Raphaël; El Ottra, Juliana H. L.; Epicoco, Cyril; Foster, Charles S. P.; Jabbour, Florian; Haevermans, Agathe; Haevermans, Thomas; Hernández, Rebeca; Little, Stefan A.; Löfstrand, Stefan; Luna, Javier A.; Massoni, Julien; Nadot, Sophie; Pamperl, Susanne; Prieu, Charlotte; Reyes, Elisabeth; dos Santos, Patrícia; Schoonderwoerd, Kristel M.; Sontag, Susanne; Soulebeau, Anaëlle; Staedler, Yannick; Tschan, Georg F.; Wing-Sze Leung, Amy; Schönenberger, Jürg

    2017-01-01

    Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm diversification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled. We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels. Although uncertainty remains for some of the characters, our reconstruction allows us to propose a new plausible scenario for the early diversification of flowers, leading to new testable hypotheses for future research on angiosperms. PMID:28763051

  14. The ancestral flower of angiosperms and its early diversification.

    PubMed

    Sauquet, Hervé; von Balthazar, Maria; Magallón, Susana; Doyle, James A; Endress, Peter K; Bailes, Emily J; Barroso de Morais, Erica; Bull-Hereñu, Kester; Carrive, Laetitia; Chartier, Marion; Chomicki, Guillaume; Coiro, Mario; Cornette, Raphaël; El Ottra, Juliana H L; Epicoco, Cyril; Foster, Charles S P; Jabbour, Florian; Haevermans, Agathe; Haevermans, Thomas; Hernández, Rebeca; Little, Stefan A; Löfstrand, Stefan; Luna, Javier A; Massoni, Julien; Nadot, Sophie; Pamperl, Susanne; Prieu, Charlotte; Reyes, Elisabeth; Dos Santos, Patrícia; Schoonderwoerd, Kristel M; Sontag, Susanne; Soulebeau, Anaëlle; Staedler, Yannick; Tschan, Georg F; Wing-Sze Leung, Amy; Schönenberger, Jürg

    2017-08-01

    Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm diversification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled. We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels. Although uncertainty remains for some of the characters, our reconstruction allows us to propose a new plausible scenario for the early diversification of flowers, leading to new testable hypotheses for future research on angiosperms.

  15. Material science lesson from the biological photosystem

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  16. Material science lesson from the biological photosystem.

    PubMed

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

    2016-01-01

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

  17. 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,…

  18. 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,…

  19. Ancestral gene synteny reconstruction improves extant species scaffolding.

    PubMed

    Anselmetti, Yoann; Berry, Vincent; Chauve, Cedric; Chateau, Annie; Tannier, Eric; Bérard, Sèverine

    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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. Mechanism of KCN inhibition of photosystem I.

    PubMed

    Berg, S P; Krogmann, D W

    1975-12-10

    Experiments with chloroplasts and purified spinach plastocyanin suggest a mechanism for KCN inhibition of Photosystem I. KCN inhibition can be bypassed by a detergent or reversed by replacement of the inactive plastocyanin. KCN bleaches and inactivates purified plastocyanin. KCN releases copper from chloroplast membranes and from purified plastocyanin. Cyanide does not bind to the apoprotein produced when plastocyanin is treated with KCN, and KCN-produced apoplastocyanin has a N-ethylmaleimide-reactive sulfhydryl group not found in holoplastocyanin. Apoplastocyanin is not active in restoring Photosystem I activity to plastocyanin-depleted membranes. Holoplastocyanin restores Photosystem I activities to plastocyanin-depleted membranes prepared from either control or KCN-treated chloroplasts to about the same extent. KCN-treated chloroplast membranes are found to have higher amounts of apoplastocyanin than do control chloroplast membranes. These results offer evidence that KCN removes the copper from plastocyanin in the chloroplast membrane, leaving the inactive apoplastocyanin which is unable to transfer electrons to Photosystem I.

  6. The Ancestral Eutherian Karyotype Is Present in Xenarthra

    PubMed Central

    Svartman, Marta; Stone, Gary; Stanyon, Roscoe

    2006-01-01

    Molecular studies have led recently to the proposal of a new super-ordinal arrangement of the 18 extant Eutherian orders. From the four proposed super-orders, Afrotheria and Xenarthra were considered the most basal. Chromosome-painting studies with human probes in these two mammalian groups are thus key in the quest to establish the ancestral Eutherian karyotype. Although a reasonable amount of chromosome-painting data with human probes have already been obtained for Afrotheria, no Xenarthra species has been thoroughly analyzed with this approach. We hybridized human chromosome probes to metaphases of species (Dasypus novemcinctus, Tamandua tetradactyla, and Choloepus hoffmanii) representing three of the four Xenarthra families. Our data allowed us to review the current hypotheses for the ancestral Eutherian karyotype, which range from 2n = 44 to 2n = 48. One of the species studied, the two-toed sloth C. hoffmanii (2n = 50), showed a chromosome complement strikingly similar to the proposed 2n = 48 ancestral Eutherian karyotype, strongly reinforcing it. PMID:16848642

  7. The ancestral eutherian karyotype is present in Xenarthra.

    PubMed

    Svartman, Marta; Stone, Gary; Stanyon, Roscoe

    2006-07-01

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

  8. When directed evolution met ancestral enzyme resurrection.

    PubMed

    Alcalde, Miguel

    2017-01-01

    The directed evolution of ancestral -resurrected- enzymes can give a new twist in protein engineering approaches towards more versatile and robust biocatalysts. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  9. 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.

  10. 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.

  11. Understanding Brassicaceae evolution through ancestral genome reconstruction.

    PubMed

    Murat, Florent; Louis, Alexandra; Maumus, Florian; Armero, Alix; Cooke, Richard; Quesneville, Hadi; Roest Crollius, Hugues; Salse, Jerome

    2015-12-10

    Brassicaceae is a family of green plants of high scientific and economic interest, including thale cress (Arabidopsis thaliana), cruciferous vegetables (cabbages) and rapeseed. We reconstruct an evolutionary framework of Brassicaceae composed of high-resolution ancestral karyotypes using the genomes of modern A. thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula. The ancestral Brassicaceae karyotype (Brassicaceae lineages I and II) is composed of eight protochromosomes and 20,037 ordered and oriented protogenes. After speciation, it evolved into the ancestral Camelineae karyotype (eight protochromosomes and 22,085 ordered protogenes) and the proto-Calepineae karyotype (seven protochromosomes and 21,035 ordered protogenes) genomes. The three inferred ancestral karyotype genomes are shown here to be powerful tools to unravel the reticulated evolutionary history of extant Brassicaceae genomes regarding the fate of ancestral genes and genomic compartments, particularly centromeres and evolutionary breakpoints. This new resource should accelerate research in comparative genomics and translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.

  12. 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.

  13. 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.

  14. Speciation as a sieve for ancestral polymorphism.

    PubMed

    Guerrero, Rafael F; Hahn, Matthew W

    2017-08-09

    Because they are considered rare, balanced polymorphisms are often discounted as crucial constituents of genome-wide variation in sequence diversity. Despite its perceived rarity, however, long-term balancing selection can elevate genetic diversity and significantly affect observed divergence between species. Here, we discuss how ancestral balanced polymorphisms can be "sieved" by the speciation process, which sorts them unequally across descendant lineages. After speciation, ancestral balancing selection is revealed by genomic regions of high divergence between species. This signature, which resembles that of other evolutionary processes, can potentially confound genomic studies of population divergence and inferences of "islands of speciation." © 2017 John Wiley & Sons Ltd.

  15. Structure of Photosystems I and II.

    PubMed

    Fromme, Petra; Grotjohann, Ingo

    2008-01-01

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

  16. 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

  17. Reconstructing ancestral gene content by coevolution.

    PubMed

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

    2010-01-01

    Inferring the gene content of ancestral genomes is a fundamental challenge in molecular evolution. Due to the statistical nature of this problem, ancestral genomes inferred by the maximum likelihood (ML) or the maximum-parsimony (MP) methods are prone to considerable error rates. In general, these errors are difficult to abolish by using longer genomic sequences or by analyzing more taxa. This study describes a new approach for improving ancestral genome reconstruction, the ancestral coevolver (ACE), which utilizes coevolutionary information to improve the accuracy of such reconstructions over previous approaches. The principal idea is to reduce the potentially large solution space by choosing a single optimal (or near optimal) solution that is in accord with the coevolutionary relationships between protein families. Simulation experiments, both on artificial and real biological data, show that ACE yields a marked decrease in error rate compared with ML or MP. Applied to a large data set (95 organisms, 4873 protein families, and 10,000 coevolutionary relationships), some of the ancestral genomes reconstructed by ACE were remarkably different in their gene content from those reconstructed by ML or MP alone (more than 10% in some nodes). These reconstructions, while having almost similar likelihood/parsimony scores as those obtained with ML/MP, had markedly higher concordance with the coevolutionary information. Specifically, when ACE was implemented to improve the results of ML, it added a large number of proteins to those encoded by LUCA (last universal common ancestor), most of them ribosomal proteins and components of the F(0)F(1)-type ATP synthase/ATPases, complexes that are vital in most living organisms. Our analysis suggests that LUCA appears to have been bacterial-like and had a genome size similar to the genome sizes of many extant organisms.

  18. 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.

  19. Regulation of photosystem I light harvesting by zeaxanthin.

    PubMed

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

    2014-06-10

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

  20. Regulation of photosystem I light harvesting by zeaxanthin

    PubMed Central

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

    2014-01-01

    In oxygenic photosynthetic eukaryotes, the hydroxylated carotenoid zeaxanthin is produced from preexisting violaxanthin upon exposure to excess light conditions. Zeaxanthin binding to components of the photosystem II (PSII) antenna system has been investigated thoroughly and shown to help in the dissipation of excess chlorophyll-excited states and scavenging of oxygen radicals. However, the functional consequences of the accumulation of the light-harvesting complex I (LHCI) proteins in the photosystem I (PSI) antenna have remained unclarified so far. In this work we investigated the effect of zeaxanthin binding on photoprotection of PSI–LHCI by comparing preparations isolated from wild-type Arabidopsis thaliana (i.e., with violaxanthin) and those isolated from the A. thaliana nonphotochemical quenching 2 mutant, in which violaxanthin is replaced by zeaxanthin. Time-resolved fluorescence measurements showed that zeaxanthin binding leads to a previously unrecognized quenching effect on PSI–LHCI fluorescence. The efficiency of energy transfer from the LHCI moiety of the complex to the PSI reaction center was down-regulated, and an enhanced PSI resistance to photoinhibition was observed both in vitro and in vivo. Thus, zeaxanthin was shown to be effective in inducing dissipative states in PSI, similar to its well-known effect on PSII. We propose that, upon acclimation to high light, PSI–LHCI changes its light-harvesting efficiency by a zeaxanthin-dependent quenching of the absorbed excitation energy, whereas in PSII the stoichiometry of LHC antenna proteins per reaction center is reduced directly. PMID:24872450

  1. Distinguishing Recent Admixture from Ancestral Population Structure

    PubMed Central

    Slatkin, Montgomery

    2017-01-01

    We develop and test two methods for distinguishing between recent admixture and ancestral population structure as explanations for greater similarity of one of two populations to an outgroup population. This problem arose when Neanderthals were found to be slightly more similar to nonAfrican than to African populations. The excess similarity is consistent with both recent admixture from Neanderthals into the ancestors of nonAfricans and subdivision in the ancestral population. Although later studies showed that there had been recent admixture, distinguishing between these two classes of models will be important in other situations, particularly when high-coverage genomes cannot be obtained for all populations. One of our two methods is based on the properties of the doubly conditioned frequency spectrum combined with the unconditional frequency spectrum. This method does not require a linkage map and can be used when there is relatively low coverage. The second method uses the extent of linkage disequilibrium among closely linked markers. PMID:28186554

  2. 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

  3. Ancestral alleles in the human genome based on population sequencing data.

    PubMed

    Park, Leeyoung

    2015-01-01

    Ancestral allele information is useful for genetics studies. Previously, the identification of ancestral alleles was primarily based on sequence alignments between species. Alternative ways to identify ancestral alleles were proposed in this study based on population sequencing data. The methods described here utilized the diversity between haplotypes harboring ancestral and newly emerged alleles. Simulations showed that these methods were reliable for identifying ancestral alleles when the variants had not aged too greatly. Application to the human genome sequencing data suggested the role of indels in maintaining the GC content in the human genome. The deletion-to-insertion ratios and GC proportions were correlated depending on the sizes of insertions and deletions in the direction of increasing GC content. There were GC-biased fixations in single base-pair insertions and AT-biased fixations in single base-pair deletions in the results based on the proposed methods. In the current study, GC-biased gene conversions in nucleotide substitutions were very slight or insignificant. In the variants of several quantitative trait loci (QTLs), slight GC-biased gene conversion was observed in nucleotide substitutions. For the QTL indels, insertions were observed more often than deletions, and deletion-biased fixation was observed, providing new insights into the evolution of functional genes.

  4. 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.

  5. Photosystem II: the reaction center of oxygenic photosynthesis.

    PubMed

    Vinyard, David J; Ananyev, Gennady M; Dismukes, G Charles

    2013-01-01

    Photosystem II (PSII) uses light energy to split water into chemical products that power the planet. The stripped protons contribute to a membrane electrochemical potential before combining with the stripped electrons to make chemical bonds and releasing O2 for powering respiratory metabolisms. In this review, we provide an overview of the kinetics and thermodynamics of water oxidation that highlights the conserved performance of PSIIs across species. We discuss recent advances in our understanding of the site of water oxidation based upon the improved (1.9-Å resolution) atomic structure of the Mn4CaO5 water-oxidizing complex (WOC) within cyanobacterial PSII. We combine these insights with recent knowledge gained from studies of the biogenesis and assembly of the WOC (called photoassembly) to arrive at a proposed chemical mechanism for water oxidation.

  6. 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.

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

    PubMed Central

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

    2011-01-01

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

  8. Oxidation-reduction signalling components in regulatory pathways of state transitions and photosystem stoichiometry adjustment in chloroplasts.

    PubMed

    Puthiyaveetil, Sujith; Ibrahim, Iskander M; Allen, John F

    2012-02-01

    State transitions and photosystem stoichiometry adjustment are two oxidation-reduction (redox)-regulated acclimatory responses in photosynthesis. State transitions are short-term adaptations that, in chloroplasts, involve reversible post-translational modification by phosphorylation of light-harvesting complex II (LHC II). Photosystem stoichiometry adjustments are long-term responses involving transcriptional regulation of reaction centre genes. Both responses are initiated by changes in light quality and are regulated by the redox state of plastoquinone (PQ). The LHC II kinase involved in the state 2 transition is a serine/threonine kinase known as STT7 in Chlamydomonas, and as STN7 in Arabidopsis. The phospho-LHC II phosphatase that produces the state 1 transition is a PP2C-type protein phosphatase currently termed both TAP38 and PPH1. In plants and algae, photosystem stoichiometry adjustment is governed by a modified two-component sensor kinase of cyanobacterial origin - chloroplast sensor kinase (CSK). CSK is a sensor of the PQ redox state. Chloroplast sigma factor 1 (SIG1) and plastid transcription kinase (PTK) are the functional partners of CSK in chloroplast gene regulation. We suggest a signalling pathway for photosystem stoichiometry adjustment. The signalling pathways of state transitions and photosystem stoichiometry adjustments are proposed to be distinct, with the two pathways sensing PQ redox state independently of each other.

  9. Unexpected changes in photosystem I function in a cytochrome c6-deficient mutant of the cyanobacterium Synechocystis PCC 6803.

    PubMed

    Ardelean, I; Matthijs, H C P; Havaux, M; Joset, F; Jeanjean, R

    2002-07-16

    Cytochrome c6, the product of the petJ gene, is a photosynthetic electron carrier in cyanobacteria, which transfers electrons to photosystem I and which is synthesised under conditions of copper deficiency to functionally replace plastocyanin. The photosystem I photochemical activity (energy storage, photoinduced P700 redox changes) was examined in a petJ-null mutant of Synechocystis PCC 6803. Surprisingly, photosystem I activity in the petJ-null mutant grown in the absence of copper was not much affected. However, in a medium with a low inorganic carbon concentration and with NH4+ ion as nitrogen source, the mutant displayed growth inhibition. Analysis showed that, especially in the latter, the isiAB operon, encoding flavodoxin and CP43', an additional chlorophyll a antenna, was strongly expressed in the mutant. These proteins are involved in photosystem I function and organisation and are proposed to assist in prevention of overoxidation of photosystem I at its lumenal side and overreduction at its stromal side.

  10. Functional Models for the Oxygen-Evolving Complex of Photosystem II

    PubMed Central

    Cady, Clyde W.; Crabtree, Robert H.; Brudvig, Gary W.

    2010-01-01

    In the last ten years, a number of advances have been made in the study of the oxygen-evolving complex (OEC) of photosystem II (PSII). Along with this new understanding of the natural system has come rapid advance in chemical models of this system. The advance of PSII model chemistry is seen most strikingly in the area of functional models where the few known systems available when this topic was last reviewed has grown into two families of model systems. In concert with this work, numerous mechanistic proposals for photosynthetic water oxidation have been proposed. Here, we review the recent efforts in functional model chemistry of the oxygen-evolving complex of photosystem II. PMID:21037800

  11. Consequences of Modification of Photosystem Stoichiometry and Amount in Cyanobacteria

    SciTech Connect

    Vermaas, Willem

    2016-12-13

    The proposed research seeks to address two interconnected, important questions that impact photosynthetic processes and that reflect key differences between the photosynthetic systems of cyanobacteria and plants or algae. The first question is what are the reasons and consequences of the high photosystem I / photosystem II (PS I/PS II) ratio in many cyanobacteria, vs. a ratio that is close to unity in many plants and algae. The corresponding hypothesis is that most of PS I functions in cyclic electron transport, and that reduction in PS I will result primarily in a shortage of ATP rather than reducing power. This hypothesis will be tested by reducing the amount of PS I by changing the promoter region of the psaAB operon in the cyanobacterium Synechocystis sp. PCC 6803 and generating a range of mutants with different PS I content and thereby different PS I/PS II ratios, with some of the mutants having a PS II/PS I ratio closer to that in plants. The resulting mutants will be probed in terms of their growth rates, electron transfer rates, and P700 redox kinetics. A second question relates to a Mehler-type reaction catalyzed by two flavoproteins, Flv1 and Flv3, that accept electrons from PS I and that potentially function as an electron safety valve leading to no useful purpose of the photosynthesis-generated electrons. The hypothesis to be tested is that Flv1 and Flv3 use the electrons for useful purposes such as cyclic electron flow around PS I. This hypothesis will be tested by analysis of a mutant strain lacking flv3, the gene for one of the flavoproteins. This research is important for a more detailed understanding of the consequences of photosystem stoichiometry and amounts in a living system. Such an understanding is critical for not only insights in the regulatory systems of the organism but also to guide the development of biological or bio-hybrid systems for solar energy conversion into fuels.

  12. Regulatory genes in the ancestral chordate genomes.

    PubMed

    Satou, Yutaka; Wada, Shuichi; Sasakura, Yasunori; Satoh, Nori

    2008-12-01

    Changes or innovations in gene regulatory networks for the developmental program in the ancestral chordate genome appear to be a major component in the evolutionary process in which tadpole-type larvae, a unique characteristic of chordates, arose. These alterations may include new genetic interactions as well as the acquisition of new regulatory genes. Previous analyses of the Ciona genome revealed that many genes may have emerged after the divergence of the tunicate and vertebrate lineages. In this paper, we examined this possibility by examining a second non-vertebrate chordate genome. We conclude from this analysis that the ancient chordate included almost the same repertory of regulatory genes, but less redundancy than extant vertebrates, and that approximately 10% of vertebrate regulatory genes were innovated after the emergence of vertebrates. Thus, refined regulatory networks arose during vertebrate evolution mainly as preexisting regulatory genes multiplied rather than by generating new regulatory genes. The inferred regulatory gene sets of the ancestral chordate would be an important foundation for understanding how tadpole-type larvae, a unique characteristic of chordates, evolved.

  13. 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. Copyright © 2015 by the Genetics Society of America.

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

    PubMed Central

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

    2015-01-01

    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

  15. DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies.

    PubMed

    Duchemin, Wandrille; Anselmetti, Yoann; Patterson, Murray; Ponty, Yann; Berard, Severine; Chauve, Cedric; Scornavacca, Celine; Daubin, Vincent; Tannier, Eric

    2017-04-08

    DeCoSTAR is a software that aims at reconstructing the organization of ancestral genes or genomes in the form of sets of neighborhood relations (adjacencies) between pairs of ancestral genes or gene domains. It can also improve the assembly of fragmented genomes by proposing evolutionary-induced adjacencies between scaffolding fragments. Ancestral genes or domains are deduced from reconciled phylogenetic trees under an evolutionary model that considers gains, losses, speciations, duplications, and transfers as possible events for gene evolution. Reconciliations are either given as input or computed with the ecceTERA package, into which DeCoSTAR is integrated. DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann-Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously-contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life. We illustrate the potential of DeCoSTAR with several applications: ancestral reconstruction of gene orders for Anopheles mosquito genomes, multidomain proteins in Drosophila, and gene fusion and fission detection in Actinobacteria.

  16. DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

    PubMed Central

    Anselmetti, Yoann; Patterson, Murray; Ponty, Yann; B�rard, S�verine; Chauve, Cedric; Scornavacca, Celine; Daubin, Vincent; Tannier, Eric

    2017-01-01

    DeCoSTAR is a software that aims at reconstructing the organization of ancestral genes or genomes in the form of sets of neighborhood relations (adjacencies) between pairs of ancestral genes or gene domains. It can also improve the assembly of fragmented genomes by proposing evolutionary-induced adjacencies between scaffolding fragments. Ancestral genes or domains are deduced from reconciled phylogenetic trees under an evolutionary model that considers gains, losses, speciations, duplications, and transfers as possible events for gene evolution. Reconciliations are either given as input or computed with the ecceTERA package, into which DeCoSTAR is integrated. DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life. We illustrate the potential of DeCoSTAR with several applications: ancestral reconstruction of gene orders for Anopheles mosquito genomes, multidomain proteins in Drosophila, and gene fusion and fission detection in Actinobacteria. Availability: http://pbil.univ-lyon1.fr/software/DeCoSTAR (Last accessed April 24, 2017). PMID:28402423

  17. 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.

  18. [Effect of dehydration on functioning of photosystems of higher plants].

    PubMed

    Karapetian, N V; Bukhov, N G

    1979-01-01

    The functional activity of both photosystems of higher plants and their thermoresistance in conditions of dehydratation of chloroplasts or subchloroplast fragments were studied. It is shown that dehydratation of the sample does not change the P700 amount capable to photooxidation. At 20 degrees in the time course of dark reduction of photooxidized P700 P(700+) in films two phases differing in rate were found. The relative contribution of each phase depends on the illumination duration. Since dehydratation blocks electron transfer between photosystems, the double phase dark reduction of P700+ in films reflects the electron flow from various components of potosystem 1 acceptor part. Dehydratation has little effect on properties of photosystem 1 acceptor part, because at low temperature the time courses of P700+ dark reduction in films and chloroplast or subchloroplast suspensions are similar. In contrast with potosystem 1, the functioning of photosystem 2, studied by light induced increase of fluorescence yield of chloroplasts, is blocked abruptly by water removal, but it could be partly restored by rehydratation of dried chloroplasts. The water removal increases the thermostability of both photosystems, however in suspension of the studied samples and also in their films photosystem 1 is more thermostable in comparison with photosystem 2.

  19. Photosynthetic quantum yield dynamics: from photosystems to leaves.

    PubMed

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

    2012-05-01

    The mechanisms underlying the wavelength dependence of the quantum yield for CO(2) fixation (α) and its acclimation to the growth-light spectrum are quantitatively addressed, combining in vivo physiological and in vitro molecular methods. Cucumber (Cucumis sativus) was grown under an artificial sunlight spectrum, shade light spectrum, and blue light, and the quantum yield for photosystem I (PSI) and photosystem II (PSII) electron transport and α were simultaneously measured in vivo at 20 different wavelengths. The wavelength dependence of the photosystem excitation balance was calculated from both these in vivo data and in vitro from the photosystem composition and spectroscopic properties. Measuring wavelengths overexciting PSI produced a higher α for leaves grown under the shade light spectrum (i.e., PSI light), whereas wavelengths overexciting PSII produced a higher α for the sun and blue leaves. The shade spectrum produced the lowest PSI:PSII ratio. The photosystem excitation balance calculated from both in vivo and in vitro data was substantially similar and was shown to determine α at those wavelengths where absorption by carotenoids and nonphotosynthetic pigments is insignificant (i.e., >580 nm). We show quantitatively that leaves acclimate their photosystem composition to their growth light spectrum and how this changes the wavelength dependence of the photosystem excitation balance and quantum yield for CO(2) fixation. This also proves that combining different wavelengths can enhance quantum yields substantially.

  20. Assessing the Accuracy of Ancestral Protein Reconstruction Methods

    PubMed Central

    Williams, Paul D; Pollock, David D; Blackburne, Benjamin P; Goldstein, Richard A

    2006-01-01

    The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of “ancestral sequences” inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a “best guess” amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated. PMID:16789817

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

    PubMed

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

    2014-08-13

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

  2. 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.

  3. Natural diterpenes from Croton ciliatoglanduliferus as photosystem II and photosystem I inhibitors in spinach chloroplasts.

    PubMed

    Morales-Flores, Félix; Aguilar, María Isabel; King-Díaz, Beatriz; de Santiago-Gómez, Jesús-Ricardo; Lotina-Hennsen, Blas

    2007-01-01

    In our search for new natural photosynthetic inhibitors that could lead to the development of "green herbicides" less toxic to environment, the diterpene labdane-8alpha,15-diol (1) and its acetyl derivative (2) were isolated for the first time from Croton ciliatoglanduliferus Ort. They inhibited photophosphorylation, electron transport (basal, phosphorylating and uncoupled) and the partial reactions of both photosystems in spinach thylakoids. Compound 1 inhibits the photosystem II (PS II) partial reaction from water to Na(+) Silicomolibdate (SiMo) and has no effect on partial reaction from diphenylcarbazide (DPC) to 2,6-dichlorophenol indophenol (DCPIP), therefore 1 inhibits at the water splitting enzyme and also inhibits PS I partial reaction from reduced phenylmetasulfate (PMS) to methylviologen (MV). Thus, it also inhibits in the span of P(700) to Iron sulfur center X (F(X)). Compound 2 inhibits both, the PS II partial reactions from water to SiMo and from DPC to DCPIP; besides this, it inhibits the photosystem I (PS I) partial reaction from reduced PMS to MV. With these results, we concluded that the targets of the natural product 2 are located at the water splitting enzyme, and at P(680) in PS II and at the span of P(700) to F(X) in PS I. The results of compounds 1 and 2 on PS II were corroborated by chlorophyll a fluorescence.

  4. 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.

  5. Deciphering the Diploid Ancestral Genome of the Mesohexaploid Brassica rapa[C][W

    PubMed Central

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

    2013-01-01

    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

  6. Fast ancestral gene order reconstruction of genomes with unequal gene content.

    PubMed

    Feijão, Pedro; Araujo, Eloi

    2016-11-11

    During evolution, genomes are modified by large scale structural events, such as rearrangements, deletions or insertions of large blocks of DNA. Of particular interest, in order to better understand how this type of genomic evolution happens, is the reconstruction of ancestral genomes, given a phylogenetic tree with extant genomes at its leaves. One way of solving this problem is to assume a rearrangement model, such as Double Cut and Join (DCJ), and find a set of ancestral genomes that minimizes the number of events on the input tree. Since this problem is NP-hard for most rearrangement models, exact solutions are practical only for small instances, and heuristics have to be used for larger datasets. This type of approach can be called event-based. Another common approach is based on finding conserved structures between the input genomes, such as adjacencies between genes, possibly also assigning weights that indicate a measure of confidence or probability that this particular structure is present on each ancestral genome, and then finding a set of non conflicting adjacencies that optimize some given function, usually trying to maximize total weight and minimizing character changes in the tree. We call this type of methods homology-based. In previous work, we proposed an ancestral reconstruction method that combines homology- and event-based ideas, using the concept of intermediate genomes, that arise in DCJ rearrangement scenarios. This method showed better rate of correctly reconstructed adjacencies than other methods, while also being faster, since the use of intermediate genomes greatly reduces the search space. Here, we generalize the intermediate genome concept to genomes with unequal gene content, extending our method to account for gene insertions and deletions of any length. In many of the simulated datasets, our proposed method had better results than MLGO and MGRA, two state-of-the-art algorithms for ancestral reconstruction with unequal gene content

  7. 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

  8. Dynamics of electron transfer in photosystem II.

    PubMed

    Burda, Kvetoslava

    2007-01-01

    Photosystem II, being a constituent of light driven photosynthetic apparatus, is a highly organized pigment-protein-lipid complex. The arrangement of PSII active redox cofactors insures efficiency of electron transfer within it. Donation of electrons extracted from water by the oxygen evolving complex to plastoquinones requires an additional activation energy. In this paper we present theoretical discussion of the anharmonic fluctuations of the protein-lipid matrix of PSII and an experimental evidence showing that the fluctuations are responsible for coupling of its donor and acceptor side. We argue that the fast collective motions liberated at temperatures higher that 200 K are crucial for the two final steps of the water splitting cycle and that one can distinguish three different dynamic regimes of PSII action which are controlled by the timescales of forward electron transfer, which vary with temperature. The three regimes of the dynamical behavior are related to different spatial domains of PSII.

  9. Ancestral vertebrate complexity of the opioid system.

    PubMed

    Larhammar, Dan; Bergqvist, Christina; Sundström, Görel

    2015-01-01

    The evolution of the opioid peptides and nociceptin/orphanin as well as their receptors has been difficult to resolve due to variable evolutionary rates. By combining sequence comparisons with information on the chromosomal locations of the genes, we have deduced the following evolutionary scenario: The vertebrate predecessor had one opioid precursor gene and one receptor gene. The two genome doublings before the vertebrate radiation resulted in three peptide precursor genes whereupon a fourth copy arose by a local gene duplication. These four precursors diverged to become the prepropeptides for endorphin (POMC), enkephalins, dynorphins, and nociceptin, respectively. The ancestral receptor gene was quadrupled in the genome doublings leading to delta, kappa, and mu and the nociceptin/orphanin receptor. This scenario is corroborated by new data presented here for coelacanth and spotted gar, representing two basal branches in the vertebrate tree. A third genome doubling in the ancestor of teleost fishes generated additional gene copies. These results show that the opioid system was quite complex already in the first vertebrates and that it has more components in teleost fishes than in mammals. From an evolutionary point of view, nociceptin and its receptor can be considered full-fledged members of the opioid system.

  10. Matrilocal residence is ancestral in Austronesian societies

    PubMed Central

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

    2009-01-01

    The nature of social life in human prehistory is elusive, yet knowing how kinship systems evolve is critical for understanding population history and cultural diversity. Post-marital residence rules specify sex-specific dispersal and kin association, influencing the pattern of genetic markers across populations. Cultural phylogenetics allows us to practise ‘virtual archaeology’ on these aspects of social life that leave no trace in the archaeological record. Here we show that early Austronesian societies practised matrilocal post-marital residence. Using a Markov-chain Monte Carlo comparative method implemented in a Bayesian phylogenetic framework, we estimated the type of residence at each ancestral node in a sample of Austronesian language trees spanning 135 Pacific societies. Matrilocal residence has been hypothesized for proto-Oceanic society (ca 3500 BP), but we find strong evidence that matrilocality was predominant in earlier Austronesian societies ca 5000–4500 BP, at the root of the language family and its early branches. Our results illuminate the divergent patterns of mtDNA and Y-chromosome markers seen in the Pacific. The analysis of present-day cross-cultural data in this way allows us to directly address cultural evolutionary and life-history processes in prehistory. PMID:19324748

  11. Investigation of water bound to photosystem I with multiquantum filtered 17 O nuclear magnetic resonance.

    PubMed

    Krzystyniak, M; Shen, Gaozhong; Golbeck, John H; Antonkine, Mikhail L

    2008-01-07

    A new analytical approach was developed to characterize the properties of water molecules bound to macromolecules in solution using 17 O nuclear magnetic resonance (NMR) relaxation. A combination of conventional (single-quantum) and triple-quantum filtered Hahn echo and inversion recovery measurements was employed. From measured relaxation rate constants, the fraction and the correlation time of bound H2 17 O molecules and the relaxation rate constant of bulk water in solution were calculated. This was done by solving analytically a set of nonlinear equations describing the overall relaxation rate constants in the presence of chemical exchange between bulk and bound water. The analytical approach shows the uniqueness of the solution for a given set of three relaxation rate constants. This important result sheds light on the data reduction problem from 17 O NMR experiments on biological systems. Water bound in photosystem I isolated from the wild type and rubA variant of the cyanobacterium Synechocystis species PCC 7002 was investigated for the first time. The analysis revealed that photosystem I isolated from the wild type binds 1720+/-110 water molecules, whereas photosystem I isolated from the rubA variant binds only 1310+/-170. The accuracy of the method proposed can be increased by further 17 O enrichment. The methodology, established for the first time in this work, allows the study of a diverse range of biological samples regardless of their size and molecular weight. Applied initially to photosystem I, this novel method has important consequences for the future investigation of the assembly of biological molecules.

  12. 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.

  13. 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.

  14. 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

    2005-01-07

    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.

  15. Multiple types of association of photosystem II and its light-harvesting antenna in partially solubilized photosystem II membranes.

    PubMed

    Boekema, E J; van Roon, H; Calkoen, F; Bassi, R; Dekker, J P

    1999-02-23

    Photosystem II is a multisubunit pigment-protein complex embedded in the thylakoid membranes of chloroplasts. It utilizes light for photochemical energy conversion, and is heavily involved in the regulation of the energy flow. We investigated the structural organization of photosystem II and its associated light-harvesting antenna by electron microscopy, multivariate statistical analysis, and classification procedures on partially solubilized photosystem II membranes from spinach. Observation by electron microscopy shortly after a mild disruption of freshly prepared membranes with the detergent n-dodecyl-alpha,D-maltoside revealed the presence of several large supramolecular complexes. In addition to the previously reported supercomplexes [Boekema, E. J., van Roon, H., and Dekker, J. P. (1998) FEBS Lett. 424, 95-99], we observed complexes with the major trimeric chlorophyll a/b protein (LHCII) in a third, L-type of binding position (C2S2M0-2L1-2), and two different types of megacomplexes, both identified as dimeric associations of supercomplexes with LHCII in two types of binding sites (C4S4M2-4). We conclude that the association of photosystem II and its associated light-harvesting antenna is intrinsically heterogeneous, and that the minor CP26 and CP24 proteins play a crucial role in the supramolecular organization of the complete photosystem. We suggest that different types of organization form the structural basis for photosystem II to specifically react to changing light and stress conditions, by providing different routes of excitation energy transfer.

  16. Spectral hole burning studies of photosystem II

    SciTech Connect

    Chang, Hai -Chou

    1995-09-26

    Low temperature absorption and hole burning spectroscopies were applied to the D1-D2-cyt b559 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 Qy-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 ~1 cm-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.

  17. Interaction of ascorbate with photosystem I.

    PubMed

    Trubitsin, Boris V; Mamedov, Mahir D; Semenov, Alexey Yu; Tikhonov, Alexander N

    2014-11-01

    Ascorbate is one of the key participants of the antioxidant defense in plants. In this work, we have investigated the interaction of ascorbate with the chloroplast electron transport chain and isolated photosystem I (PSI), using the EPR method for monitoring the oxidized centers [Formula: see text] and ascorbate free radicals. Inhibitor analysis of the light-induced redox transients of P700 in spinach thylakoids has demonstrated that ascorbate efficiently donates electrons to [Formula: see text] via plastocyanin. Inhibitors (DCMU and stigmatellin), which block electron transport between photosystem II and Pc, did not disturb the ascorbate capacity for electron donation to [Formula: see text]. Otherwise, inactivation of Pc with CN(-) ions inhibited electron flow from ascorbate to [Formula: see text]. This proves that the main route of electron flow from ascorbate to [Formula: see text] runs through Pc, bypassing the plastoquinone (PQ) pool and the cytochrome b 6 f complex. In contrast to Pc-mediated pathway, direct donation of electrons from ascorbate to [Formula: see text] is a rather slow process. Oxidized ascorbate species act as alternative oxidants for PSI, which intercept electrons directly from the terminal electron acceptors of PSI, thereby stimulating photooxidation of P700. We investigated the interaction of ascorbate with PSI complexes isolated from the wild type cells and the MenB deletion strain of cyanobacterium Synechocystis sp. PCC 6803. In the MenB mutant, PSI contains PQ in the quinone-binding A1-site, which can be substituted by high-potential electron carrier 2,3-dichloro-1,4-naphthoquinone (Cl2NQ). In PSI from the MenB mutant with Cl2NQ in the A1-site, the outflow of electrons from PSI is impeded due to the uphill electron transfer from A1 to the iron-sulfur cluster FX and further to the terminal clusters FA/FB, which manifests itself as a decrease in a steady-state level of [Formula: see text]. The addition of ascorbate promoted photooxidation

  18. 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

  19. 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.

  20. Small Cab-like proteins retard degradation of photosystem II-associated chlorophyll in Synechocystis sp. PCC 6803: kinetic analysis of pigment labeling with 15N and 13C.

    PubMed

    Vavilin, Dmitrii; Yao, Danny; Vermaas, Wim

    2007-12-28

    Isotope (Na(15)NO(3), ((15)NH(4))SO(4) or [(13)C]glucose) labeling was used to analyze chlorophyll synthesis and degradation rates in a set of Synechocystis mutants that lacked single or multiple small Cab-like proteins (SCPs), as well as photosystem I or II. When all five small Cab-like proteins were inactivated in the wild-type background, chlorophyll stability was not affected unless the scpABCDE(-) strain was grown at a moderately high light intensity of 100-300 micromol photons m(-2) s(-1). However, the half-life time of chlorophyll was 5-fold shorter in the photosystem I-less/scpABCDE(-) strain than in the photosystem I-less strain even when grown at low light intensity (~3 micromol photons m(-2) s(-1)) (32 +/- 5 and 161 +/- 25 h, respectively). In other photosystem I-less mutants that lacked one to four of the scp genes the chlorophyll lifetime was in between these two values, with the chlorophyll lifetime generally decreasing with an increasing number of inactivated scps. In contrast, the chlorophyll biosynthesis rate was only marginally affected by inactivation of scps except when all five scp genes were deleted. Small Cab-like protein deficiency did not significantly affect photoinhibition or turnover of photosystem II-associated beta-carotene. It is concluded that SCPs do not alter the stability of functional photosystem II complexes but retard the degradation of photosystem II-associated chlorophyll, consistent with the proposed involvement of SCPs in photosystem II re-assembly or/and repair processes by temporarily binding chlorophyll while photosystem II protein components are being replaced.

  1. 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

  2. Photoinactivation of Photosystem II in Prochlorococcus and Synechococcus

    PubMed Central

    Murphy, Cole D.; Roodvoets, Mitchell S.; Austen, Emily J.; Dolan, Allison; Barnett, Audrey

    2017-01-01

    The marine picocyanobacteria Synechococcus and Prochlorococcus numerically dominate open ocean phytoplankton. Although evolutionarily related they are ecologically distinct, with different strategies to harvest, manage and exploit light. We grew representative strains of Synechococcus and Prochlorococcus and tracked their susceptibility to photoinactivation of Photosystem II under a range of light levels. As expected blue light provoked more rapid photoinactivation than did an equivalent level of red light. The previous growth light level altered the susceptibility of Synechococcus, but not Prochlorococcus, to this photoinactivation. We resolved a simple linear pattern when we expressed the yield of photoinactivation on the basis of photons delivered to Photosystem II photochemistry, plotted versus excitation pressure upon Photosystem II, the balance between excitation and downstream metabolism. A high excitation pressure increases the generation of reactive oxygen species, and thus increases the yield of photoinactivation of Photosystem II. Blue photons, however, retained a higher baseline photoinactivation across a wide range of excitation pressures. Our experiments thus uncovered the relative influences of the direct photoinactivation of Photosystem II by blue photons which dominates under low to moderate blue light, and photoinactivation as a side effect of reactive oxygen species which dominates under higher excitation pressure. Synechococcus enjoyed a positive metabolic return upon the repair or the synthesis of a Photosystem II, across the range of light levels we tested. In contrast Prochlorococcus only enjoyed a positive return upon synthesis of a Photosystem II up to 400 μmol photons m-2 s-1. These differential cost-benefits probably underlie the distinct photoacclimation strategies of the species. PMID:28129341

  3. Photosystem II: the engine of life.

    PubMed

    Barber, James

    2003-02-01

    Photosystem II (PS II) is a multisubunit membrane protein complex, which uses light energy to oxidize water and reduce plastoquinone. High-resolution electron cryomicroscopy and X-ray crystallography are revealing the structure of this important molecular machine. Both approaches have contributed to our understanding of the organization of the transmembrane helices of higher plant and cyanobacterial PS II and both indicate that PS II normally functions as a dimer. However the high-resolution electron density maps derived from X-ray crystallography currently at 3.7/3.8 A, have allowed assignments to be made to the redox active cofactors involved in the light-driven water-plastoquinone oxidoreductase activity and to the chlorophyll molecules that absorb and transfer energy to the reaction centre. In particular the X-ray work has identified density that can accommodate the four manganese atoms which catalyse the water-oxidation process. The Mn cluster is located at the lumenal surface of the DI protein and approximately 7 A from the redox active tyrosine residue (YZ) which acts an electron/proton transfer link to the primary oxidant P680.+. The lower resolution electron microscopy studies, however, are providing structural models of larger PS II supercomplexes that are ideal frameworks in which to incorporate the X-ray derived structures.

  4. 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.

  5. Antimycobacterial N-alkoxyphenylhydroxynaphthalenecarboxamides affecting photosystem II.

    PubMed

    Gonec, Tomas; Kralova, Katarina; Pesko, Matus; Jampilek, Josef

    2017-03-21

    N-(Alkoxyphenyl)-2-hydroxynaphthalene-1-carboxamides (series A) and N-(alkoxyphenyl)-1-hydroxynaphthalene-2-carboxamides (series B) affecting photosystem (PS) II inhibited photosynthetic electron transport (PET) in spinach chloroplasts. Their inhibitory activity depended on the compound lipophilicity as well as on the position of the alkoxy substituent. The most potent PET inhibitors were 2-hydroxy-N-phenylnaphthalene-1-carboxamide and N-[3-(but-2-yloxy)phenyl]-2-hydroxynaphthalene-1-carboxamide within series A (IC50=28.9 and 42.5µM, respectively) and 1-hydroxy-N-(3-propoxyphenyl)naphthalene-2-carboxamide and 1-hydroxy-N-(3-ethoxyphenyl)-naphthalene-2-carboxamide (IC50=2.0 and 3.1µM, respectively) within series B. The inhibitory activity of C'(3) or C'(4) alkoxy substituted compounds of series B was considerably higher than that of C'(2) ones within series A. The PET-inhibiting activities of both series were compared with the PET inhibition of isomeric N-alkoxyphenyl-3-hydroxynaphthalene-2-carboxamides (series C) reported recently. Interactions of the studied compounds with chlorophyll a and aromatic amino acids present in pigment-protein complexes mainly in PS II were documented by fluorescence spectroscopy. The section between P680 and plastoquinone QB in the PET chain occurring on the acceptor side of PSII can be suggested as the site of action of the compounds.

  6. GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach.

    PubMed

    Baumung, R; Farkas, J; Boichard, D; Mészáros, G; Sölkner, J; Curik, I

    2015-04-01

    GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the 'classical' inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient (AHC ), defined here for the first time. AHC is defined as the number that tells how many times during pedigree segregation (gene dropping) a randomly taken allele has been in IBD status. Furthermore, GRain enables testing of heterogeneity and/or purging of inbreeding depression with respect to different founders/ancestors by calculating partial coefficients for all previously obtained coefficients.

  7. 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

  8. 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.

  9. 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

  10. Photoprotection of photosystems in fluctuating light intensities.

    PubMed

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

    2015-05-01

    Oxygenic photosynthetic organisms experience strong fluctuations in light intensity in their natural terrestrial and aquatic growth environments. Recent studies with both plants and cyanobacteria have revealed that Photosystem (PS) I is the potential target of damage upon abrupt changes in light intensity. Photosynthetic organisms have, however, developed powerful mechanisms in order to protect their photosynthetic apparatus against such potentially hazardous light conditions. Although the electron transfer chain has remained relatively unchanged in both plant chloroplasts and their cyanobacterial ancestors, the photoprotective and regulatory mechanisms of photosynthetic light reactions have experienced conspicuous evolutionary changes. In cyanobacteria, the specific flavodiiron proteins (Flv1 and Flv3) are responsible for safeguarding PSI under rapidly fluctuating light intensities, whilst the thylakoid located terminal oxidases are involved in the protection of PSII during 12h diurnal cycles involving abrupt, square-wave, changes from dark to high light. Higher plants such as Arabidopsis thaliana have evolved different protective mechanisms. In particular, the PGR5 protein controls electron flow during sudden changes in light intensity by allowing the regulation mostly via the Cytochrome b6f complex. Besides the function of PGR5, plants have also acquired other dynamic regulatory mechanisms, among them the STN7-related LHCII protein phosphorylation that is similarly responsible for protection against rapid changes in the light environment. The green alga Chlamydomonas reinhardtii, as an evolutionary intermediate between cyanobacteria and higher plants, probably possesses both protective mechanisms. In this review, evolutionarily different photoprotective mechanisms under fluctuating light conditions are described and their contributions to cyanobacterial and plant photosynthesis are discussed. © The Author 2014. Published by Oxford University Press on behalf of

  11. 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

  12. 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

  13. 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.

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

    PubMed

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

    2013-12-01

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

  15. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates.

    PubMed

    Huang, Ruiqi; Hippauf, Frank; Rohrbeck, Diana; Haustein, Maria; Wenke, Katrin; Feike, Janie; Sorrelle, Noah; Piechulla, Birgit; Barkman, Todd J

    2012-02-21

    In this study, we investigated the role for ancestral functional variation that may be selected upon to generate protein functional shifts using ancestral protein resurrection, statistical tests for positive selection, forward and reverse evolutionary genetics, and enzyme functional assays. Data are presented for three instances of protein functional change in the salicylic acid/benzoic acid/theobromine (SABATH) lineage of plant secondary metabolite-producing enzymes. In each case, we demonstrate that ancestral nonpreferred activities were improved upon in a daughter enzyme after gene duplication, and that these functional shifts were likely coincident with positive selection. Both forward and reverse mutagenesis studies validate the impact of one or a few sites toward increasing activity with ancestrally nonpreferred substrates. In one case, we document the occurrence of an evolutionary reversal of an active site residue that reversed enzyme properties. Furthermore, these studies show that functionally important amino acid replacements result in substrate discrimination as reflected in evolutionary changes in the specificity constant (k(cat)/K(M)) for competing substrates, even though adaptive substitutions may affect K(M) and k(cat) separately. In total, these results indicate that nonpreferred, or even latent, ancestral protein activities may be coopted at later times to become the primary or preferred protein activities.

  16. An experimental phylogeny to benchmark ancestral sequence reconstruction

    PubMed Central

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

    2016-01-01

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

  17. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates

    PubMed Central

    Huang, Ruiqi; Hippauf, Frank; Rohrbeck, Diana; Haustein, Maria; Wenke, Katrin; Feike, Janie; Sorrelle, Noah; Piechulla, Birgit; Barkman, Todd J.

    2012-01-01

    In this study, we investigated the role for ancestral functional variation that may be selected upon to generate protein functional shifts using ancestral protein resurrection, statistical tests for positive selection, forward and reverse evolutionary genetics, and enzyme functional assays. Data are presented for three instances of protein functional change in the salicylic acid/benzoic acid/theobromine (SABATH) lineage of plant secondary metabolite-producing enzymes. In each case, we demonstrate that ancestral nonpreferred activities were improved upon in a daughter enzyme after gene duplication, and that these functional shifts were likely coincident with positive selection. Both forward and reverse mutagenesis studies validate the impact of one or a few sites toward increasing activity with ancestrally nonpreferred substrates. In one case, we document the occurrence of an evolutionary reversal of an active site residue that reversed enzyme properties. Furthermore, these studies show that functionally important amino acid replacements result in substrate discrimination as reflected in evolutionary changes in the specificity constant (kcat/KM) for competing substrates, even though adaptive substitutions may affect KM and kcat separately. In total, these results indicate that nonpreferred, or even latent, ancestral protein activities may be coopted at later times to become the primary or preferred protein activities. PMID:22315396

  18. Oxygen evolving complex in photosystem II: better than excellent.

    PubMed

    Najafpour, Mohammad Mahdi; Govindjee

    2011-09-28

    The Oxygen Evolving Complex in photosystem II, which is responsible for the oxidation of water to oxygen in plants, algae and cyanobacteria, contains a cluster of one calcium and four manganese atoms. This cluster serves as a model for the splitting of water by energy obtained from sunlight. The recent published data on the mechanism and the structure of photosystem II provide a detailed architecture of the oxygen-evolving complex and the surrounding amino acids. Biomimetically, we expect to learn some strategies from this natural system to synthesize an efficient catalyst for water oxidation, that is necessary for artificial photosynthesis.

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

    PubMed Central

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

    2002-01-01

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

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

    PubMed

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

    2013-09-01

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

  1. Simultaneous regulation of antenna size and photosystem I/II stoichiometry in Arabidopsis thaliana.

    PubMed

    Jia, Ting; Ito, Hisashi; Tanaka, Ayumi

    2016-11-01

    The photosystem I/II ratio increased when antenna size was enlarged by transient induction of CAO in chlorophyll b -less mutants, thus indicating simultaneous regulation of antenna size and photosystem I/II stoichiometry. Regulation of antenna size and photosystem I/II stoichiometry is an indispensable strategy for plants to acclimate to changes to light environments. When plants grown in high-light conditions are transferred to low-light conditions, the peripheral antennae of photosystems are enlarged. A change in the photosystem I/II ratio is also observed under the same light conditions. However, our knowledge of the correlation between antenna size modulation and variation in photosystem I/II stoichiometry remains limited. In this study, chlorophyll a oxygenase was transiently induced in Arabidopsis thaliana chlorophyll b-less mutants, ch1-1, to alter the antenna size without changing environmental conditions. In addition to the accumulation of chlorophyll b, the levels of the peripheral antenna complexes of both photosystems gradually increased, and these were assembled to the core antenna of both photosystems. However, the antenna size of photosystem II was greater than that of photosystem I. Immunoblot analysis of core antenna proteins showed that the number of photosystem I increased, but not that of photosystem II, resulting in an increase in the photosystem I/II ratio. These results clearly indicate that antenna size adjustment was coupled with changes in photosystem I/II stoichiometry. Based on these results, the physiological importance of simultaneous regulation of antenna size and photosystem I/II stoichiometry is discussed in relation to acclimation to light conditions.

  2. The Microcephalin Ancestral Allele in a Neanderthal Individual

    PubMed Central

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

    2010-01-01

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

  3. Ancestral Genomes, Sex, and the Population Structure of Trypanosoma cruzi

    PubMed Central

    Bastos-Rodrigues, Luciana; Gonçalves, Vanessa F; Teixeira, Santuza M. R; Chiari, Egler; Junqueira, Ângela C. V; Fernandes, Octavio; Macedo, Andréa M; Machado, Carlos Renato; Pena, Sérgio D. J

    2006-01-01

    Acquisition of detailed knowledge of the structure and evolution of Trypanosoma cruzi populations is essential for control of Chagas disease. We profiled 75 strains of the parasite with five nuclear microsatellite loci, 24Sα RNA genes, and sequence polymorphisms in the mitochondrial cytochrome oxidase subunit II gene. We also used sequences available in GenBank for the mitochondrial genes cytochrome B and NADH dehydrogenase subunit 1. A multidimensional scaling plot (MDS) based in microsatellite data divided the parasites into four clusters corresponding to T. cruzi I (MDS-cluster A), T. cruzi II (MDS-cluster C), a third group of T. cruzi strains (MDS-cluster B), and hybrid strains (MDS-cluster BH). The first two clusters matched respectively mitochondrial clades A and C, while the other two belonged to mitochondrial clade B. The 24Sα rDNA and microsatellite profiling data were combined into multilocus genotypes that were analyzed by the haplotype reconstruction program PHASE. We identified 141 haplotypes that were clearly distributed into three haplogroups (X, Y, and Z). All strains belonging to T. cruzi I (MDS-cluster A) were Z/Z, the T. cruzi II strains (MDS-cluster C) were Y/Y, and those belonging to MDS-cluster B (unclassified T. cruzi) had X/X haplogroup genotypes. The strains grouped in the MDS-cluster BH were X/Y, confirming their hybrid character. Based on these results we propose the following minimal scenario for T. cruzi evolution. In a distant past there were at a minimum three ancestral lineages that we may call, respectively, T. cruzi I, T. cruzi II, and T. cruzi III. At least two hybridization events involving T. cruzi II and T. cruzi III produced evolutionarily viable progeny. In both events, the mitochondrial recipient (as identified by the mitochondrial clade of the hybrid strains) was T. cruzi II and the mitochondrial donor was T. cruzi III. PMID:16609729

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

    PubMed

    Briscoe, Adriana D

    2008-06-01

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

  5. Ancestral and novel roles of Pax family genes in mollusks.

    PubMed

    Scherholz, Maik; Redl, Emanuel; Wollesen, Tim; de Oliveira, André Luiz; Todt, Christiane; Wanninger, Andreas

    2017-03-16

    Pax genes are transcription factors with significant roles in cell fate specification and tissue differentiation during animal ontogeny. Most information on their tempo-spatial mode of expression is available from well-studied model organisms where the Pax-subfamilies Pax2/5/8, Pax6, and Paxα/β are mainly involved in the development of the central nervous system (CNS), the eyes, and other sensory organs. In certain taxa, Pax2/5/8 seems to be additionally involved in the development of excretion organs. Data on expression patterns in lophotrochozoans, and in particular in mollusks, are very scarce for all the above-mentioned Pax-subfamilies, which hampers reconstruction of their putative ancestral roles in bilaterian animals. Thus, we studied the developmental expression of Pax2/5/8, Pax6, and the lophotrochozoan-specific Paxβ in the worm-shaped mollusk Wirenia argentea, a member of Aplacophora that together with Polyplacophora forms the Aculifera, the proposed sister taxon to all primarily single-shelled mollusks (Conchifera). All investigated Pax genes are expressed in the developing cerebral ganglia and in the ventral nerve cords, but not in the lateral nerve cords of the tetraneural nervous system. Additionally, Pax2/5/8 is expressed in epidermal spicule-secreting or associated cells of the larval trunk and in the region of the developing protonephridia. We found no indication for an involvement of the investigated Pax genes in the development of larval or adult sensory organs of Wirenia argentea. Pax2/5/8 seems to have a conserved role in the development of the CNS, whereas expression in the spicule-secreting tissues of aplacophorans and polyplacophorans suggests co-option in aculiferan skeletogenesis. The Pax6 expression pattern in Aculifera largely resembles the common bilaterian expression during CNS development. All data available on Paxβ expression argue for a common role in lophotrochozoan neurogenesis.

  6. Quality control of Photosystem II: reversible and irreversible protein aggregation decides the fate of Photosystem II under excessive illumination

    PubMed Central

    Yamamoto, Yasusi; Hori, Haruka; Kai, Suguru; Ishikawa, Tomomi; Ohnishi, Atsuki; Tsumura, Nodoka; Morita, Noriko

    2013-01-01

    In response to excessive light, the thylakoid membranes of higher plant chloroplasts show dynamic changes including the degradation and reassembly of proteins, a change in the distribution of proteins, and large-scale structural changes such as unstacking of the grana. Here, we examined the aggregation of light-harvesting chlorophyll-protein complexes and Photosystem II core subunits of spinach thylakoid membranes under light stress with 77K chlorophyll fluorescence; aggregation of these proteins was found to proceed with increasing light intensity. Measurement of changes in the fluidity of thylakoid membranes with fluorescence polarization of diphenylhexatriene showed that membrane fluidity increased at a light intensity of 500–1,000 μmol photons m-2 s-1, and decreased at very high light intensity (1,500 μmol photons m-2 s-1). The aggregation of light-harvesting complexes at moderately high light intensity is known to be reversible, while that of Photosystem II core subunits at extremely high light intensity is irreversible. It is likely that the reversibility of protein aggregation is closely related to membrane fluidity: increases in fluidity should stimulate reversible protein aggregation, whereas irreversible protein aggregation might decrease membrane fluidity. When spinach leaves were pre-illuminated with moderately high light intensity, the qE component of non-photochemical quenching and the optimum quantum yield of Photosystem II increased, indicating that Photosystem II/light-harvesting complexes rearranged in the thylakoid membranes to optimize Photosystem II activity. Transmission electron microscopy revealed that the thylakoids underwent partial unstacking under these light stress conditions. Thus, protein aggregation is involved in thylakoid dynamics and regulates photochemical reactions, thereby deciding the fate of Photosystem II. PMID:24194743

  7. 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.

  8. Quality control of Photosystem II: where and how does the degradation of the D1 protein by FtsH proteases start under light stress?--Facts and hypotheses.

    PubMed

    Yoshioka, Miho; Yamamoto, Yasusi

    2011-01-01

    Degradation of the reaction center-binding D1 protein of Photosystem II is central in photoinhibition of Photosystem II. In higher plant chloroplasts, Photosystem II complexes are abundant in the grana. It has been suggested that the Photosystem II complexes containing photodamaged D1 protein migrate for their repair from the grana to the non-appressed stroma thylakoids, where the photodamaged D1 protein is degraded by a specific protease(s) such as filamentation temperature sensitive H (FtsH) protease. There are several possible ways to activate the FtsH proteases. As FtsH is a membrane-bound ATP-dependent metalloprotease, it requires ATP and zinc as essential part of its catalytic mechanism. It is also suggested that a membrane protein(s) associated with FtsH is required for modulation of the FtsH activity. Here, we propose several possible mechanisms for activation of the proteases, which depend on oligomerization of the monomer subunits. In relation to the oligomerization of FtsH subunits, we also suggest unique distribution of active FtsH hexamers on the thylakoids: hexamers of the FtsH proteases are localized near the Photosystem II complexes at the grana. Degradation of the D1 protein probably takes place in the grana rather than in the stroma thylakoids to circumvent long-distance migration of both the Photosystem II complexes containing the photodamaged D1 protein and the proteases. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. 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…

  10. 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…

  11. Covalently Binding the Photosystem I to Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Kaniber, S.; Frolov, L.; Simmel, F. C.; Holleitner, A. W.; Carmeli, C.; Carmeli, I.

    2010-01-01

    We present a chemical route to covalently couple the photosystem I (PS I) to carbon nanotubes (CNTs). Small linker molecules are used to connect the PS I to the CNTs. Hybrid systems, consisting of CNTs and the PS I, promise new photo-induced transport phenomena due to the outstanding electro-optical properties of the robust cyanobacteria membrane protein PS I.

  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. Light-harvesting superstructures of green plant chloroplasts lacking photosystems.

    PubMed

    Belgio, Erica; Ungerer, Petra; Ruban, Alexander V

    2015-10-01

    The light-harvesting antenna of higher plant photosystem II (LHCII) is the major photosynthetic membrane component encoded by an entire family of homologous nuclear genes. On the contrary, the great majority of proteins of photosystems and electron transport components are encoded by the chloroplast genome. In this work, we succeeded in gradually inhibiting the expression of the chloroplast genes that led to the disappearance of the photosystem complexes, mimicking almost total photoinhibition. The treated plants, despite displaying only some early signs of senescence, sustained their metabolism and growth for several weeks. The only major remaining membrane component was LHCII antenna that formed superstructures - stacks of dozens of thylakoids or supergrana. Freeze-fracture electron microscopy revealed specific organization, directly displaying frequently bifurcated membranes with reduced or totally absent photosystem II (PSII) reaction centre complexes. Our findings show that it is possible to accumulate large amounts of light-harvesting membranes, organized into three-dimensional structures, in the absence of reaction centre complexes. This points to the reciprocal role of LHCII and PSII in self-assembly of the three-dimensional matrix of the photosynthetic membrane, dictating its size and flexible adaptation to the light environment.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  15. A practical approach to detect ancestral haplotypes in livestock populations.

    PubMed

    Sánchez-Molano, Enrique; Tsiokos, Dimitrios; Chatziplis, Dimitrios; Jorjani, Hossein; Degano, Lorenzo; Diaz, Clara; Rossoni, Attilio; Schwarzenbacher, Hermann; Seefried, Franz; Varona, Luis; Vicario, Daniele; Nicolazzi, Ezequiel L; Banos, Georgios

    2016-06-24

    The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle. The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content. In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations.

  16. 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

  17. The Effect of Recombination on the Reconstruction of Ancestral Sequences

    PubMed Central

    Arenas, Miguel; Posada, David

    2010-01-01

    While a variety of methods exist to reconstruct ancestral sequences, all of them assume that a single phylogeny underlies all the positions in the alignment and therefore that recombination has not taken place. Using computer simulations we show that recombination can severely bias ancestral sequence reconstruction (ASR), and quantify this effect. If recombination is ignored, the ancestral sequences recovered can be quite distinct from the grand most recent common ancestor (GMRCA) of the sample and better resemble the concatenate of partial most recent common ancestors (MRCAs) at each recombination fragment. When independent phylogenetic trees are assumed for the different recombinant segments, the estimation of the fragment MRCAs improves significantly. Importantly, we show that recombination can change the biological predictions derived from ASRs carried out with real data. Given that recombination is widespread on nuclear genes and in particular in RNA viruses and some bacteria, the reconstruction of ancestral sequences in these cases should consider the potential impact of recombination and ideally be carried out using approaches that accommodate recombination. PMID:20124027

  18. 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…

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

    PubMed

    Schulze, Anja; Rice, Mary E

    2009-01-01

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

  20. Isolation of Ancestral Sylvatic Dengue Virus Type 1, Malaysia

    PubMed Central

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

    2010-01-01

    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

  1. 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.

  2. A multi-functional tubulovesicular network as the ancestral eukaryotic endomembrane system.

    PubMed

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

    2015-03-24

    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.

  3. 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

  4. 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. Copyright 2001 John Wiley & Sons, Inc.

  5. Directing electron transfer within Photosystem I by breaking H-bonds in the cofactor branches

    PubMed Central

    Li, Yajing; van der Est, Art; Lucas, Marie Gabrielle; Ramesh, V. M.; Gu, Feifei; Petrenko, Alexander; Lin, Su; Webber, Andrew N.; Rappaport, Fabrice; Redding, Kevin

    2006-01-01

    Photosystem I has two branches of cofactors down which light-driven electron transfer (ET) could potentially proceed, each consisting of a pair of chlorophylls (Chls) and a phylloquinone (PhQ). Forward ET from PhQ to the next ET cofactor (FX) is described by two kinetic components with decay times of ≈20 and ≈200 ns, which have been proposed to represent ET from PhQB and PhQA, respectively. Immediately preceding each quinone is a Chl (ec3), which receives a H-bond from a nearby tyrosine. To decrease the reduction potential of each of these Chls, and thus modify the relative yield of ET within the targeted branch, this H-bond was removed by conversion of each Tyr to Phe in the green alga Chlamydomonas reinhardtii. Together, transient optical absorption spectroscopy performed in vivo and transient electron paramagnetic resonance data from thylakoid membranes showed that the mutations affect the relative amplitudes, but not the lifetimes, of the two kinetic components representing ET from PhQ to FX. The mutation near ec3A increases the fraction of the faster component at the expense of the slower component, with the opposite effect seen in the ec3B mutant. We interpret this result as a decrease in the relative use of the targeted branch. This finding suggests that in Photosystem I, unlike type II reaction centers, the relative efficiency of the two branches is extremely sensitive to the energetics of the embedded redox cofactors. PMID:16467143

  6. Directing electron transfer within Photosystem I by breaking H-bonds in the cofactor branches.

    PubMed

    Li, Yajing; van der Est, Art; Lucas, Marie Gabrielle; Ramesh, V M; Gu, Feifei; Petrenko, Alexander; Lin, Su; Webber, Andrew N; Rappaport, Fabrice; Redding, Kevin

    2006-02-14

    Photosystem I has two branches of cofactors down which light-driven electron transfer (ET) could potentially proceed, each consisting of a pair of chlorophylls (Chls) and a phylloquinone (PhQ). Forward ET from PhQ to the next ET cofactor (FX) is described by two kinetic components with decay times of approximately 20 and approximately 200 ns, which have been proposed to represent ET from PhQB and PhQA, respectively. Immediately preceding each quinone is a Chl (ec3), which receives a H-bond from a nearby tyrosine. To decrease the reduction potential of each of these Chls, and thus modify the relative yield of ET within the targeted branch, this H-bond was removed by conversion of each Tyr to Phe in the green alga Chlamydomonas reinhardtii. Together, transient optical absorption spectroscopy performed in vivo and transient electron paramagnetic resonance data from thylakoid membranes showed that the mutations affect the relative amplitudes, but not the lifetimes, of the two kinetic components representing ET from PhQ to F(X). The mutation near ec3A increases the fraction of the faster component at the expense of the slower component, with the opposite effect seen in the ec3B mutant. We interpret this result as a decrease in the relative use of the targeted branch. This finding suggests that in Photosystem I, unlike type II reaction centers, the relative efficiency of the two branches is extremely sensitive to the energetics of the embedded redox cofactors.

  7. Amorphous manganese-calcium oxides as a possible evolutionary origin for the CaMn₄ cluster in photosystem II.

    PubMed

    Najafpour, Mohammad Mahdi

    2011-06-01

    In this paper a few calcium-manganese oxides and calcium-manganese minerals are studied as catalysts for water oxidation. The natural mineral marokite is also studied as a catalyst for water oxidation for the first time. Marokite is made up of edge-sharing Mn(3+) in a distorted octahedral environment and eight-coordinate Ca(2+) centered polyhedral layers. The structure is similar to recent models of the oxygen evolving complex in photosystem II. Thus, the oxygen evolving complex in photosystem II does not have an unusual structure and could be synthesized hydrothermally. Also in this paper, oxygen evolution is studied with marokite (CaMn₂O₄), pyrolusite (MnO₂) and compared with hollandite (Ba(0.2)Ca(0.15)K(0.3)Mn(6.9)Al(0.2)Si(0.3)O(16)), hausmannite (Mn₃O₄), Mn₂O₃.H₂O, Ca Mn₃O₆.H₂O, CaMn₄O₈.H₂O, CaMn₂O₄.H₂O and synthetic marokite (CaMn₂O₄). I propose that the origin of the oxygen evolving complex in photosystem II resulted from absorption of calcium and manganese ions that were precipitated together in the archean oceans by protocyanobacteria because of changing pH from ~5 to ~8-10. As reported in this paper, amorphous calcium-manganese oxides with different ratios of manganese and calcium are effective catalysts for water oxidation. The bond types and lengths of the calcium and manganese ions in the calcium-manganese oxides are directly comparable to those in the OEC. This primitive structure of these amorphous calcium-manganese compounds could be changed and modified by environmental groups (amino acids) to form the oxygen evolving complex in photosystem II.

  8. 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

  9. Photoinactivation of photosystem II: is there more than one way to skin a cat?

    PubMed

    Ohad, Itzhak; Berg, Alex; Berkowicz, Simon M; Kaplan, Aaron; Keren, Nir

    2011-05-01

    We briefly review the main mechanisms proposed for photodamage to photosystem II (PSII), at the donor and acceptor sides, and then discuss the mechanism whereby filamentous cyanobacteria inhabiting biological sand crusts such as Microcoleus sp. are able to avoid serious damage to their photosynthetic machinery. We show that the decline in fluorescence following exposure to excess light does not reflect a reduction in PSII activity but rather the activation of a non-radiative charge recombination in PSII. Furthermore, we show that the difference in the thermoluminescent peak temperature intensities in these organisms, in the presence and absence of inhibitors such as dichlorophenyl-dimethylurea (DCMU), is smaller than observed in model organisms suggesting that the redox gap between Q(A)⁻ and P₆₈₀+ is smaller. On the basis of these data, we propose that this could enable an alternative, pheophytin-independent recombination, thereby minimizing the damaging ¹O₂ production associated with radiative recombination.

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

    PubMed Central

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

    2002-01-01

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

  11. Inferring the Early Evolution of Translation: Ancestral Reconstruction, Compositional Analysis, and Functional Specificity

    NASA Astrophysics Data System (ADS)

    Fournier, G. P.; Gogarten, J. P.

    2010-04-01

    Using ancestral sequence reconstruction and compositional analysis, it is possible to reconstruct the ancestral functions of many enzymes involved in protein synthesis, elucidating the early functional evolution of the translation machinery and genetic code.

  12. Evolution of complex resistance transposons from an ancestral mercury transposon.

    PubMed

    Tanaka, M; Yamamoto, T; Sawai, T

    1983-03-01

    The molecular interrelationship of a transposon family which confers multiple antibiotic resistance and is assumed to have been generated from an ancestral mercury transposon was analyzed. Initially, the transposons Tn2613 (7.2 kilobases), encoding mercury resistance, and Tn2608 (13.5 kilobases), encoding mercury, streptomycin, and sulfonamide resistances, were isolated and their structures were analyzed. Next, the following transposons were compared with respect to their genetic and physical maps: Tn2613 and Tn501, encoding mercury resistance; Tn2608 and Tn21, encoding mercury, streptomycin, and sulfonamide resistance; Tn2607 and Tn4, encoding streptomycin, sulfonamide, and ampicillin resistance; and Tn2603, encoding mercury, streptomycin, sulfonamide, and ampicillin resistance. The results suggest that the transposons encoding multiple resistance were evolved from an ancestral mercury transposon.

  13. Single-crossover recombination and ancestral recombination trees.

    PubMed

    Baake, Ellen; von Wangenheim, Ute

    2014-05-01

    We consider the Wright-Fisher model for a population of [Formula: see text] individuals, each identified with a sequence of a finite number of sites, and single-crossover recombination between them. We trace back the ancestry of single individuals from the present population. In the [Formula: see text] limit without rescaling of parameters or time, this ancestral process is described by a random tree, whose branching events correspond to the splitting of the sequence due to recombination. With the help of a decomposition of the trees into subtrees, we calculate the probabilities of the topologies of the ancestral trees. At the same time, these probabilities lead to a semi-explicit solution of the deterministic single-crossover equation. The latter is a discrete-time dynamical system that emerges from the Wright-Fisher model via a law of large numbers and has been waiting for a solution for many decades.

  14. Structure of photosystem II and substrate binding at room temperature

    SciTech Connect

    Young, Iris D.; Ibrahim, Mohamed; Chatterjee, Ruchira; Gul, Sheraz; Fuller, Franklin D.; Koroidov, Sergey; Brewster, Aaron S.; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G.; Stan, Claudiu A.; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Vo Pham, Long; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A.; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T.; Andi, Babak; Orville, Allen M.; Glownia, James M.; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S.; Lane, Thomas J.; Aquila, Andy; Koglin, Jason E.; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Moriarty, Nigel W.; Liebschner, Dorothee; Afonine, Pavel V.; Waterman, David G.; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I.; Brunger, Axel T.; Zwart, Petrus H.; Adams, Paul D.; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K.; Kern, Jan; Yachandra, Vittal K.; Yano, Junko

    2016-11-21

    We report light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution. A detailed understanding of the O–O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL7 provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. Lastly, this approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond

  15. Structure of photosystem II and substrate binding at room temperature

    DOE PAGES

    Young, Iris D.; Ibrahim, Mohamed; Chatterjee, Ruchira; ...

    2016-11-21

    We report light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution. A detailed understanding of the O–O bond formation mechanismmore » remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL7 provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. Lastly, this approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.« less

  16. Structure of photosystem II and substrate binding at room temperature.

    PubMed

    Young, Iris D; Ibrahim, Mohamed; Chatterjee, Ruchira; Gul, Sheraz; Fuller, Franklin D; Koroidov, Sergey; Brewster, Aaron S; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G; Stan, Claudiu A; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Vo Pham, Long; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T; Andi, Babak; Orville, Allen M; Glownia, James M; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S; Lane, Thomas J; Aquila, Andy; Koglin, Jason E; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y; Uervirojnangkoorn, Monarin; Moriarty, Nigel W; Liebschner, Dorothee; Afonine, Pavel V; Waterman, David G; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I; Brunger, Axel T; Zwart, Petrus H; Adams, Paul D; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K; Kern, Jan; Yachandra, Vittal K; Yano, Junko

    2016-12-15

    Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

  17. Structure of photosystem II and substrate binding at room temperature

    PubMed Central

    Gul, Sheraz; Fuller, Franklin; Koroidov, Sergey; Brewster, Aaron S.; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G.; Stan, Claudiu A.; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Long Vo, Pham; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A.; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T.; Andi, Babak; Orville, Allen M.; Glownia, James M.; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S.; Lane, Thomas J.; Aquila, Andy; Koglin, Jason E.; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Moriarty, Nigel W.; Liebschner, Dorothee; Afonine, Pavel V.; Waterman, David G.; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I.; Brunger, Axel T.; Zwart, Petrus H.; Adams, Paul D.; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K.; Kern, Jan; Yachandra, Vittal K.; Yano, Junko

    2016-01-01

    Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment-protein complex, couples the one-electron photochemistry at the reaction center with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC) (Fig. 1a, Extended Data Fig. 1). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4)1, where S1 is the dark stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution2,3. A detailed understanding of the O-O bond formation mechanism remains a challenge, and elucidating the structures of the OEC in the different S-states, as well as the binding of the two substrate waters to the catalytic site4-6, is a prerequisite for this purpose. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage free, room temperature (RT) structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å structure of PS II7 at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, RT measurements are required to study the structural landscape of proteins under functional conditions8,9, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analog, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10-13. Thus, this approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms. PMID:27871088

  18. Resurrection of an ancestral 5S rRNA.

    PubMed

    Lu, Qing; Fox, George E

    2011-07-22

    In addition to providing phylogenetic relationships, tree making procedures such as parsimony and maximum likelihood can make specific predictions of actual historical sequences. Resurrection of such sequences can be used to understand early events in evolution. In the case of RNA, the nature of parsimony is such that when applied to multiple RNA sequences it typically predicts ancestral sequences that satisfy the base pairing constraints associated with secondary structure. The case for such sequences being actual ancestors is greatly improved, if they can be shown to be biologically functional. A unique common ancestral sequence of 28 Vibrio 5S ribosomal RNA sequences predicted by parsimony was resurrected and found to be functional in the context of the E. coli cellular environment. The functionality of various point variants and intermediates that were constructed as part of the resurrection were examined in detail. When separately introduced the changes at single stranded positions and individual double variants at base-paired positions were also viable. An additional double variant was examined at a different base-paired position and it was also valid. The results show that at least in the case of the 5S rRNAs considered here, ancestors predicted by parsimony are likely to be realistic when the prediction is not overly influenced by single outliers. It is especially noteworthy that the phenotype of the predicted ancestors could be anticipated as a cumulative consequence of the phenotypes of the individual variants that comprised them. Thus, point mutation data is potentially useful in evaluating the reasonableness of ancestral sequences predicted by parsimony or other methods. The results also suggest that in the absence of significant tertiary structure constraints double variants that preserve pairing in stem regions will typically be accepted. Overall, the results suggest that it will be feasible to resurrect additional meaningful 5S rRNA ancestors as well

  19. Cyclic electron transport around photosystem I: genetic approaches.

    PubMed

    Shikanai, Toshiharu

    2007-01-01

    The light reactions in photosynthesis convert light energy into chemical energy in the form of ATP and drive the production of NADPH from NADP+. The reactions involve two types of electron flow in the chloroplast. While linear electron transport generates both ATP and NADPH, photosystem I cyclic electron transport is exclusively involved in ATP synthesis. The physiological significance of photosystem I cyclic electron transport has been underestimated, and our knowledge of the machineries involved remains very limited. However, recent genetic approaches using Arabidopsis thaliana have clarified the essential functions of this electron flow in both photoprotection and photosynthesis. Based on several lines of evidence presented here, it is necessary to reconsider the fundamental mechanisms of chloroplast energetics.

  20. 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

  1. Ancestral facial morphology of Old World higher primates.

    PubMed

    Benefit, B R; McCrossin, M L

    1991-06-15

    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.

  2. 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.

  3. 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

  4. Cases In Which Ancestral Maximum Likelihood Will Be Confusingly Misleading.

    PubMed

    Handelman, Tomer; Chor, Benny

    2017-03-02

    Ancestral maximum likelihood (AML) is a phylogenetic tree reconstruction criteria that "lies between" maximum parsimony (MP) and maximum likelihood (ML). ML has long been known to be statistically consistent. On the other hand, Felsenstein (1978) showed that MP is statistically inconsistent, and even positively misleading: There are cases where the parsimony criteria, applied to data generated according to one tree topology, will be optimized on a different tree topology. The question of weather AML is statistically consistent or not has been open for a long time. Mosel, Roch, and Steel (2009) have shown that AML can "shrink" short tree edges, resulting in a star tree with no internal resolution, which yields a better AML score than the original (resolved) model. This result implies that AML is statistically inconsistent, but not that it is positively misleading, because the star tree is compatible with any other topology. We show that AML is confusingly misleading: For some simple, four taxa (resolved) tree, the ancestral likelihood optimization criteria is maximized on an incorrect (resolved) tree topology, as well as on a star tree (both with specific edge lengths), while the tree with the original, correct topology, has strictly lower ancestral likelihood. Interestingly, the two short edges in the incorrect, resolved tree topology are of length zero, and are not adjacent, so this resolved tree is in fact a simple path. While for MP, the underlying phenomenon can be described as long edge attraction, it turns out that here we have long edge repulsion.

  5. Chlorophyll triplet states associated with photosystem II of thylakoids.

    PubMed

    Santabarbara, Stefano; Bordignon, Enrica; Jennings, Robert C; Carbonera, Donatella

    2002-06-25

    The analysis of FDMR thylakoid spectra, determined at multiple emission wavelengths, by a global decomposition technique, has revealed the presence of three previously undescribed triplet populations at emission wavelengths characteristic of Photosystem II chlorophyll/protein complexes. Their zero-field splitting parameters have been determined in order to compare them with the well-studied PSII recombination triplet state. None of these triplets have the zero-field splitting parameters characteristic of the recombination triplet and are therefore probably not generated directly in the reaction center. On the basis of their microwave-induced emission spectra, it is suggested that two are probably generated in the core complex(es) while the third may be generated in the external antenna. These triplets are formed under nonreducing redox conditions, when the recombination triplet is undetectable. It is suggested that they may be involved in the photoinhibitory damage of Photosystem II. The triplet-minus-singlet spectrum associated with the recombination triplet state has been determined for thylakoids after reduction of the secondary acceptors. Its main peak is at 685 nm, slightly red shifted with respect to earlier reports, with a weak signal, of opposite sign at approximately 675 nm. The 685 nm peak indicates that at cryogenic temperatures, the triplet is located on the long-wavelength chlorophyll state present in the reaction center complex of Photosystem II (D1.D2.Cytb(559) complex). From the absence of a clear structure in the 680 nm absorption region, this long-wavelength absorbing state does not appear to be strongly coupled to P(680), though it must be associated with one of the "inner core" pigments recently identified in the photosystem II crystallographic structure [Zouni et al. (2001) Nature 408, 739-743].

  6. Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification.

    PubMed

    Harrington, S; Reeder, T W

    2017-02-01

    The binary-state speciation and extinction (BiSSE) model has been used in many instances to identify state-dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant-rate birth-death models often inappropriately favours the BiSSE model when diversification rates vary in a state-independent fashion. The newly developed HiSSE model enables researchers to identify state-dependent diversification rates while accounting for state-independent diversification at the same time. The HiSSE model also allows researchers to test state-dependent models against appropriate state-independent null models that have the same number of parameters as the state-dependent models being tested. We reanalyse two data sets that originally used BiSSE to reconstruct ancestral states within squamate reptiles and reached surprising conclusions regarding the evolution of toepads within Gekkota and viviparity across Squamata. We used this new method to demonstrate that there are many shifts in diversification rates across squamates. We then fit various HiSSE submodels and null models to the state and phylogenetic data and reconstructed states under these models. We found that there is no single, consistent signal for state-dependent diversification associated with toepads in gekkotans or viviparity across all squamates. Our reconstructions show limited support for the recently proposed hypotheses that toepads evolved multiple times independently in Gekkota and that transitions from viviparity to oviparity are common in Squamata. Our results highlight the importance of considering an adequate pool of models and null models when estimating diversification rate parameters and reconstructing ancestral states. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  7. 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

    2015-07-08

    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.

  8. Time-resolved quasielastic neutron scattering studies of native photosystems.

    PubMed

    Pieper, Jörg

    2010-01-01

    The internal molecular dynamics of proteins plays an important role in a number of functional processes in native photosystems. Prominent examples include the photocycle of bacteriorhodopsin and electron transfer in the reaction center of plant photosystem II. In this regard, the recently developed technique of time-resolved quasielastic neutron scattering with laser excitation opens up new perspectives for the study of protein/membrane dynamics in specific functional states of even complex systems. The first direct observation of a functionally modulated protein dynamics has just recently been reported for the model system bacteriorhodopsin (Pieper et al., Phys. Rev. Lett. 100, 2008, 228103.), where a transient softening of the protein was observed on a timescale of approximately 1 ms along with the large-scale structural change in the M-intermediate of bacteriorhodopsin. In contrast, photosystem II membrane fragments with inhibited electron transfer show a suppression of protein dynamics approximately 160 mus after the actinic laser flash (Pieper and Renger, Biochemistry 48, 2009, 6111). This effect may reflect aggregation-like conformational changes capable of dissipation of excess excitation energy to prevent photodamage in the absence of Q(A)-->Q(B) electron transfer. These findings indicate that proteins exhibit a remarkable flexibility to accommodate different functional processes. This contribution will discuss methodical aspects, challenges, and recent applications of laser-excited, time-resolved quasielastic neutron scattering.

  9. Photoelectric responses of oxygen-evolving complexes of photosystem II

    PubMed

    Mamedov; Beshta; Gurovskaya; Mamedova; Neverov; Samuilov; Semenov

    1999-05-01

    The generation of a transmembrane electric potential difference induced by a series of laser flashes was studied by the direct electrometrical method in proteoliposomes containing oxygen-evolving particles of photosystem II. In addition to the fast stage of generation of the membrane potential, which is due to electron transfer from the redox active tyrosine residue Tyr-161 (YZ) to the primary quinone acceptor QA, electrogenic stages corresponding to the S1 --> S2 (tau = 30 &mgr;sec), S2 --> S3 (tau = 240 &mgr;sec), and S3 --> S4 --> S0 (tau = 6.2 msec) transitions of the oxygen-evolving complex (OEC) were observed. The amplitudes of the photoelectric responses show that the contribution of the OEC to the overall electrogenicity is small. The parameters of the electrogenic reactions of the OEC as measured in photosystem II preparations containing the peripheral proteins of 23 and 17 kD were similar to those of photosystem II preparations devoid of these peptides. It is concluded that neither the 23- nor the 17-kD proteins are involved in the electrogenic reactions of the OEC.

  10. Cyclic electron flow around photosystem I is essential for photosynthesis.

    PubMed

    Munekage, Yuri; Hashimoto, Mihoko; Miyake, Chikahiro; Tomizawa, Ken-ichi; Endo, Tsuyoshi; Tasaka, Masao; Shikanai, Toshiharu

    2004-06-03

    Photosynthesis provides at least two routes through which light energy can be used to generate a proton gradient across the thylakoid membrane of chloroplasts, which is subsequently used to synthesize ATP. In the first route, electrons released from water in photosystem II (PSII) are eventually transferred to NADP+ by way of photosystem I (PSI). This linear electron flow is driven by two photochemical reactions that function in series. The cytochrome b6f complex mediates electron transport between the two photosystems and generates the proton gradient (DeltapH). In the second route, driven solely by PSI, electrons can be recycled from either reduced ferredoxin or NADPH to plastoquinone, and subsequently to the cytochrome b6f complex. Such cyclic flow generates DeltapH and thus ATP without the accumulation of reduced species. Whereas linear flow from water to NADP+ is commonly used to explain the function of the light-dependent reactions of photosynthesis, the role of cyclic flow is less clear. In higher plants cyclic flow consists of two partially redundant pathways. Here we have constructed mutants in Arabidopsis thaliana in which both PSI cyclic pathways are impaired, and present evidence that cyclic flow is essential for efficient photosynthesis.

  11. Imaging the Photosystem I/Photosystem II chlorophyll ratio inside the leaf.

    PubMed

    Wientjes, Emilie; Philippi, John; Borst, Jan Willem; van Amerongen, Herbert

    2017-03-01

    Oxygenic photosynthesis is driven by photosystems I (PSI) and II (PSII). In plants the number of chlorophylls of PSI versus PSII is adjusted to the light irradiance spectrum. On a timescale of days, this is regulated at the level of protein concentration. Instead, on a timescale of minutes, it is regulated by the dynamic association of light-harvesting complex II with either PSI or PSII. Thus far very diverse values have been reported for the PSI/PSII chlorophyll ratio, ranging from 0.54 to 1.4. The methods used require the isolation of chloroplasts and are time consuming. We present a fluorescence lifetime imaging approach that quantifies the PSI/PSII Chl ratio of chloroplasts directly in their natural leaf environment. In wild type Arabidopsis thaliana plants, grown under white light, the PSI/PSII chlorophyll ratio appeared to be 0.99±0.09 at the adaxial side and 0.83±0.05 at the abaxial side of the leaf. When these plants were acclimated to far red light for several days the PSI/PSII chlorophyll ratio decreased by more than a factor of 3 to compensate for the ineffective far red light absorption of PSII. This shows how plants optimize their light-harvesting capacity to the specific light conditions they encounter. Zooming in on single chloroplasts inside the leaf allowed to study the grana/stroma membrane network and their PSI/PSII chlorophyll ratios. The developed method will be useful to study dynamic processes in chloroplasts in intact leaves which involve changes in the grana and the stroma membranes such as state transitions. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. DNA clone encoding a photosystem I protein with homology to photosystem II chlorophyll a/b-binding polypeptides

    SciTech Connect

    Hoffman, N.E.; Pichersky, E.; Malik, V.S.; Castresana, C.; Ko, K.; Darr, S.C.; Cashmore, A.R.

    1987-12-01

    The authors report here the isolation and nucleotide sequence of a complete cDNA clone encoding a photosystem I (PS I) polypeptide that is recognized by a monoclonal antibody made against photosystem II (PS II) chlorophyll a/b-binding (CAB) proteins. The deduced sequence of this PS I protein shows 30% overall identity to PS II CAB sequences, and two long segments within this protein show 50% and 65% identity to the corresponding segments in the PS II CAB polypeptides. Even though the sequence of this PS I CAB protein is substantially divergent from PS II CAB sequences, their hydropathy plots are very similar and suggest they all traverse the thylakoid membrane three times. A segment of the PS I CAB polypeptide shows similarity to the functionally analogous ..beta.. subunits of the antenna proteins of purple bacteria. In contrast, no homology was observed between these bacterial proteins and PS II CAB polypeptides.

  13. A retrieval algorithm to evaluate the Photosystem I and Photosystem II spectral contributions to leaf chlorophyll fluorescence at physiological temperatures.

    PubMed

    Palombi, Lorenzo; Cecchi, Giovanna; Lognoli, David; Raimondi, Valentina; Toci, Guido; Agati, Giovanni

    2011-09-01

    A new computational procedure to resolve the contribution of Photosystem I (PSI) and Photosystem II (PSII) to the leaf chlorophyll fluorescence emission spectra at room temperature has been developed. It is based on the Principal Component Analysis (PCA) of the leaf fluorescence emission spectra measured during the OI photochemical phase of fluorescence induction kinetics. During this phase, we can assume that only two spectral components are present, one of which is constant (PSI) and the other variable in intensity (PSII). Application of the PCA method to the measured fluorescence emission spectra of Ficus benjamina L. evidences that the temporal variation in the spectra can be ascribed to a single spectral component (the first principal component extracted by PCA), which can be considered to be a good approximation of the PSII fluorescence emission spectrum. The PSI fluorescence emission spectrum was deduced by difference between measured spectra and the first principal component. A single-band spectrum for the PSI fluorescence emission, peaked at about 735 nm, and a 2-band spectrum with maxima at 685 and 740 nm for the PSII were obtained. A linear combination of only these two spectral shapes produced a good fit for any measured emission spectrum of the leaf under investigation and can be used to obtain the fluorescence emission contributions of photosystems under different conditions. With the use of our approach, the dynamics of energy distribution between the two photosystems, such as state transition, can be monitored in vivo, directly at physiological temperatures. Separation of the PSI and PSII emission components can improve the understanding of the fluorescence signal changes induced by environmental factors or stress conditions on plants.

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

    PubMed Central

    Franchin, Cinzia; Arrigoni, Giorgio

    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

  15. 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

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

    PubMed

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

    2015-03-22

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

  17. On the question of the light-harvesting role of β-carotene in photosystem II and photosystem I core complexes.

    PubMed

    Stamatakis, Kostas; Tsimilli-Michael, Merope; Papageorgiou, George C

    2014-08-01

    β-Carotene is the only carotenoid present in the core complexes of Photosystems I and II. Its proximity to chlorophyll a molecules enables intermolecular electronic interactions, including β-carotene to chlorophyll a electronic excitation transfers. However, it has been well documented that, compared to chlorophylls and to phycobilins, the light harvesting efficiency of β-carotenes for photosynthetic O2 evolution is poor. This is more evident in cyanobacteria than in plants and algae because they lack accessory light harvesting pigments with absorptions that overlap the β-carotene absorption. In the present work we investigated the light harvesting role of β-carotenes in the cyanobacterium Synechococcus sp. PCC 7942 using selective β-carotene excitation and selective Photosystem detection of photo-induced electron transport to and from the intersystem plastoquinones (the plastoquinone pool). We report that, although selectively excited β-carotenes transfer electronic excitation to the chlorophyll a of both photosystems, they enable only the oxidation of the plastoquinone pool by Photosystem I but not its reduction by Photosystem II. This may suggest a light harvesting role for the β-carotenes of the Photosystem I core complex but not for those of the Photosystem II core complex. According to the present investigation, performed with whole cyanobacterial cells, the lower photosynthesis yields measured with β-Car-absorbed light can be attributed to the different excitation trapping efficiencies in the reaction centers of PSI and PSII.

  18. 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

  19. 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.

  20. Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences

    PubMed Central

    Leclercq, Mickael; Diallo, Abdoulaye Baniré; Blanchette, Mathieu

    2017-01-01

    MicroRNAs (miRNA) are short single-stranded RNA molecules derived from hairpin-forming precursors that play a crucial role as post-transcriptional regulators in eukaryotes and viruses. In the past years, many microRNA target genes (MTGs) have been identified experimentally. However, because of the high costs of experimental approaches, target genes databases remain incomplete. Although several target prediction programs have been developed in the recent years to identify MTGs in silico, their specificity and sensitivity remain low. Here, we propose a new approach called MirAncesTar, which uses ancestral genome reconstruction to boost the accuracy of existing MTGs prediction tools for human miRNAs. For each miRNA and each putative human target UTR, our algorithm makes uses of existing prediction tools to identify putative target sites in the human UTR, as well as in its mammalian orthologs and inferred ancestral sequences. It then evaluates evidence in support of selective pressure to maintain target site counts (rather than sequences), accounting for the possibility of target site turnover. It finally integrates this measure with several simpler ones using a logistic regression predictor. MirAncesTar improves the accuracy of existing MTG predictors by 26% to 157%. Source code and prediction results for human miRNAs, as well as supporting evolutionary data are available at http://cs.mcgill.ca/∼blanchem/mirancestar. PMID:27899600

  1. Making sense of the past: hyperstability of ancestral thioredoxins explained by free energy simulations.

    PubMed

    Cortés Cabrera, Álvaro; Sánchez-Murcia, Pedro A; Gago, Federico

    2017-08-30

    Thioredoxin (Trx), a small and globular protein, is present in all kinds of organisms, from Archea to higher mammals. Throughout evolution, the Trx sequence has undergone subtle modifications to adapt to varying environmental conditions. The high degree of sequence conservation makes Trx very amenable to ancestral protein reconstruction techniques. In this work, we address the study of the structural and energetic determinants of thermostability in E. coli Trx using a dataset of mutations inspired by ancestral reconstruction. We compute, from first principles, the expected contribution of 19 different amino acid substitutions to the stability (ΔΔG) and the melting temperature (ΔTm) of the protein. We also describe the specific changes in structure and protein dynamics responsible for the stabilizing or destabilizing effects of these mutations. Our results point to local and independent changes for most of the variants. Our predictions are accurate enough to substantiate the proposal of new hypotheses regarding evolutionary relationships between mutations, as in the case of T89R, P68A and G74S or K90L and F102A, and reach beyond the initial set to suggest improved variants, such as K90I or K90Y.

  2. 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

  3. 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

  4. Ancestral Components of Admixed Genomes in a Mexican Cohort

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2011-12-01

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

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

    PubMed

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

    2015-07-01

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

  7. 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.

  8. Blue-light reception in Phycomyces phototropism: evidence for two photosystems operating in low- and high-intensity ranges

    SciTech Connect

    Galland, P.; Lipson, E.D.

    1987-01-01

    Phototropism in the fungus Phycomyces is mediated by two photosystems that are optimized for the low-intensity region (below 10(-6) W X m-2) and the high-intensity region (above 10(-6) W X m-2). These photosystems can be distinguished under special experimental conditions, in which sporangiophores grown in the dark are suddenly exposed to continuous unilateral light. With this treatment, the bending occurs in two steps. Below 10(-6) W X m-2, an early-response component (15-min latency) and a late-response component (50- to 70-min latency) are observed that are mediated by photosystem I. Above 10(-6) W X m-2, the early component is augmented by an intermediate component with a 40-min delay that is mediated by photosystem II. The two photosystems are distinguished further by their wavelength sensitivities and adaptation kinetics. Photosystem I is more effective at 334, 347, and 550 nm than photosystem II, but it is less effective at 383 nm. At wavelength 450 nm, the dark-adaptation kinetics associated with photosystem I are approximately half as fast as those associated with photosystem II. However, the light-adaptation kinetics of photosystem I are approximately equal to 3 times faster than the kinetics associated with photosystem II. The existence of two photosystems clarifies several behavioral features of Phycomyces and helps explain how the sporangiophore can manage the full range of 10 decades.

  9. The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate.

    PubMed

    Richardson, Aaron O; Rice, Danny W; Young, Gregory J; Alverson, Andrew J; Palmer, Jeffrey D

    2013-04-15

    The mitochondrial genomes of flowering plants vary greatly in size, gene content, gene order, mutation rate and level of RNA editing. However, the narrow phylogenetic breadth of available genomic data has limited our ability to reconstruct these traits in the ancestral flowering plant and, therefore, to infer subsequent patterns of evolution across angiosperms. We sequenced the mitochondrial genome of Liriodendron tulipifera, the first from outside the monocots or eudicots. This 553,721 bp mitochondrial genome has evolved remarkably slowly in virtually all respects, with an extraordinarily low genome-wide silent substitution rate, retention of genes frequently lost in other angiosperm lineages, and conservation of ancestral gene clusters. The mitochondrial protein genes in Liriodendron are the most heavily edited of any angiosperm characterized to date. Most of these sites are also edited in various other lineages, which allowed us to polarize losses of editing sites in other parts of the angiosperm phylogeny. Finally, we added comprehensive gene sequence data for two other magnoliids, Magnolia stellata and the more distantly related Calycanthus floridus, to measure rates of sequence evolution in Liriodendron with greater accuracy. The Magnolia genome has evolved at an even lower rate, revealing a roughly 5,000-fold range of synonymous-site divergence among angiosperms whose mitochondrial gene space has been comprehensively sequenced. Using Liriodendron as a guide, we estimate that the ancestral flowering plant mitochondrial genome contained 41 protein genes, 14 tRNA genes of mitochondrial origin, as many as 7 tRNA genes of chloroplast origin, >700 sites of RNA editing, and some 14 colinear gene clusters. Many of these gene clusters, genes and RNA editing sites have been variously lost in different lineages over the course of the ensuing ∽200 million years of angiosperm evolution.

  10. What computational chemistry and magnetic resonance reveal concerning the oxygen evolving centre in Photosystem II.

    PubMed

    Terrett, Richard; Petrie, Simon; Stranger, Rob; Pace, Ron J

    2016-09-01

    Density Functional Theory (DFT) computational studies of the Mn4/Ca Oxygen Evolving Complex (OEC) region of Photosystem II in the paramagnetic S2 and S3 states of the water oxdizing catalytic cycle are described. These build upon recent advances in computationally understanding the detailed S1 state OEC geometries, revealed by the recent high resolution Photosystem II crystal structures of Shen et al., at 1.90Å and 1.95Å (Petrie et al., 2015, Angew. Chem. Int. Ed., 54, 7120). The models feature a 'Low Oxidation Paradigm' assumption for the mean Mn oxidation states in the functional enzyme, with the mean oxidation levels being 3.0, 3.25 and 3.5 in S1, S2 and S3, respectively. These calculations are used to infer magnetic exchange interactions within the coupled OEC cluster, particularly in the Electron Paramagnetic Resonance (EPR)-visible S2 and S3 states. Detailed computational estimates of the intrinsic magnitudes and molecular orientations of the (55)Mn hyperfine tensors in the S2 state are presented. These parameters, together with the resultant spin projected hyperfine values are compared with recent appropriate experimental EPR data (Continuous Wave (CW), Electron-Nuclear Double Resonance (ENDOR) and ELDOR (Electron-Electron Double Resonance)-Detected Nuclear Magnetic Resonance (EDNMR)) from the OEC. It is found that an effective Coupled Dimer magnetic organization of the four Mn in the OEC cluster in the S2 and S3 states is able to quantitatively rationalize the observed (55)Mn hyperfine data. This is consistent with structures we propose to represent the likely state of the OEC in the catalytically active form of the enzyme. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Moderate Heat Stress Stimulates Repair of Photosystem II During Photoinhibition in Synechocystis sp. PCC 6803.

    PubMed

    Ueno, Mamoru; Sae-Tang, Penporn; Kusama, Yuri; Hihara, Yukako; Matsuda, Mami; Hasunuma, Tomohisa; Nishiyama, Yoshitaka

    2016-11-01

    Examination of the effects of high temperature on the photoinhibition of photosystem II (PSII) in the cyanobacterium Synechocystis sp. PCC 6803 revealed that the extent of photoinhibition of PSII was lower at moderately high temperatures (35-42 °C) than at 30 °C. Photodamage to PSII, as determined in the presence of chloramphenicol, which blocks the repair of PSII, was accelerated at the moderately high temperatures but the effects of repair were greater than those of photodamage. The synthesis de novo of the D1 protein, which is essential for the repair of PSII, was enhanced at 38 °C. Electron transport and the synthesis of ATP were also enhanced at 38 °C, while levels of reactive oxygen species fell. Inhibition of the Calvin-Benson cycle with glycolaldehyde abolished the enhancement of repair of PSII at 38 °C, suggesting that an increase in the activity of the Calvin-Benson cycle might be required for the enhancement of repair at moderately high temperatures. The synthesis de novo of metabolic intermediates of the Calvin-Benson cycle, such as 3-phosphoglycerate, was also enhanced at 38 °C. We propose that moderate heat stress might enhance the repair of PSII by stimulating the synthesis of ATP and depressing the production of reactive oxygen species, via the stimulation of electron transport and suppression of the accumulation of excess electrons on the acceptor side of photosystem I, which might be driven by an increase in the activity of the Calvin-Benson cycle. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  12. Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance.

    PubMed

    Delgado, Asunción; Arco, Rocio; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2017-05-09

    Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli. Unlike E. coli thioredoxin, however, these ancestral thioredoxins are not efficiently recruited by the bacteriophage T7 for its replisome and therefore prevent phage propagation in E. coli. These results suggest an approach to the engineering of virus resistance. Diseases caused by viruses may have a devastating effect in agriculture. We discuss how the suggested approach could be applied to the engineering of plant virus resistance. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  13. Ancestral vascular tube formation and its adoption by tumors.

    PubMed

    Kucera, Tomás; Lammert, Eckhard

    2009-10-01

    Similar to growing and metabolically active tissues, tumors require a dense vasculature to gain access to oxygen and nutrients. However, blood vessels in tumors differ from vessels in normal tissues in many respects. In particular, the tumor vasculature is in an active state of angiogenesis or vasculogenesis, and it is immature and leaky. Blood vessels are multicellular tubes formed by polarized endothelial cells, which face the patent vascular lumen with their apical cell surface, whereas their basal cell surface faces extracellular matrix on the outside of the vessels. The same cell polarity can be found in other tubular structures, such as in the bronchial tubes of the lung or the kidney tubules. In contrast, blood vessels in invertebrates often have a vascular lumen lined by basal cell surfaces. These vessels are often formed by a process named 'ancestral vascular tube formation'. Here, we discuss the hypothesis that the supply of tumors with blood can be achieved by both endothelial cell-lined tubes as well as tubes formed by the tumor cells themselves using the ancestral vascular tube formation mechanism. We discuss this hypothesis with a particular focus on gastrointestinal tumors.

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

    PubMed Central

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

    2015-01-01

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

  15. A new photosystem II electron transfer inhibitor from Sorghum bicolor.

    PubMed

    Rimando, A M; Dayan, F E; Czarnota, M A; Weston, L A; Duke, S O

    1998-07-01

    Our study of the mechanism(s) by which sorgoleone (1) acts as a photosystem II (PS II) inhibitor led to the isolation of a new benzoquinone derivative, 2-hydroxy-5-ethoxy-3-[(Z,Z)-8',11', 14'-pentadecatriene]-rho-benzoquinone (2), from the root exudate of sorghum. The structure of 2, which is being given the name 5-ethoxy-sorgoleone, was determined by spectroscopic means. A methoxy derivative (3) of 1 was also prepared. Both 2 and 3 caused a reduction in oxygen evolution by thylakoid membranes and induced variable chlorophyll fluorescence. These compounds, however, were less active inhibitors of PS II than 1.

  16. Structural/Functional Role of Chloride in Photosystem II

    PubMed Central

    Rivalta, Ivan; Amin, Muhamed; Luber, Sandra; Vassiliev, Serguei; Pokhrel, Ravi; Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren; Kamiya, Nobuo; Bruce, Doug; Brudvig, Gary W.; Gunner, M. R.; Batista, Victor S.

    2011-01-01

    Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 Å resolution. We find that chloride depletion induces formation of a salt-bridge between D2-K317 and D1-D61 that could suppress proton transfer to the lumen. PMID:21678923

  17. 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.

  18. 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

  19. 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.

  20. Growth under Red Light Enhances Photosystem II Relative to Photosystem I and Phycobilisomes in the Red Alga Porphyridium cruentum1

    PubMed Central

    Cunningham, Francis X.; Dennenberg, Ronald J.; Jursinic, Paul A.; Gantt, Elisabeth

    1990-01-01

    Acclimation of the photosynthetic apparatus to light absorbed primarily by photosystem I (PSI) or by photosystem II (PSII) was studied in the unicellular red alga Porphyridium cruentum (ATCC 50161). Cultures grown under green light of 15 microeinsteins per square meter per second (PSII light; absorbed predominantly by the phycobilisomes) exhibited a PSII/PSI ratio of 0.26 ± 0.05. Under red light (PSI light; absorbed primarily by chlorophyll) of comparable quantum flux, cells contained nearly five times as many PSII per PSI (1.21 ± 0.10), and three times as many PSII per cell. About 12% of the chlorophyll was attributed to PSII in green light, 22% in white light, and 39% in red light-grown cultures. Chlorophyll antenna sizes appeared to remain constant at about 75 chlorophyll per PSII and 140 per PSI. Spectral quality had little effect on cell content or composition of the phycobilisomes, thus the number of PSII per phycobilisome was substantially greater in red light-grown cultures (4.2 ± 0.6) than in those grown under green (1.6 ± 0.3) or white light (2.9 ± 0.1). Total photosystems (PSI + PSII) per phycobilisome remained at about eight in each case. Carotenoid content and composition was little affected by the spectral composition of the growth light. Zeaxanthin comprised more than 50% (mole/mole), β-carotene about 40%, and cryptoxanthin about 4% of the carotenoid pigment. Despite marked changes in the light-harvesting apparatus, red and green light-grown cultures have generation times equal to that of cultures grown under white light of only one-third the quantum flux. PMID:16667597

  1. 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

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

    PubMed

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

    2016-01-28

    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.

  3. 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

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

    PubMed Central

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

    2003-01-01

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

  5. 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.

  6. Pigment exchange of photosystem II reaction center by chlorophyll d.

    PubMed

    Tomo, Tatsuya; Hirano, Emi; Nagata, Junko; Nakazato, Katsuyoshi

    2005-06-01

    Pigment exchanges among photosystem reaction centers (RCs) are useful for the identification and functional analysis of chromophores in photosynthetic organisms. Pigment replacement within the spinach Photosystem II RC was performed with Chl d derived from the oxygenic alga Acaryochloris marina, using a protocol similar to that reported previously [Gall et al. (1998) FEBS Lett 434: 88-92] based on the incubation of reaction centers with an excess of other pigments. In this study, we analyzed Chl d-modified monomeric RC which was separated from Chl d-modified dimeric RC by size-exclusion chromatography. Based on the assumption of a constant ratio of two Pheo a molecules per RC, the number of Chl a molecules in Chl d-modified monomeric RCs was found to decrease from six to four. The absorption spectrum of the Chl d-modified monomeric RC at room temperature showed a large peak at 699.5 nm originating from Chl d and a small peak at 672.5 nm orignating from Chl a. Photoaccumulation of the Pheo a- in Chl d-modified monomeric RC, in the presence of sodium dithionate and methyl viologen, did not differ significantly from that in control RC, showing that the Chl d-modified monomeric RC retains its charge separation activity and photochemically active Pheo a.

  7. 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.

  8. Structural analysis of photosystem I polypeptides using chemical crosslinking.

    PubMed

    Armbrust, T S; Odom, W R; Guikema, J A

    1994-07-01

    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.

  9. Engineering of an alternative electron transfer path in photosystem II

    PubMed Central

    Larom, Shirley; Salama, Faris; Schuster, Gadi; Adir, Noam

    2010-01-01

    The initial steps of oxygenic photosynthetic electron transfer occur within photosystem II, an intricate pigment/protein transmembrane complex. Light-driven electron transfer occurs within a multistep pathway that is efficiently insulated from competing electron transfer pathways. The heart of the electron transfer system, composed of six linearly coupled redox active cofactors that enable electron transfer from water to the secondary quinone acceptor QB, is mainly embedded within two proteins called D1 and D2. We have identified a site in silico, poised in the vicinity of the QA intermediate quinone acceptor, which could serve as a potential binding site for redox active proteins. Here we show that modification of Lysine 238 of the D1 protein to glutamic acid (Glu) in the cyanobacterium Synechocystis sp. PCC 6803, results in a strain that grows photautotrophically. The Glu thylakoid membranes are able to perform light-dependent reduction of exogenous cytochrome c with water as the electron donor. Cytochrome c photoreduction by the Glu mutant was also shown to significantly protect the D1 protein from photodamage when isolated thylakoid membranes were illuminated. We have therefore engineered a novel electron transfer pathway from water to a soluble protein electron carrier without harming the normal function of photosystem II. PMID:20457933

  10. Structure, function and regulation of plant photosystem I.

    PubMed

    Jensen, Poul Erik; Bassi, Roberto; Boekema, Egbert J; Dekker, Jan P; Jansson, Stefan; Leister, Dario; Robinson, Colin; Scheller, Henrik Vibe

    2007-05-01

    Photosystem I (PSI) is a multisubunit protein complex located in the thylakoid membranes of green plants and algae, where it initiates one of the first steps of solar energy conversion by light-driven electron transport. In this review, we discuss recent progress on several topics related to the functioning of the PSI complex, like the protein composition of the complex in the plant Arabidopsis thaliana, the function of these subunits and the mechanism by which nuclear-encoded subunits can be inserted into or transported through the thylakoid membrane. Furthermore, the structure of the native PSI complex in several oxygenic photosynthetic organisms and the role of the chlorophylls and carotenoids in the antenna complexes in light harvesting and photoprotection are reviewed. The special role of the 'red' chlorophylls (chlorophyll molecules that absorb at longer wavelength than the primary electron donor P700) is assessed. The physiology and mechanism of the association of the major light-harvesting complex of photosystem II (LHCII) with PSI during short term adaptation to changes in light quality and quantity is discussed in functional and structural terms. The mechanism of excitation energy transfer between the chlorophylls and the mechanism of primary charge separation is outlined and discussed. Finally, a number of regulatory processes like acclimatory responses and retrograde signalling is reviewed with respect to function of the thylakoid membrane. We finish this review by shortly discussing the perspectives for future research on PSI.

  11. 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.

  12. Differential loss of ancestral gene families as a source of genomic divergence in animals.

    PubMed Central

    Hughes, Austin L; Friedman, Robert

    2004-01-01

    A phylogenetic approach was used to reconstruct the pattern of an apparent loss of 2106 ancestral gene families in four animal genomes (Caenorhabditis elegans, Drosophila melanogaster, human and fugu). Substantially higher rates of loss of ancestral gene families were found in the invertebrates than in the vertebrates. These results indicate that the differential loss of ancestral gene families can be a significant factor in the evolutionary diversification of organisms. PMID:15101434

  13. Estimation of ancestral inbreeding effects on stillbirth, calving ease and birthweight in German Holstein dairy cattle.

    PubMed

    Hinrichs, D; Bennewitz, J; Wellmann, R; Thaller, G

    2015-02-01

    In this study, the effect of different measurements of ancestral inbreeding on birthweight, calving ease and stillbirth were analysed. Three models were used to estimate the effect of ancestral inbreeding, and the estimated regression coefficient of phenotypic data on different measurements of ancestral inbreeding was used to quantify the effect of ancestral inbreeding. The first model included only one measurement of inbreeding, whereas the second model included the classical inbreeding coefficients and one alternative inbreeding coefficient. The third model included the classical inbreeding coefficients, the interaction between classical inbreeding and ancestral inbreeding, and the classical inbreeding coefficients of the dam. Phenotypic data for this study were collected from February 1998 to December 2008 on three large commercial milk farms. During this time, 36,477 calving events were recorded. All calves were weighed after birth, and 8.08% of the calves died within 48 h after calving. Calving ease was recorded on a scale between 1 and 4 (1 = easy birth, 4 = surgery), and 69.95, 20.91, 8.92 and 0.21% of the calvings were scored with 1, 2, 3 and 4, respectively. The average inbreeding coefficient of inbred animals was 0.03, and average ancestral inbreeding coefficients were 0.08 and 0.01, depending on how ancestral inbreeding was calculated. Approximately 26% of classically non-inbred animals showed ancestral inbreeding. Correlations between different inbreeding coefficients ranged between 0.46 and 0.99. No significant effect of ancestral inbreeding was found for calving ease, because the number of animals with reasonable high level of ancestral inbreeding was too low. Significant effects of ancestral inbreeding were estimated for birthweight and stillbirth. Unfavourable effects of ancestral inbreeding were observed for birthweight. However, favourable purging effects were estimated for stillbirth, indicating that purging could be partly beneficial for genetic

  14. 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.

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

    PubMed Central

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

    2012-01-01

    Ancestral sequence reconstruction is essential to a variety of evolutionary studies. Here, we present the FastML web server, a user-friendly tool for the reconstruction of ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in which each gap, possibly spanning multiples sites, is coded as binary data. FastML then reconstructs ancestral indel states assuming a continuous time Markov process. FastML provides the most likely ancestral sequences, integrating both indels and characters; (ii) FastML accounts for uncertainty in ancestral states: it provides not only the posterior probabilities for each character and indel at each sequence position, but also a sample of ancestral sequences from this posterior distribution, and a list of the k-most likely ancestral sequences; (iii) FastML implements a large array of evolutionary models, which makes it generic and applicable for nucleotide, protein and codon sequences; and (iv) a graphical representation of the results is provided, including, for example, a graphical logo of the inferred ancestral sequences. The utility of FastML is demonstrated by reconstructing ancestral sequences of the Env protein from various HIV-1 subtypes. FastML is freely available for all academic users and is available online at http://fastml.tau.ac.il/. PMID:22661579

  16. 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.

  17. Female song is widespread and ancestral in songbirds.

    PubMed

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

    2014-03-04

    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.

  18. Computational analysis and functional expression of ancestral copepod luciferase.

    PubMed

    Takenaka, Yasuhiro; Noda-Ogura, Akiko; Imanishi, Tadashi; Yamaguchi, Atsushi; Gojobori, Takashi; Shigeri, Yasushi

    2013-10-10

    We recently reported the cDNA sequences of 11 copepod luciferases from the superfamily Augaptiloidea in the order Calanoida. They were classified into two groups, Metridinidae and Heterorhabdidae/Lucicutiidae families, by phylogenetic analyses. To elucidate the evolutionary processes, we have now further isolated 12 copepod luciferases from Augaptiloidea species (Metridia asymmetrica, Metridia curticauda, Pleuromamma scutullata, Pleuromamma xiphias, Lucicutia ovaliformis and Heterorhabdus tanneri). Codon-based synonymous/nonsynonymous tests of positive selection for 25 identified copepod luciferases suggested that positive Darwinian selection operated in the evolution of Heterorhabdidae luciferases, whereas two types of Metridinidae luciferases had diversified via neutral mechanism. By in silico analysis of the decoded amino acid sequences of 25 copepod luciferases, we inferred two protein sequences as ancestral copepod luciferases. They were expressed in HEK293 cells where they exhibited notable luciferase activity both in intracellular lysates and cultured media, indicating that the luciferase activity was established before evolutionary diversification of these copepod species.

  19. Experimental evidence for the thermophilicity of ancestral life.

    PubMed

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

    2013-07-02

    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.

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

    NASA Astrophysics Data System (ADS)

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

    1984-03-01

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

  1. 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

  2. Palaeohistological Evidence for Ancestral High Metabolic Rate in Archosaurs.

    PubMed

    Legendre, Lucas J; Guénard, Guillaume; Botha-Brink, Jennifer; Cubo, Jorge

    2016-11-01

    Metabolic heat production in archosaurs has played an important role in their evolutionary radiation during the Mesozoic, and their ancestral metabolic condition has long been a matter of debate in systematics and palaeontology. The study of fossil bone histology provides crucial information on bone growth rate, which has been used to indirectly investigate the evolution of thermometabolism in archosaurs. However, no quantitative estimation of metabolic rate has ever been performed on fossils using bone histological features. Moreover, to date, no inference model has included phylogenetic information in the form of predictive variables. Here we performed statistical predictive modeling using the new method of phylogenetic eigenvector maps on a set of bone histological features for a sample of extant and extinct vertebrates, to estimate metabolic rates of fossil archosauromorphs. This modeling procedure serves as a case study for eigenvector-based predictive modeling in a phylogenetic context, as well as an investigation of the poorly known evolutionary patterns of metabolic rate in archosaurs. Our results show that Mesozoic theropod dinosaurs exhibit metabolic rates very close to those found in modern birds, that archosaurs share a higher ancestral metabolic rate than that of extant ectotherms, and that this derived high metabolic rate was acquired at a much more inclusive level of the phylogenetic tree, among non-archosaurian archosauromorphs. These results also highlight the difficulties of assigning a given heat production strategy (i.e., endothermy, ectothermy) to an estimated metabolic rate value, and confirm findings of previous studies that the definition of the endotherm/ectotherm dichotomy may be ambiguous.

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

    PubMed Central

    2013-01-01

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

  4. 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

  5. Ancestral European roots of Helicobacter pylori in India.

    PubMed

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

    2007-06-20

    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. 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. 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.

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

    PubMed Central

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

    2012-01-01

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

  7. Conversion of the spin state of the manganese complex in photosystem II induced by near-infrared light.

    PubMed

    Boussac, A; Girerd, J J; Rutherford, A W

    1996-06-04

    The manganese complex (Mn4) which is responsible for water oxidation in photosystem II is EPR detectable in the S2 state, one of the five redox states of the enzyme cycle. The S2 state is observable at 10 K either as a multiline signal (spin 1/2) or as a signal at g = 4.1 (spin 3/2 or spin 5/2). It is shown here that at around 150 K the state responsible for the multiline signal is converted to that responsible for the g = 4.1 signal upon the absorption of infrared light. This conversion is fully reversible at 200 K. The action spectrum of this conversion has its maximum at 820 nm (12 200 cm-1) and is similar to the intervalence charge transfer band in di-mu-oxo-(MnIIIMnIV) model systems. It is suggested that the conversion of the multiline signal to the g = 4.1 signal results from absorption of infrared light by the Mn cluster itself, resulting in electron transfer from MnIII to MnIV. The g = 4.1 signal is thus proposed to arise from a state which differs from that which gives rise to the multiline signal only in terms of this change in its valence distribution. The near-infrared light effect was observed in the S2 state of Sr(2+)-reconstituted photosystem II and in Ca(2+)-depleted, EGTA (or citrate-)-treated photosystem II but not in ammonia-treated photosystem II. Earlier results in the literature which showed that the g = 4.1 state was preferentially formed by illumination at 130 K are reinterpreted as being the result of two photochemical events: the first being photosynthetic charge separation resulting in an S2 state which gives rise to the multiline signal and the second being the conversion of this state to the g = 4.1 state due to the simultaneous and inadvertent presence of 820 nm light in the broad-band illumination given. There is therefore no reason to consider the state responsible for the g = 4.1 signal as a precursor of that which gives rise to the multiline signal.

  8. Purification and crystallization of oxygen-evolving photosystem II core complex from thermophilic cyanobacteria.

    PubMed

    Shen, Jian-Ren; Kawakami, Keisuke; Koike, Hiroyuki

    2011-01-01

    This chapter describes the purification and crystallization of oxygen-evolving photosystem II core dimer complex from a thermophilic cyanobacterium Thermosynechococcus vulcanus. Procedures used for purification of photosystem II from the cyanobacterium involves cultivation of cells, isolation of thylakoid membranes, purification of crude and pure photosystem II core complexes by detergent solubilization, followed by differential centrifugation and column chromatography. The purified core dimer particles were successfully used for crystallization, and the methods and conditions used for crystallization are presented. These purification and crystallization procedures can be applied for another thermophilic cyanobacterium T. elongatus.

  9. Chlorophyll composition and photochemical activity of photosystems detached from chloroplast grana and stroma lamellae.

    PubMed

    Gasanov, R A; French, C S

    1973-07-01

    A stroma fraction that has photosystem 1 activity and grana lamellae fractions that have activities for both photosystems were isolated by differential centrifugation of a needle valve homogenate. Subsequent fractions, corresponding to photosystems 1 (F-1D) and 2 (F-2D) were isolated by digitonin treatment of the grana lamellae (P-10K) and compared with respect to their chlorophyll composition and electron transport activities.Fraction F-2D from grana lamellae having photosystem 2 activity is primarily active in photosystem 2 and contains only the four major forms of chlorophyll a with a predominance of chlorophyll a 677 nm. This fraction differs from the original grana membranes in the absence of the longwavelength form of chlorophyll a and in the widening of the absorption band of chlorophyll a 682 nm from 10.9 to 15.6 nm.Photosystem 1 particles from grana and stroma both have high photosystem 1 activity but differ from each other in the proportions of the four major forms of chlorophyll a. The short-wavelength forms of chlorophyll a and also chlorophyll b 650 nm in particles from grana lamellae comprise relatively more total area than these same forms in the particles from stroma. In addition, the fraction corresponding to photosystem 1 from grana lamellae is not shifted to the long-wavelength side of the main absorption maximum, as compared to the photosystem 2 particles from grana and the original grana membrane fraction; this is usually observed in fractions that have photosystem 1 activity. Furthermore, the longest wavelength form of chlorophyll a in the photosystem 1 particles from grana is at 700 nm, while in the same fraction from stroma, it is at 706 nm.The half-width of the four main forms of chlorophyll a and both forms of chlorophyll b in the photosystem 1 fraction from grana is narrower than that of the corresponding forms in the same fraction from stroma. This may indicate a different packing of pigment molecules that are aggregated on the surface

  10. 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

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

    PubMed

    Mayer, Georg; Harzsch, Steffen

    2007-07-15

    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). 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. 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.

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

    PubMed

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

    2012-11-01

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

  15. 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

  16. A new photosystem II reaction center component (4.8 kDa protein) encoded by chloroplast genome.

    PubMed

    Ikeuchi, M; Inoue, Y

    1988-12-05

    The photosystem II reaction center complex, so-called D1-D2-cytochrome b-559 complex, isolated from higher plants contains a new component of about 4.8 kDa [(1988) Plant Cell Physiol. 29, 1233-1239]. The partial amino acid sequence of this component from spinach was determined after release of N-terminal blockage. The determined sequence matched an open reading frame (ORF36) of the chloroplast genome from tobacco and liverwort, which is located downstream from the psbK gene and forms an operon with psbK. The predicted product consists of 36 amino acid residues and has a single membrane-spanning segment. High homology between the tobacco and liverwort genes, and its presence in the reaction center complex suggest an important role for this component in the photosystem II complex. Since this gene corresponds to a part of the formerly designated psbI gene, we propose to revise the definition of psbI as the gene encoding the 4.8 kDa reaction center component.

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

    PubMed

    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.

  18. 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.

  19. Estimating ancestral ranges: testing methods with a clade of neotropical lizards (iguania: liolaemidae).

    PubMed

    Díaz Gómez, Juan Manuel

    2011-01-01

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

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

    PubMed Central

    Díaz Gómez, Juan Manuel

    2011-01-01

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

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

    PubMed

    Schrago, Carlos G

    2014-08-01

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

  2. Enumeration of Ancestral Configurations for Matching Gene Trees and Species Trees.

    PubMed

    Disanto, Filippo; Rosenberg, Noah A

    2017-09-01

    Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the recursive computation of the conditional probability under the multispecies coalescent model of a gene tree topology given a species tree, the cost of this computation being affected by the number of ancestral configurations of the gene tree in the species tree. For matching gene trees and species trees, we obtain enumerative results on ancestral configurations. We study ancestral configurations in balanced and unbalanced families of trees determined by a given seed tree, showing that for seed trees with more than one taxon, the number of ancestral configurations increases for both families exponentially in the number of taxa n. For fixed n, the maximal number of ancestral configurations tabulated at the species tree root node and the largest number of labeled histories possible for a labeled topology occur for trees with precisely the same unlabeled shape. For ancestral configurations at the root, the maximum increases with [Formula: see text], where [Formula: see text] is a quadratic recurrence constant. Under a uniform distribution over the set of labeled trees of given size, the mean number of root ancestral configurations grows with [Formula: see text] and the variance with ∼[Formula: see text]. The results provide a contribution to the combinatorial study of gene trees and species trees.

  3. Isolation of Plant Photosystem II Complexes by Fractional Solubilization

    PubMed Central

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

    2015-01-01

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

  4. 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

  5. Light regulation of pigment and photosystem biosynthesis in cyanobacteria.

    PubMed

    Ho, Ming-Yang; Soulier, Nathan T; Canniffe, Daniel P; Shen, Gaozhong; Bryant, Donald A

    2017-04-06

    Most cyanobacteria are obligate oxygenic photoautotrophs, and thus their growth and survival is highly dependent on effective utilization of incident light. Cyanobacteria have evolved a diverse set of phytochromes and cyanobacteriochromes (CBCRs) that allow cells to respond to light in the range from ∼300nm to ∼750nm. Together with associated response regulators, these photosensory proteins control many aspects of cyanobacterial physiology and metabolism. These include far-red light photoacclimation (FaRLiP), complementary chromatic acclimation (CCA), low-light photoacclimation (LoLiP), photosystem content and stoichiometry (long-term adaptation), short-term acclimation (state transitions), circadian rhythm, phototaxis, photomorphogenesis/development, and cellular aggregation. This minireview highlights some discoveries concerning phytochromes and CBCRs as well as two acclimation processes that improve light harvesting and energy conversion under specific irradiance conditions: FaRLiP and CCA.

  6. Evidence for direct binding of glycerol to photosystem I.

    PubMed

    Hussels, Martin; Brecht, Marc

    2011-08-04

    The interaction between glycerol and photosystem I (PSI) was investigated using low temperature single-molecule spectroscopy. PSI complexes were dissolved in three different solutions: in buffer solution, in 66% glycerol/buffer solution, and in 66% glycerol/buffer solution that was afterwards diluted by buffer; the final glycerol concentration was <1‰. Mean fluorescence spectra and intercomplex heterogeneity of PSI complexes in 66% glycerol/buffer solution and in the re-diluted solution show high similarity, but differ from complexes in buffer solution indicating that the glycerol concentration is not the determining factor modifying the spectral properties. However, the exposure of PSI to a high glycerol concentration during sample preparation affects PSI and the effect is maintained if glycerol is removed from the solution.

  7. Colocalization of Polyphenol Oxidase and Photosystem II Proteins.

    PubMed

    Lax, A R; Vaughn, K C

    1991-05-01

    Polyphenol oxidase (PPO) appears to be ubiquitous in higher plants but, as yet, no function has been ascribed to it. Herein, we report on the localization of PPO based upon biochemical fractionation of chloroplast membranes in Vicia faba (broad bean) into various complexes and immunocytochemical electron microscopic investigations. Sucrose density gradient fractionations of thylakoid membranes after detergent solubilization reveals that PPO protein (by reactivity with anti-PPO antibody) and activity (based upon ability to oxidize di-dihydroxyphenylalanine) are found only in fractions enriched in photosystem II (PSII). Furthermore, of the PSII particles isolated using three different protocols utilizing several plant species, all had PPO. Immunogold localization of PPO on thin sections reveals exclusive thylakoid labeling with a distribution pattern consistent with other PSII proteins (80% grana, 20% stroma). These data strongly indicate that PPO is at least peripherally associated with the PSII complex.

  8. 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.

  9. Long-range energy transport in photosystem II.

    PubMed

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

    2016-06-28

    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.

  10. 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

  11. 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.

  12. 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

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

    PubMed

    Jennings, Robert C; Zucchelli, Giuseppe

    2014-12-01

    We have investigated the concept of the so-called "antenna entropy" of higher plant photosystems. Several interesting points emerge: 1. In the case of a photosystemwhich harbours an excited state, the “antenna entropy” is equivalent to the configurational (mixing) entropy of a thermodynamic canonical ensemble. The energy associated with this parameter has been calculated for a hypothetical isoenergetic photosystem, photosystem I and photosystem II, and comes out in the range of 3.5 - 8% of the photon energy considering 680 nm. 2. The “antenna entropy” seems to be a rather unique thermodynamic phenomenon, in as much as it does not modify the free energy available for primary photochemistry, as has been previously suggested. 3. It is underlined that this configurational (mixing) entropy, unlike heat dispersal in a thermal system, does not involve energy dilution. This points out an important difference between thermal and electronic energy dispersal. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. An energetic comparison of different models for the oxygen evolving complex of photosystem II.

    PubMed

    Siegbahn, Per E M

    2009-12-30

    The computed total energy from a cluster model DFT calculation is used to discriminate between different suggested models for the oxygen evolving complex of photosystem II. The comparison between different structures rules out several suggestions. Only one suggested structure remains.

  15. 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.

  16. 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.

  17. Constitution and energetics of photosystem I and photosystem II in the chlorophyll d-dominated cyanobacterium Acaryochloris marina.

    PubMed

    Tomo, Tatsuya; Allakhverdiev, Suleyman I; Mimuro, Mamoru

    2011-01-01

    This mini review presents current topics of discussion about photosystem (PS) I and PS II of photosynthesis in the Acaryochloris marina. A. marina is a photosynthetic cyanobacterium in which chlorophyll (Chl) d is the major antenna pigment (>95%). However, Chl a is always present in a few percent. Chl d absorbs light with a wavelength up to 30 nm red-shifted from Chl a. Therefore, the chlorophyll species of the special pair in PS II has been a matter of debate because if Chl d was the special pair component, the overall energetics must be different in A. marina. The history of this field indicates that a purified sample is necessary for the reliable identification and characterization of the special pair. In view of the spectroscopic data and the redox potential of pheophytin, we discuss the nature of special pair constituents and the localization of the enigmatic Chl a.

  18. Light saturation curves show competence of the water splitting complex in inactive Photosystem II reaction centers.

    PubMed

    Nedbal, L; Gibas, C; Whitmarsh, J

    1991-12-01

    Photosystem II complexes of higher plants are structurally and functionally heterogeneous. While the only clearly defined structural difference is that Photosystem II reaction centers are served by two distinct antenna sizes, several types of functional heterogeneity have been demonstrated. Among these is the observation that in dark-adapted leaves of spinach and pea, over 30% of the Photosystem II reaction centers are unable to reduce plastoquinone to plastoquinol at physiologically meaningful rates. Several lines of evidence show that the impaired reaction centers are effectively inactive, because the rate of oxidation of the primary quinone acceptor, QA, is 1000 times slower than in normally active reaction centers. However, there are conflicting opinions and data over whether inactive Photosystem II complexes are capable of oxidizing water in the presence of certain artificial electron acceptors. In the present study we investigated whether inactive Photosystem II complexes have a functional water oxidizing system in spinach thylakoid membranes by measuring the flash yield of water oxidation products as a function of flash intensity. At low flash energies (less that 10% saturation), selected to minimize double turnovers of reaction centers, we found that in the presence of the artificial quinone acceptor, dichlorobenzoquinone (DCBQ), the yield of proton release was enhanced 20±2% over that observed in the presence of dimethylbenzoquinone (DMBQ). We argue that the extra proton release is from the normally inactive Photosystem II reaction centers that have been activated in the presence of DCBQ, demonstrating their capacity to oxidize water in repetitive flashes, as concluded by Graan and Ort (Biochim Biophys Acta (1986) 852: 320-330). The light saturation curves indicate that the effective antenna size of inactive reaction centers is 55±12% the size of active Photosystem II centers. Comparison of the light saturation dependence of steady state oxygen evolution

  19. Possible rules for the ancestral origin of Hox gene collinearity.

    PubMed

    Gaunt, Stephen J; Gaunt, Alexander L

    2016-12-07

    The Hox gene cluster is believed to have formed from a single ProtoHox gene by repeated cycles of the following events: tandem gene duplication, mutation to generate a new expression boundary along the embryonic axis, and acquisition of a new Hox patterning function. The Hox cluster in Bilateria evolved in compliance with the so-called collinearity rule. That is, the order of the genes along the chromosome corresponds with the order of their embryonic expression domains along the head-tail axis. Gaunt (2015) suggested that collinearity may have arisen as a mechanism to minimise the incidence of boundaries between active and inactive genes within the Hox cluster. We now attempt to clarify the model by presenting it in the form of three rules: 1) no two Hox genes may persist in the same cluster with the same anterior boundary of activity in the same tissue; 2) an inactive Hox gene must not be flanked by two active Hox genes; 3) an active Hox gene must not be flanked by two inactive genes. We provide evidence and illustrative computer simulations to show that these rules, which can apply only to partially overlapping patterns of Hox activity, may account for the ancestral origin of Hox gene collinearity.

  20. Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.

    PubMed

    Peris, David; Arias, Armando; Orlić, Sandi; Belloch, Carmela; Pérez-Través, Laura; Querol, Amparo; Barrio, Eladio

    2017-03-01

    Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several worldwide distributed wild Saccharomyces species and their hybrids isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in mitochondrial region COX2-ORF1, likely mediated by either the activity of the protein encoded by the ORF1 (F-SceIII) gene, a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur among strains of the same species and among strains of different species, which suggests a complex model of Saccharomyces evolution that involves several ancestral hybridization events in wild environments.

  1. 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

  2. Ancestral TSH mechanism signals summer in a photoperiodic mammal.

    PubMed

    Hanon, Elodie A; Lincoln, Gerald A; Fustin, Jean-Michel; Dardente, Hugues; Masson-Pévet, Mireille; Morgan, Peter J; Hazlerigg, David G

    2008-08-05

    In mammals, day-length-sensitive (photoperiodic) seasonal breeding cycles depend on the pineal hormone melatonin, which modulates secretion of reproductive hormones by the anterior pituitary gland [1]. It is thought that melatonin acts in the hypothalamus to control reproduction through the release of neurosecretory signals into the pituitary portal blood supply, where they act on pituitary endocrine cells [2]. Contrastingly, we show here that during the reproductive response of Soay sheep exposed to summer day lengths, the reverse applies: Melatonin acts directly on anterior-pituitary cells, and these then relay the photoperiodic message back into the hypothalamus to control neuroendocrine output. The switch to long days causes melatonin-responsive cells in the pars tuberalis (PT) of the anterior pituitary to increase production of thyrotrophin (TSH). This acts locally on TSH-receptor-expressing cells in the adjacent mediobasal hypothalamus, leading to increased expression of type II thyroid hormone deiodinase (DIO2). DIO2 initiates the summer response by increasing hypothalamic tri-iodothyronine (T3) levels. These data and recent findings in quail [3] indicate that the TSH-expressing cells of the PT play an ancestral role in seasonal reproductive control in vertebrates. In mammals this provides the missing link between the pineal melatonin signal and thyroid-dependent seasonal biology.

  3. Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity

    PubMed Central

    Howard, Conor J; Hanson-Smith, Victor; Kennedy, Kristopher J; Miller, Chad J; Lou, Hua Jane; Johnson, Alexander D; Turk, Benjamin E; Holt, Liam J

    2014-01-01

    Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs) require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs, and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases. DOI: http://dx.doi.org/10.7554/eLife.04126.001 PMID:25310241

  4. Color vision of ancestral organisms of higher primates.

    PubMed

    Nei, M; Zhang, J; Yokoyama, S

    1997-06-01

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

  5. 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.

  6. Estimating Causal Effects with Ancestral Graph Markov Models

    PubMed Central

    Malinsky, Daniel; Spirtes, Peter

    2017-01-01

    We present an algorithm for estimating bounds on causal effects from observational data which combines graphical model search with simple linear regression. We assume that the underlying system can be represented by a linear structural equation model with no feedback, and we allow for the possibility of latent variables. Under assumptions standard in the causal search literature, we use conditional independence constraints to search for an equivalence class of ancestral graphs. Then, for each model in the equivalence class, we perform the appropriate regression (using causal structure information to determine which covariates to include in the regression) to estimate a set of possible causal effects. Our approach is based on the “IDA” procedure of Maathuis et al. (2009), which assumes that all relevant variables have been measured (i.e., no unmeasured confounders). We generalize their work by relaxing this assumption, which is often violated in applied contexts. We validate the performance of our algorithm on simulated data and demonstrate improved precision over IDA when latent variables are present. PMID:28217244

  7. 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

  8. 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

  9. Ancestral role of caudal genes in axis elongation and segmentation.

    PubMed

    Copf, Tijana; Schröder, Reinhard; Averof, Michalis

    2004-12-21

    caudal (cad/Cdx) genes are essential for the formation of posterior structures in Drosophila, Caenorhabditis elegans, and vertebrates. In contrast to Drosophila, the majority of arthropods generate their segments sequentially from a posteriorly located growth zone, a process known as short-germ development. caudal homologues are expressed in the growth zone of diverse short-germ arthropods, but until now their functional role in these animals had not been studied. Here, we use RNA interference to examine the function of caudal genes in two short-germ arthropods, the crustacean Artemia franciscana and the beetle Tribolium castaneum. We show that, in both species, caudal is required for the formation of most body segments. In animals with reduced levels of caudal expression, axis elongation stops, resulting in severe truncations that remove most trunk segments. We also show that caudal function is required for the early phases of segmentation and Hox gene expression. The observed phenotypes suggest that in arthropods caudal had an ancestral role in axis elongation and segmentation, and was required for the formation of most body segments. Similarities to the function of vertebrate Cdx genes in the presomitic mesoderm, from which somites are generated, indicate that this role may also predate the origin of the Bilateria.

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

    PubMed Central

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

    2013-01-01

    Telomerase is a ribonucleoprotein with an intrinsic telomerase RNA (TER) component. Within yeasts, TER is remarkably large and presents little similarity in secondary structure to vertebrate or ciliate TERs. To better understand the evolution of fungal telomerase, we identified 74 TERs from Pezizomycotina and Taphrinomycotina subphyla, sister clades to budding yeasts. We initially identified TER from Neurospora crassa using a novel deep-sequencing–based approach, and homologous TER sequences from available fungal genome databases by computational searches. Remarkably, TERs from these non-yeast fungi have many attributes in common with vertebrate TERs. Comparative phylogenetic analysis of highly conserved regions within Pezizomycotina TERs revealed two core domains nearly identical in secondary structure to the pseudoknot and CR4/5 within vertebrate TERs. We then analyzed N. crassa and Schizosaccharomyces pombe telomerase reconstituted in vitro, and showed that the two RNA core domains in both systems can reconstitute activity in trans as two separate RNA fragments. Furthermore, the primer-extension pulse-chase analysis affirmed that the reconstituted N. crassa telomerase synthesizes TTAGGG repeats with high processivity, a common attribute of vertebrate telomerase. Overall, this study reveals the common ancestral cores of vertebrate and fungal TERs, and provides insights into the molecular evolution of fungal TER structure and function. PMID:23093598

  11. Photosystem I reduction in diatoms: as complex as the green lineage systems but less efficient.

    PubMed

    Bernal-Bayard, Pilar; Molina-Heredia, Fernando P; Hervás, Manuel; Navarro, José A

    2013-12-03

    Diatoms occupy a key branch in the evolutionary tree of oxygen-evolving photosynthetic organisms. Here, the electron transfer reaction mechanism from cytochrome c₆ to photosystem I from the diatom Phaeodactylum tricornutum has been analyzed by laser-flash absorption spectroscopy. Kinetic traces of photosystem I reduction fit to biphasic curves, the analysis of the observed rate constants indicating that electron transfer occurs in a cytochrome c₆/photosystem I transient complex, which undergoes a reorganization process from the initial encounter complex to the optimized final configuration. The mild ionic strength dependence of the rate constants makes evident the relatively weak electrostatically attractive nature of the interaction. Taken together, these results indicate that the "red" Phaeodactylum system is less efficient than "green" systems, both in the formation of the properly arranged (cytochrome c₆/photosystem I) complex and in the electron transfer itself. The results obtained from cross-reactions with cytochrome c₆ and photosystem I from cyanobacteria, green algae, and plants shed light on the different evolutionary pathway of the electron transfer to photosystem I in diatoms with regard to the way that it evolved in higher plants.

  12. 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.

  13. Characterization of a Purified Photosystem II-Phycobilisome Particle Preparation from Porphyridium cruentum1

    PubMed Central

    Chereskin, Barbara M.; Clement-Metral, Jenny D.; Gantt, Elisabeth

    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 O2-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 O2 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 O2 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. PMID:16664110

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

    PubMed

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

    2014-07-08

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

  15. Accumulation of the Type IV prepilin triggers degradation of SecY and YidC and inhibits synthesis of Photosystem II proteins in the cyanobacterium Synechocystis PCC 6803.

    PubMed

    Linhartová, Markéta; Bučinská, Lenka; Halada, Petr; Ječmen, Tomáš; Setlík, Jiří; Komenda, Josef; Sobotka, Roman

    2014-09-01

    Type IV pilins are bacterial proteins that are small in size but have a broad range of functions, including motility, transformation competence and secretion. Although pilins vary in sequence, they possess a characteristic signal peptide that has to be removed by the prepilin peptidase PilD during pilin maturation. We generated a pilD (slr1120) null mutant of the cyanobacterium Synechocystis 6803 that accumulates an unprocessed form of the major pilin PilA1 (pPilA1) and its non-glycosylated derivative (NpPilA1). Notably, the pilD strain had aberrant membrane ultrastructure and did not grow photoautotrophically because the synthesis of Photosystem II subunits was abolished. However, other membrane components such as Photosystem I and ATP synthase were synthesized at levels comparable to the control strain. Proliferation of the pilD strain was rescued by elimination of the pilA1 gene, demonstrating that PilA1 prepilin inhibited the synthesis of Photosystem II. Furthermore, NpPilA1 co-immunoprecipitated with the SecY translocase and the YidC insertase, and both of these essential translocon components were degraded in the mutant. We propose that unprocessed prepilins inactivate an identical pool of translocons that function in the synthesis of both pilins and the core subunits of Photosystem II. © 2014 John Wiley & Sons Ltd.

  16. Improvement of Bacillus circulans beta-amylase activity attained using the ancestral mutation method.

    PubMed

    Yamashiro, Kan; Yokobori, Shin-ichi; Koikeda, Satoshi; Yamagishi, Akihiko

    2010-07-01

    Thermostabilization of enzymes is one of the greatest challenges of protein engineering. The ancestral mutation method, which introduces ancestral residues into a target enzyme, has previously been developed and used to improve the thermostabilities of thermophilic enzymes. Herein, we report a study that used the ancestral mutation method to improve the thermostability of Bacillus circulans beta-amylase, a mesophilic enzyme. A bacterial, common-ancestral beta-amylase sequence was inferred using a phylogenetic tree composed of higher plant and bacterial amylase sequences. Eighteen mutants containing ancestral residues were designed, expressed in Escherichia coli and purified. Several of these mutants were more thermostable than that of the wild-type amylase. Notably, one mutant had both greater activity and greater thermostability. The relationship between the extent to which the amino acid residues within 5 A of the mutation site were evolutionarily conserved and the extent to which thermostability was improved was examined. Apparently, it is necessary to conserve the residues surrounding an ancestral residue if thermostability is to be improved by the ancestral mutation method.

  17. Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere.

    PubMed

    Akanuma, Satoshi

    2017-08-06

    Understanding the evolution of ancestral life, and especially the ability of some organisms to flourish in the variable environments experienced in Earth's early biosphere, requires knowledge of the characteristics and the environment of these ancestral organisms. Information about early life and environmental conditions has been obtained from fossil records and geological surveys. Recent advances in phylogenetic analysis, and an increasing number of protein sequences available in public databases, have made it possible to infer ancestral protein sequences possessed by ancient organisms. However, the in silico studies that assess the ancestral base content of ribosomal RNAs, the frequency of each amino acid in ancestral proteins, and estimate the environmental temperatures of ancient organisms, show conflicting results. The characterization of ancestral proteins reconstructed in vitro suggests that ancient organisms had very thermally stable proteins, and therefore were thermophilic or hyperthermophilic. Experimental data supports the idea that only thermophilic ancestors survived the catastrophic increase in temperature of the biosphere that was likely associated with meteorite impacts during the early history of Earth. In addition, by expanding the timescale and including more ancestral proteins for reconstruction, it appears as though the Earth's surface temperature gradually decreased over time, from Archean to present.

  18. On the Number of Non-equivalent Ancestral Configurations for Matching Gene Trees and Species Trees.

    PubMed

    Disanto, Filippo; Rosenberg, Noah A

    2017-09-14

    An ancestral configuration is one of the combinatorially distinct sets of gene lineages that, for a given gene tree, can reach a given node of a specified species tree. Ancestral configurations have appeared in recursive algebraic computations of the conditional probability that a gene tree topology is produced under the multispecies coalescent model for a given species tree. For matching gene trees and species trees, we study the number of ancestral configurations, considered up to an equivalence relation introduced by Wu (Evolution 66:763-775, 2012) to reduce the complexity of the recursive probability computation. We examine the largest number of non-equivalent ancestral configurations possible for a given tree size n. Whereas the smallest number of non-equivalent ancestral configurations increases polynomially with n, we show that the largest number increases with [Formula: see text], where k is a constant that satisfies [Formula: see text]. Under a uniform distribution on the set of binary labeled trees with a given size n, the mean number of non-equivalent ancestral configurations grows exponentially with n. The results refine an earlier analysis of the number of ancestral configurations considered without applying the equivalence relation, showing that use of the equivalence relation does not alter the exponential nature of the increase with tree size.

  19. Highly resolved proton matrix ENDOR of oriented photosystem II membranes in the S2 state.

    PubMed

    Nagashima, Hiroki; Mino, Hiroyuki

    2013-10-01

    Proton matrix ENDOR was performed to investigate the protons close to the manganese cluster in oriented samples of photosystem II (PS II). Eight pairs of ENDOR signals were detected in oriented PS II membranes. At an angle of θ=0° between the membrane normal vector n and the external field H0, five pairs of ENDOR signals were exchangeable in D2O medium and three pairs were not exchangeable in D2O medium. The hyperfine splitting of 3.60MHz at θ=0° increased to 3.80MHz at θ=90°. The non-exchangeable signals with 1.73MHz hyperfine splitting at θ=0°, which were assigned to a proton in an amino acid residue, were not detected at θ=90° in oriented PS II or in non-oriented PS II. Highly resolved spectra show that only limited numbers of protons were detected by CW-ENDOR spectra, although many protons were located near the CaMn4O5 cluster. The detected exchangeable protons were proposed to arise from the protons belonging to the water molecules, labeled W1-W4 in the 1.9Å crystal structure, directly ligated to the CaMn4O5 cluster, and nearby amino-acid residue.

  20. Two equilibration pools of chlorophylls in the Photosystem I core antenna of Chlamydomonas reinhardtii.

    PubMed

    Gibasiewicz, Krzysztof; Ramesh, V M; Lin, Su; Redding, Kevin; Woodbury, Neal W; Webber, Andrew N

    2007-04-01

    Femtosecond transient absorption spectroscopy was applied for a comparative study of excitation decay in several different Photosystem I (PSI) core preparations from the green alga Chlamydomonas reinhardtii. For PSI cores with a fully interconnected network of chlorophylls, the excitation energy was equilibrated over a pool of chlorophylls absorbing at approximately 683 nm, independent of excitation wavelength [Gibasiewicz et al. J Phys Chem B 105:11498-11506, 2001; J Phys Chem B 106:6322-6330, 2002]. In preparations with impaired connectivity between chlorophylls, we have found that the spectrum of chlorophylls connected to the reaction center (i.e., with approximately 20 ps decay time) over which the excitation is equilibrated becomes excitation-wavelength-dependent. Excitation at 670 nm is finally equilibrated over chlorophylls absorbing at approximately 675 nm, whereas excitation at 695 nm or 700 nm is equilibrated over chlorophylls absorbing at approximately 683 nm. This indicates that in the vicinity of the reaction center there are two spectrally different and spatially separated pools of chlorophylls that are equally capable of effective excitation energy transfer to the reaction center. We propose that they are related to the two groups of central PSI core chlorophylls lying on the opposite sides of reaction center.

  1. Destabilization of the oxygen evolving complex of photosystem II by Al3+.

    PubMed

    Hasni, Imed; Hamdani, Saber; Carpentier, Robert

    2013-01-01

    The inhibitory effect of Al(3+) on photosynthetic electron transport was investigated in isolated thylakoid membranes of spinach. A combination of oxygen evolution, chlorophyll fluorescence induction (FI) and decay and thermoluminescence measurements have been used to characterize photosystem II (PSII) electron transport in the presence of this toxic metal cation. Our results show that below 3 mm, Al(3+) already caused a destabilization of the Mn4 O5 Ca cluster of the oxygen evolving complex (OEC). At these concentrations, an increase in the relative amplitude of the first phase (OJ) of FI curve and retardation of the fluorescence decay kinetics following excitation with a single turnover flash were also observed. A transmembrane structural modification of PSII polypeptides due to the interaction of Al(3+) at the OEC is proposed to retard electron transfer between the quinones QA and QB . Above 3 mm, Al(3+) strongly retarded fluorescence induction and significantly reduced Fv /Fm together with the maximal amplitude of chlorophyll fluorescence induced by a single turnover flash. This chlorophyll fluorescence quenching was attributed to the formation of P680(+) due to inhibition of electron transfer between tyrosine 161 of D1 subunit and P680.

  2. 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

  3. The plastoquinol-plastoquinone exchange mechanism in photosystem II: insight from molecular dynamics simulations.

    PubMed

    Zobnina, Veranika; Lambreva, Maya D; Rea, Giuseppina; Campi, Gaetano; Antonacci, Amina; Scognamiglio, Viviana; Giardi, Maria Teresa; Polticelli, Fabio

    2017-01-01

    In the photosystem II (PSII) of oxygenic photosynthetic organisms, the reaction center (RC) core mediates the light-induced electron transfer leading to water splitting and production of reduced plastoquinone molecules. The reduction of plastoquinone to plastoquinol lowers PSII affinity for the latter and leads to its release. However, little is known about the role of protein dynamics in this process. Here, molecular dynamics simulations of the complete PSII complex embedded in a lipid bilayer have been used to investigate the plastoquinol release mechanism. A distinct dynamic behavior of PSII in the presence of plastoquinol is observed which, coupled to changes in charge distribution and electrostatic interactions, causes disruption of the interactions seen in the PSII-plastoquinone complex and leads to the "squeezing out" of plastoquinol from the binding pocket. Displacement of plastoquinol closes the second water channel, recently described in a 2.9 Å resolution PSII structure (Guskov et al. in Nat Struct Mol Biol 16:334-342, 2009), allowing to rule out the proposed "alternating" mechanism of plastoquinol-plastoquinone exchange, while giving support to the "single-channel" one. The performed simulations indicated a pivotal role of D1-Ser264 in modulating the dynamics of the plastoquinone binding pocket and plastoquinol-plastoquinone exchange via its interaction with D1-His252 residue. The effects of the disruption of this hydrogen bond network on the PSII redox reactions were experimentally assessed in the D1 site-directed mutant Ser264Lys.

  4. Photosystem II heterogeneity of in hospite zooxanthellae in scleractinian corals exposed to bleaching conditions.

    PubMed

    Hill, Ross; PeterJ, Ralph

    2006-01-01

    Increased ocean temperatures are thought to be triggering mass coral bleaching events around the world. The intracellular symbiotic zooxanthellae (genus Symbiodinium) are expelled from the coral host, which is believed to be a response to photosynthetic damage within these symbionts. Several sites of impact have been proposed, and here we probe the functional heterogeneity of Photosystem II (PSII) in three coral species exposed to bleaching conditions. As length of exposure to bleaching conditions (32 degrees C and 350 micromol photons m(-2) s(-1)) increased, the QA- reoxidation kinetics showed a rise in the proportion of inactive PSII centers (PSIIx), where QB was unable to accept electrons. PSIIx contributed up to 20% of the total PSII centers in Pocillopora damicornis, 35% in Acropora nobilis and 14% in Cyphastrea serailia. Changes in Fv/Fm and amplitude of the J step along fast induction curves were found to be highly dependent upon the proportion of PSIIx centers within the total pool of PSII reaction centers. Determination of PSII antenna size revealed that under control conditions in the three coral species up to 60% of PSII centers were lacking peripheral light-harvesting complexes (PSIIbeta). In P. damicornis, the proportion of PSIIbeta increased under bleaching conditions and this could be a photoprotective mechanism in response to excess light. The rapid increases in PSIIx and PSIIbeta observed in these corals under bleaching conditions indicates these physiological processes are involved in the initial photochemical damage to zooxanthellae.

  5. Hominoid seminal protein evolution and ancestral mating behavior.

    PubMed

    Carnahan, Sarah J; Jensen-Seaman, Michael I

    2008-10-01

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

  6. 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

  7. Ancestral Heterogeneity in a Bi-ethnic Stroke Population

    PubMed Central

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

    2011-01-01

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

  8. 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.

  9. Geography disentangles introgression from ancestral polymorphism in Lake Malawi cichlids.

    PubMed

    Mims, Meryl C; Darrin Hulsey, C; Fitzpatrick, Benjamin M; Streelman, J Todd

    2010-03-01

    Phenotypically diverse Lake Malawi cichlids exhibit similar genomes. The extensive sharing of genetic polymorphism among forms has both intrigued and frustrated biologists trying to understand the nature of diversity in this and other rapidly evolving systems. Shared polymorphism might result from hybridization and/or the retention of ancestrally polymorphic alleles. To examine these alternatives, we used new genomic tools to characterize genetic differentiation in widespread, geographically structured populations of Labeotropheus fuelleborni and Metriaclima zebra. These phenotypically distinct species share mitochondrial DNA (mtDNA) haplotypes and show greater mtDNA differentiation among localities than between species. However, Bayesian analysis of nuclear single nucleotide polymorphism (SNP) data revealed two distinct genetic clusters corresponding perfectly to morphologically diagnosed L. fuelleborni and M. zebra. This result is a function of the resolving power of the multi-locus dataset, not a conflict between nuclear and mitochondrial partitions. Locus-by-locus analysis showed that mtDNA differentiation between species (F(CT)) was nearly identical to the median single-locus SNP F(CT). Finally, we asked whether there is evidence for gene flow at sites of co-occurrence. We used simulations to generate a null distribution for the level of differentiation between co-occurring populations of L. fuelleborni and M. zebra expected if there was no hybridization. The null hypothesis was rejected for the SNP data; populations that co-occur at rock reef sites were slightly more similar than expected by chance, suggesting recent gene flow. The coupling of numerous independent markers with extensive geographic sampling and simulations utilized here provides a framework for assessing the prevalence of gene flow in recently diverged species.

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

    PubMed

    Estabrook, Barry

    2010-01-01

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

  11. Plausibility of inferred ancestral phenotypes and the evaluation of alternative models of limb evolution in scincid lizards.

    PubMed

    Skinner, Adam; Lee, Michael S Y

    2010-06-23

    Phylogenetic approaches to inferring ancestral character states are becoming increasingly sophisticated; however, the potential remains for available methods to yield strongly supported but inaccurate ancestral state estimates. The consistency of ancestral states inferred for two or more characters affords a useful criterion for evaluating ancestral trait reconstructions. Ancestral state estimates for multiple characters that entail plausible phenotypes when considered together may reasonably be assumed to be reliable. However, the accuracy of inferred ancestral states for one or more characters may be questionable where combined reconstructions imply implausible phenotypes for a proportion of internal nodes. This criterion for assessing reconstructed ancestral states is applied here in evaluating inferences of ancestral limb morphology in the scincid lizard clade Lerista. Ancestral numbers of digits for the manus and pes inferred assuming the models that best fit the data entail ancestral digit configurations for many nodes that differ fundamentally from configurations observed among known species. However, when an alternative model is assumed for the pes, inferred ancestral digit configurations are invariably represented among observed phenotypes. This indicates that a suboptimal model for the pes (and not the model providing the best fit to the data) yields accurate ancestral state estimates.

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

    PubMed

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

    2014-06-01

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

  13. 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.

  14. 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.

  15. Femtosecond transient spectroscopy and excitonic interactions in Photosystem I.

    PubMed

    Melkozernov, A N; Lin, S; Blankenship, R E

    2000-02-24

    Ultrafast dynamics of excitation transfer in the Photosystem I (PSI) core antenna from the cyanobacterium Synechocystis sp. PCC 6803 were detected at 77 K by using femtosecond transient absorption spectroscopy with selective excitation at 700, 695, and 710 nm. At low temperature, the efficiency of uphill energy transfer in the core antenna significantly decreases. As a result, the spectral profile of the PSI equilibrated antenna shifts to lower energies because of a change of chlorophyll (Chl) excited-state distribution. Observed on a 2-ns time scale, P700 photooxidation spectra are largely excitation wavelength independent. In the early time spectra, excitation of P700 induces transient photobleaching at 698 nm accompanied by a resonant photobleaching band at 683 nm decaying within 250-300 fs. Chemical oxidation of P700 does not affect the transient band at 683 nm. This band is also present in 200-fs spectra induced by selective excitation of Chls at 710 nm (red pigments C708), which suggests that this high-energy transition may reflect an excitonic interaction between pigments of the reaction center and closely located red pigments. Possible candidates for the interacting molecules in the 4-angstroms crystal structure of cyanobacterial PSI are discussed.

  16. Functional architecture of higher plant photosystem II supercomplexes.

    PubMed

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

    2009-10-07

    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 C(2)S(2)M(2) 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 C(2)S(2)M(2) at 12 A 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.

  17. Dynamics of the Special Pair of Chlorophylls of Photosystem II.

    PubMed

    Narzi, Daniele; Bovi, Daniele; De Gaetano, Pietro; Guidoni, Leonardo

    2016-01-13

    Cholophylls are at the basis of the photosynthetic energy conversion mechanisms in algae, plants, and cyanobacteria. In photosystem II, the photoproduced electrons leave a special pair of chlorophylls (namely, P(D1) and P(D2)) that becomes cationic. This oxidizing pair [P(D1),P(D2)](+), in turn, triggers a cascade of oxidative events, eventually leading to water splitting and oxygen evolution. In the present work, using quantum mechanics/molecular mechanics calculations, we investigate the electronic structure and the dynamics of the P(D1)P(D2) special pair in both its oxidized and reduced states. In agreement with previously reported static calculations, the symmetry between the two chlorophylls was found to be broken, the positive charge being preferentially located on P(D1). Nevertheless, this study reveals for the first time that large charge fluctuations occur along dynamics, temporarily inverting the charge preference for the two branches. Finally, a vibrational analysis pinpointed that such charge fluctuations are strongly coupled to specific modes of the special pair.

  18. 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.

  19. Universality of energy and electron transfer processes in photosystem I.

    PubMed

    Hastings, G; Hoshina, S; Webber, A N; Blankenship, R E

    1995-11-28

    Femtosecond transient absorption spectroscopy has been used to investigate the photoinduced energy and electron transfer processes in photosystem I (PS I) particles from cyanobacteria, green algae, and higher plants. At room temperature, the kinetics observed in all three species are very similar: Following 590 nm excitation, an equilibration process(es) with a 3.7-7.5 ps lifetime was observed, followed by a 19-24 ps process that is associated with trapping. In all three species long-wavelength pigments (pigments that absorb at longer wavelengths than the primary electron donor) were observed. The difference spectrum associated with reduction of the primary electron acceptor [Ao(-)-Ao) difference spectrum] was obtained for all three species. The (Ao(-)-Ao) difference spectra obtained from measurements using detergent-isolated PS I particles from spinach and Chlamydomonas reinhardtii are similar but clearly membrane fragments. In all three species the reduced primary electron acceptor (Ao(-)) is reoxidized extremely rapidly, in about 20 ps. The difference spectrum associated with Ao reduction appears to contain contributions from more than a single chlorophyll pigment.

  20. Femtosecond photodichroism studies of isolated photosystem II reaction centers.

    PubMed

    Wiederrecht, G P; Seibert, M; Govindjee; Wasielewski, M R

    1994-09-13

    Photosynthetic conversion of light energy into chemical potential begins in reaction center protein complexes, where rapid charge separation occurs with nearly unit quantum efficiency. Primary charge separation was studied in isolated photosystem II reaction centers from spinach containing 6 chlorophyll a, 2 pheophytin a (Pheo), 1 cytochrome b559, and 2 beta-carotene molecules. Time-resolved pump-probe kinetic spectroscopy was carried out with 105-fs time resolution and with the pump laser polarized parallel, perpendicular, and at the magic angle (54.7 degrees) relative to the polarized probe beam. The time evolution of the transient absorption changes due to the formation of the oxidized primary electron donor P680+ and the reduced primary electron acceptor Pheo- were measured at 820 nm and 545 nm, respectively. In addition, kinetics were obtained at 680 nm, the wavelength ascribed to the Qy transition of the primary electron donor P680 in the reaction center. At each measured probe wavelength the kinetics of the transient absorption changes can be fit to two major kinetic components. The relative amplitudes of these components are strongly dependent on the polarization of the pump beam relative to that of the probe. At the magic angle, where no photoselection occurs, the amplitude of the 3-ps component, which is indicative of the charge separation, dominates. When the primary electron acceptor Pheo is reduced prior to P680 excitation, the 3-ps component is eliminated.

  1. 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.

  2. Spectroscopic properties of photosystem II reaction center revisited.

    PubMed

    Gelzinis, Andrius; Abramavicius, Darius; Ogilvie, Jennifer P; Valkunas, Leonas

    2017-09-21

    Photosystem II (PSII) is the only biological system capable of splitting water to molecular oxygen. Its reaction center (RC) is responsible for the primary charge separation that drives the water oxidation reaction. In this work, we revisit the spectroscopic properties of the PSII RC using the complex time-dependent Redfield (ctR) theory for optical lineshapes [A. Gelzinis et al., J. Chem. Phys. 142, 154107 (2015)]. We obtain the PSII RC model parameters (site energies, disorder, and reorganization energies) from the fits of several spectra and then further validate the model by calculating additional independent spectra. We obtain good to excellent agreement between theory and calculations. We find that overall our model is similar to some of the previous asymmetric exciton models of the PSII RC. On the other hand, our model displays differences from previous work based on the modified Redfield theory. We extend the ctR theory to describe the Stark spectrum and use its fit to obtain the parameters of a single charge transfer state included in our model. Our results suggest that ChlD1(+)PheoD1(-) is most likely the primary charge transfer state, but that the Stark spectrum of the PSII RC is probably also influenced by other states.

  3. 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

  4. (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.

  5. 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).

  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. 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

  8. Spectroscopic properties of photosystem II reaction center revisited

    NASA Astrophysics Data System (ADS)

    Gelzinis, Andrius; Abramavicius, Darius; Ogilvie, Jennifer P.; Valkunas, Leonas

    2017-09-01

    Photosystem II (PSII) is the only biological system capable of splitting water to molecular oxygen. Its reaction center (RC) is responsible for the primary charge separation that drives the water oxidation reaction. In this work, we revisit the spectroscopic properties of the PSII RC using the complex time-dependent Redfield (ctR) theory for optical lineshapes [A. Gelzinis et al., J. Chem. Phys. 142, 154107 (2015)]. We obtain the PSII RC model parameters (site energies, disorder, and reorganization energies) from the fits of several spectra and then further validate the model by calculating additional independent spectra. We obtain good to excellent agreement between theory and calculations. We find that overall our model is similar to some of the previous asymmetric exciton models of the PSII RC. On the other hand, our model displays differences from previous work based on the modified Redfield theory. We extend the ctR theory to describe the Stark spectrum and use its fit to obtain the parameters of a single charge transfer state included in our model. Our results suggest that C h lD1 +P h e oD1 - is most likely the primary charge transfer state, but that the Stark spectrum of the PSII RC is probably also influenced by other states.

  9. Origins of Water Molecules in the Photosystem II Crystal Structure.

    PubMed

    Sakashita, Naoki; Watanabe, Hiroshi C; Ikeda, Takuya; Saito, Keisuke; Ishikita, Hiroshi

    2017-06-20

    The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region. In the same channel, a diamond-shaped cluster of water molecules formed near redox-active TyrZ in MD simulations. Reorientation of the D2-Leu352 side chain resulted in formation of a hexagonal water network at the Cl(-)2 binding site. Water molecules could not enter the main region of the O4-water chain, which proceeds from the O4 site of the Mn4CaO5 cluster. However, in the O4-water chain, the two water binding sites that are most distant from the protein bulk surface were occupied by water molecules that approached along the E65/E312 channel, one of which formed an H-bond with the O4 site. These findings provide key insights into the significance of the channel ends, which may utilize water molecules during the PSII photocycle.

  10. Proteomic analysis of photosystem I components from different plant species.

    PubMed

    Zolla, Lello; Rinalducci, Sara; Timperio, Anna Maria

    2007-06-01

    In this study, the photosystem I (PSI) highly hydrophobic proteins present within stroma lamellae of the thylakoid membrane were separated by RP-HPLC and identified either by in-solution trypsin digestion peptide fragment fingerprinting or by the close correspondence between the intact mass measurements (IMMs) and those expected from the DNA sequence. Protein identification performed by MS/MS was as reliable as IMMs. Thus, IMM is an easy and valid method for identifying proteins that have no PTMs. This paper reports the M(r) for all PSI proteins in ten different species, including those whose genes have not yet been cloned. Lhca5 was revealed unequivocally in four species, corroborating that it is indeed a protein belonging to the light-harvesting antenna of PSI. In all species examined, the product of the Lhca6 gene has never been revealed. Concerning core proteins, Psa-O has been revealed in three species; isoforms of Psa-D and Psa-E have been found in both monocots and dicots. Small proteins like Psa-I and Psa-J are well separated and identified. RP-HPLC produces reliable fingerprints and reveals that the relative amounts of PSI proteins appear to be markedly different.

  11. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Ultrafast energy transfer within the photosystem II core complex.

    PubMed

    Pan, Jie; Gelzinis, Andrius; Chorošajev, Vladimir; Vengris, Mikas; Senlik, S Seckin; Shen, Jian-Ren; Valkunas, Leonas; Abramavicius, Darius; Ogilvie, Jennifer P

    2017-06-14

    We report 2D electronic spectroscopy on the photosystem II core complex (PSII CC) at 77 K under different polarization conditions. A global analysis of the high time-resolution 2D data shows rapid, sub-100 fs energy transfer within the PSII CC. It also reveals the 2D spectral signatures of slower energy equilibration processes occurring on several to hundreds of picosecond time scales that are consistent with previous work. Using a recent structure-based model of the PSII CC [Y. Shibata, S. Nishi, K. Kawakami, J. R. Shen and T. Renger, J. Am. Chem. Soc., 2013, 135, 6903], we simulate the energy transfer in the PSII CC by calculating auxiliary time-resolved fluorescence spectra. We obtain the observed sub-100 fs evolution, even though the calculated electronic energy shows almost no dynamics at early times. On the other hand, the electronic-vibrational interaction energy increases considerably over the same time period. We conclude that interactions with vibrational degrees of freedom not only induce population transfer between the excitonic states in the PSII CC, but also reshape the energy landscape of the system. We suggest that the experimentally observed ultrafast energy transfer is a signature of excitonic-polaron formation.

  13. Femtosecond photodischroism studies of isolated photosystem II reaction centers

    SciTech Connect

    Wiederrecht, G.P.; Wasielewski, M.R.; Siebert, M.; Govindjee

    1994-09-13

    Photosynthetic conversion of light energy into chemical potential begins in reaction center protein complexes, where rapid charge separation occurs with nearly unit quantum efficiency. Primary charge separation was studied in isolated photosystem II reaction centers from spinach containing 6 chlorophyll a, 2 pheophytin a (Pheo), 1 cytochrome b{sub 559}, and 2 {beta}-carotene molecules. Time-resolved pump-probe kinetic spectroscopy was carried out with 105-fs time resolution and with the pump laser polarized parallel, perpendicular, and at the magic angle (54.7{degrees}) relative to the polarized probe beam. The time evolution of the oxidized primary electron donor P680{sup +} and the reduced primary electron acceptor Pheo{sup {minus}} were measured at 820 nm and 545 nm, respectively. In addition, kinetics were obtained at 680 nm, the wavelength ascribed to the Q{sub y} transition of the primary electron donor P680 in the reaction center. At each measured probe wavelength the kinetics of the transient absorption changes can be fit to two major kinetic components. The relative amplitudes of these components are strongly dependent on the polarization of the pump beam relative to that of the probe. At the magic angle, where no photoselection occurs, the amplitude of the 3-ps component, which is indicative of the charge separation, dominates. When the primary electron acceptor Pheo is reduced prior to P680 excitation, the 3-ps component is eliminated. 48 refs., 6 figs., 1 tab.

  14. Electron transfer in native and mutated photosystem I reaction centers

    NASA Astrophysics Data System (ADS)

    Savikhin, Sergei; Xu, Wu; Chitnis, Parag; Struve, Walter

    2002-03-01

    Femtosecond time-resolved absorption difference studies were performed on photosystem I complexes from the cyanobacterium Synechocystis sp. PCC 6803. The overal electron transfer from the special pair P700 to the secondary acceptor A1 has been shown to be 10 ps, twice shorter than the previously estimated value. Similar studies were performed on more than 10 genetically engineered species, where protein structure was altered in the visinity of the reaction center (RC). The functioning of the PS I complex was found to be extremelly sensitive to the protein sequence in the immediate proximity of the RC: less than half of the studied mutations resulted in photosynthetically active complexes, and all of the latter had electron transfer dynamics indistinguishable from that of the wild type. Most of the mutations in the other areas of the PS I, including antenna, did not affect the photosynthetic function of this complex radically. These results confirm the extreme importance of the precise RC structure and demonstrate why millions of years of evolution resulted in only two types of topologically similar RC's shared by all photosynthetic organisms.

  15. 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.

  16. Widely Divergent Transcriptional Patterns Between SLE Patients of Different Ancestral Backgrounds in Sorted Immune Cell Populations

    PubMed Central

    Rosenzweig, Elizabeth; Rao, Swapna; Ko, Kichul; Niewold, Timothy B.

    2015-01-01

    Systemic lupus erythematosus (SLE) is a complex autoimmune disease of uncertain etiology. Patients from different ancestral backgrounds demonstrate differences in clinical manifestations and autoantibody profiles. We examined genome-wide transcriptional patterns in major immune cell subsets across different ancestral backgrounds. Peripheral blood was collected from African-American (AA) and European-American (EA) SLE patients and controls. CD4 T-cells, CD8 T-cells, monocytes, and B cells were purified by flow sorting, and each cell subset from each subject was run on a genome-wide expression array. Cases were compared to controls of the same ancestral background. The overlap in differentially expressed gene (DEG) lists between different cell types from the same ancestral background was modest (<10%), and only 5-8% overlap in DEG lists was observed when comparing the same cell type between different ancestral backgrounds. IFN-stimulated gene (ISG) expression was not up-regulated synchronously in all cell types from a given patient, for example a given subject could have high ISG expression in T and B cells, but not in monocytes. AA subjects demonstrated more concordance in ISG expression between cell types from the same individual, and AA patients demonstrated significant down-regulation of metabolic gene expression which was not observed in EA patients. ISG expression was significantly decreased in B cells in patients taking immunosuppressants, while ISGs in other cell types did not differ with medication use. In conclusion, gene expression was strikingly different between immune cell subsets and between ancestral backgrounds in SLE patients. These findings emphasize the critical importance of studying multiple ancestral backgrounds and multiple cell types in gene expression studies. Ancestral backgrounds which are not studied will not benefit from personalized medicine strategies in SLE. PMID:25921064

  17. Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals

    PubMed Central

    Danchin, Etienne GJ; Gouret, Philippe; Pontarotti, Pierre

    2006-01-01

    Background Gene losses played a role which may have been as important as gene and genome duplications and rearrangements, in modelling today species' genomes from a common ancestral set of genes. The set and diversity of protein-coding genes in a species has direct output at the functional level. While gene losses have been reported in all the major lineages of the metazoan tree of life, none have proposed a focus on specific losses in the vertebrates and mammals lineages. In contrast, genes lost in protostomes (i.e. arthropods and nematodes) but still present in vertebrates have been reported and extensively detailed. This probable over-anthropocentric way of comparing genomes does not consider as an important phenomena, gene losses in species that are usually described as "higher". However reporting universally conserved genes throughout evolution that have recently been lost in vertebrates and mammals could reveal interesting features about the evolution of our genome, particularly if these losses can be related to losses of capability. Results We report 11 gene families conserved throughout eukaryotes from yeasts (such as Saccharomyces cerevisiae) to bilaterian animals (such as Drosophila melanogaster or Caenorhabditis elegans). This evolutionarily wide conservation suggests they were present in the last common ancestors of fungi and metazoan animals. None of these 11 gene families are found in human nor mouse genomes, and their absence generally extends to all vertebrates. A total of 8 out of these 11 gene families have orthologs in plants, suggesting they were present in the Last Eukaryotic Common Ancestor (LECA). We investigated known functional information for these 11 gene families. This allowed us to correlate some of the lost gene families to loss of capabilities. Conclusion Mammalian and vertebrate genomes lost evolutionary conserved ancestral genes that are probably otherwise not dispensable in eukaryotes. Hence, the human genome, which is generally

  18. 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

    2016-06-27

    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.

  19. Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

    PubMed Central

    Miklós, István

    2009-01-01

    Homologous genes originate from a common ancestor through vertical inheritance, duplication, or horizontal gene transfer. Entire homolog families spawned by a single ancestral gene can be identified across multiple genomes based on protein sequence similarity. The sequences, however, do not always reveal conclusively the history of large families. To study the evolution of complete gene repertoires, we propose here a mathematical framework that does not rely on resolved gene family histories. We show that so-called phylogenetic profiles, formed by family sizes across multiple genomes, are sufficient to infer principal evolutionary trends. The main novelty in our approach is an efficient algorithm to compute the likelihood of a phylogenetic profile in a model of birth-and-death processes acting on a phylogeny. We examine known gene families in 28 archaeal genomes using a probabilistic model that involves lineage- and family-specific components of gene acquisition, duplication, and loss. The model enables us to consider all possible histories when inferring statistics about archaeal evolution. According to our reconstruction, most lineages are characterized by a net loss of gene families. Major increases in gene repertoire have occurred only a few times. Our reconstruction underlines the importance of persistent streamlining processes in shaping genome composition in Archaea. It also suggests that early archaeal genomes were as complex as typical modern ones, and even show signs, in the case of the methanogenic ancestor, of an extremely large gene repertoire. PMID:19570746

  20. 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

  1. Expression of the Drosophila homeobox gene, Distal-less supports an ancestral role in neural development

    PubMed Central

    Plavicki, Jessica S.; Squirrell, Jayne M.; Eliceiri, Kevin W.; Boekhoff-Falk, Grace

    2015-01-01

    Background Distal-less (Dll) encodes a homeodomain transcription factor expressed in developing appendages of organisms throughout metazoan phylogeny. Based on earlier observations in the limbless nematode Caenorhabditis elegans and the primitive chordate amphioxus, it was proposed that Dll had an ancestral function in nervous system development. Consistent with this hypothesis, Dll is necessary for the development of both peripheral and central components of the Drosophila olfactory system. Furthermore, vertebrate homologs of Dll, the Dlx genes, play critical roles in mammalian brain development. Results Using fluorescent immunohistochemistry of fixed samples and multiphoton microscopy of living Drosophila embryos we show that Dll is expressed in the embryonic, larval and adult CNS and PNS in embryonic and larval neurons, brain and ventral nerve cord (VNC) glia, as well as in PNS structures associated with chemosensation. In adult flies, Dll expression is expressed in the optic lobes, central brain regions and the antennal lobes. Conclusions Characterization of Dll expression in the developing nervous system supports a role of Dll in neural development and function and establishes an important basis for determining the specific functional roles of Dll in Drosophila development and for comparative studies of Drosophila Dll functions with those of its vertebrate counterparts. PMID:26472170

  2. Ancestral origins of the prion protein gene D178N mutation in the Basque Country.

    PubMed

    Rodríguez-Martínez, Ana B; Barreau, Christian; Coupry, Isabelle; Yagüe, Jordi; Sánchez-Valle, Raquel; Galdós-Alcelay, Luis; Ibáñez, Agustín; Digón, Antón; Fernández-Manchola, Ignacio; Goizet, Cyril; Castro, Azucena; Cuevas, Nerea; Alvarez-Alvarez, Maite; de Pancorbo, Marian M; Arveiler, Benoît; Zarranz, Juan J

    2005-06-01

    Fatal familial insomnia (FFI) and familial Creutzfeldt-Jakob disease (fCJD) are familial prion diseases with autosomal dominant inheritance of the D178N mutation. FFI has been reported in at least 27 pedigrees around the world. Twelve apparently unrelated FFI and fCJD pedigrees with the characteristic D178N mutation have been reported in the Prion Diseases Registry of the Basque Country since 1993. The high incidence of familial prion diseases in this region may reflect a unique ancestral origin of the chromosome carrying this mutation. In order to investigate this putative founder effect, we developed "happy typing", a new approach to the happy mapping method, which consists of the physical isolation of large haploid genomic DNA fragments and their analysis by the Polymerase Chain Reaction in order to perform haplotypic analysis instead of pedigree analysis. Six novel microsatellite markers, located in a 150-kb genomic segment flanking the PRNP gene were characterized for typing haploid DNA fragments of 285 kb in size. A common haplotype was found in patients from the Basque region, strongly suggesting a founder effect. We propose that "happy typing" constitutes an efficient method for determining disease-associated haplotypes, since the analysis of a single affected individual per pedigree should provide sufficient evidence.

  3. S3 State of the O2-Evolving Complex of Photosystem II: Insights from QM/MM, EXAFS, and Femtosecond X-ray Diffraction.

    PubMed

    Askerka, Mikhail; Wang, Jimin; Vinyard, David J; Brudvig, Gary W; Batista, Victor S

    2016-02-23

    The oxygen-evolving complex (OEC) of photosystem II has been studied in the S3 state by electron paramagnetic resonance, extended X-ray absorption fine structure (EXAFS), and femtosecond X-ray diffraction (XRD). However, the actual structure of the OEC in the S3 state has yet to be established. Here, we apply hybrid quantum mechanics/molecular mechanics methods and propose a structural model that is consistent with EXAFS and XRD. The model supports binding of water ligands to the cluster in the S2 → S3 transition through a carousel rearrangement around Mn4, inspired by studies of ammonia binding.

  4. 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

  5. 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.

  6. Circular spectropolarimetric sensing of chiral photosystems in decaying leaves

    NASA Astrophysics Data System (ADS)

    Patty, C. H. Lucas; Visser, Luuk J. J.; Ariese, Freek; Buma, Wybren Jan; Sparks, William B.; van Spanning, Rob J. M.; Röling, Wilfred F. M.; Snik, Frans

    2017-03-01

    Circular polarization spectroscopy has proven to be an indispensable tool in photosynthesis research and (bio)molecular research in general. Oxygenic photosystems typically display an asymmetric Cotton effect around the chlorophyll absorbance maximum with a signal ≤ 1 % . In vegetation, these signals are the direct result of the chirality of the supramolecular aggregates. The circular polarization is thus directly influenced by the composition and architecture of the photosynthetic macrodomains, and is thereby linked to photosynthetic functioning. Although ordinarily measured only on a molecular level, we have developed a new spectropolarimetric instrument, TreePol, that allows for both laboratory and in-the-field measurements. Through spectral multiplexing, TreePol is capable of fast measurements with a sensitivity of ∼ 1 *10-4 and is therefore suitable of non-destructively probing the molecular architecture of whole plant leaves. We have measured the chiroptical evolution of Hedera helix leaves for a period of 22 days. Spectrally resolved circular polarization measurements (450-900 nm) on whole leaves in transmission exhibit a strong decrease in the polarization signal over time after plucking, which we accredit to the deterioration of chiral macro-aggregates. Chlorophyll a levels measured over the same period by means of UV-vis absorption and fluorescence spectroscopy showed a much smaller decrease. With these results we are able to distinguish healthy from deteriorating leaves. Hereby we indicate the potency of circular polarization spectroscopy on whole and intact leaves as a nondestructive tool for structural and plant stress assessment. Additionally, we underline the establishment of circular polarization signals as remotely accessible means of detecting the presence of extraterrestrial life.

  7. Distinctive photosystem II photoinactivation and protein dynamics in marine diatoms.

    PubMed

    Wu, Hongyan; Cockshutt, Amanda M; McCarthy, Avery; Campbell, Douglas A

    2011-08-01

    Diatoms host chlorophyll a/c chloroplasts distinct from green chloroplasts. Diatoms now dominate the eukaryotic oceanic phytoplankton, in part through their exploitation of environments with variable light. We grew marine diatoms across a range of temperatures and then analyzed their PSII function and subunit turnover during an increase in light to mimic an upward mixing event. The small diatom Thalassiosira pseudonana initially responds to increased photoinactivation under blue or white light with rapid acceleration of the photosystem II (PSII) repair cycle. Increased red light provoked only modest PSII photoinactivation but triggered a rapid clearance of a subpool of PsbA. Furthermore, PsbD and PsbB content was greater than PsbA content, indicating a large pool of partly assembled PSII repair cycle intermediates lacking PsbA. The initial replacement rates for PsbD (D2) were, surprisingly, comparable to or higher than those for PsbA (D1), and even the supposedly stable PsbB (CP47) dropped rapidly upon the light shift, showing a novel aspect of rapid protein subunit turnover in the PSII repair cycle in small diatoms. Under sustained high light, T. pseudonana induces sustained nonphotochemical quenching, which correlates with stabilization of PSII function and the PsbA pool. The larger diatom Coscinodiscus radiatus showed generally similar responses but had a smaller allocation of PSII complexes relative to total protein content, with nearly equal stiochiometries of PsbA and PsbD subunits. Fast turnover of multiple PSII subunits, pools of PSII repair cycle intermediates, and photoprotective induction of nonphotochemical quenching are important interacting factors, particularly for small diatoms, to withstand and exploit high, fluctuating light.

  8. Entrapment of photosystem I within self-assembled films.

    PubMed

    Kincaid, Helen A; Niedringhaus, Tom; Ciobanu, Madalina; Cliffel, David E; Jennings, G Kane

    2006-09-12

    We have developed a process to incorporate an integral membrane protein, Photosystem I (PSI), into an organic thin film at an electrode surface and thereby insulate the protein complex on the surface while mimicking its natural environment. The PSI complex, which is primarily more hydrophobic on the exterior than interior, is hydrophobically confined in vivo within the thylakoid membrane. To mimic the thylakoid membrane and entrap PSI on an electrode, we have designed a series of steps using a thin self-assembled monolayer (SAM) to adsorb and orient PSI followed by exposures to longer-chained methyl-terminated alkanethiols that place exchange with components of the original SAM in the interprotein domains. In this process, PSI is first adsorbed onto a HOC(6)S/Au substrate through a short exposure to a dilute solution of the protein to achieve a protein coverage of approximately 25%. The PSI/HOC(6)S/Au substrate is then placed into a solution containing one of various longer-chained alkanethiols including C(22)SH or C(18)OC(19)SH. Changes in thickness, interfacial capacitance, infrared spectra, and surface wettability were used to assess the extent of backfilling by the long-chained thiols. The coverage of the protein layer and the solvent used for backfilling affected the rate and quality of the SAM formed in the interprotein regions. After exposure of the PSI layer to solvents containing alkanethiols, there was only minor loss of protein on the surface and no real change in protein secondary structure as evidenced by reflectance absorption infrared spectroscopy.

  9. Biogenesis of photosystem II complexes: transcriptional, translational, and posttranslational regulation

    PubMed Central

    1986-01-01

    The integral membrane proteins of photosystem II (PS II) reaction center complexes are encoded by chloroplast genomes. These proteins are absent from thylakoids of PS II mutants of algae and vascular plants as a result of either chloroplast or nuclear gene mutations. To resolve the molecular basis for the concurrent absence of the PS II polypeptides, protein synthesis rates and mRNA levels were measured in mutants of Chlamydomonas reinhardtii that lack PS II. The analyses show that one nuclear gene product regulates the levels of transcripts from the chloroplast gene encoding the 51-kD chlorophyll a-binding polypeptide (polypeptide 5) but is not involved in the synthesis of other chloroplast mRNAs. Another nuclear product is specifically required for translation of mRNA encoding the 32-34-kD polypeptide, D1. The absence of either D1 or polypeptide 5 does not eliminate the synthesis and thylakoid insertion of two other integral membrane proteins of PS II, the chlorophyll a-binding polypeptide of 46 kD (polypeptide 6) and the 30-kD "D1-like" protein, D2. However, these two unassembled subunits cannot be properly processed and/or are degraded in the mutants even though they reside in the membrane. In addition, pulse labeling of the nuclear mutants and a chloroplast mutant that does not synthesize D1 mRNA indicates that synthesis of polypeptide 5 and D1 is coordinated at the translational level. A model is presented to explain how absence of one of the two proteins could lead to translational arrest of the other. PMID:3533953

  10. Rapid formation of the stable tyrosyl radical in photosystem II.

    PubMed

    Faller, P; Debus, R J; Brettel, K; Sugiura, M; Rutherford, A W; Boussac, A

    2001-12-04

    Two symmetrically positioned redox active tyrosine residues are present in the photosystem II (PSII) reaction center. One of them, TyrZ, is oxidized in the ns-micros time scale by P680+ and reduced rapidly (micros to ms) by electrons from the Mn complex. The other one, TyrD, is stable in its oxidized form and seems to play no direct role in enzyme function. Here, we have studied electron donation from these tyrosines to the chlorophyll cation (P680+) in Mn-depleted PSII from plants and cyanobacteria. In particular, a mutant lacking TyrZ was used to investigate electron donation from TyrD. By using EPR and time-resolved absorption spectroscopy, we show that reduced TyrD is capable of donating an electron to P680+ with t1/2 approximately equal to 190 ns at pH 8.5 in approximately half of the centers. This rate is approximately 10(5) times faster than was previously thought and similar to the TyrZ donation rate in Mn-depleted wild-type PSII (pH 8.5). Some earlier arguments put forward to rationalize the supposedly slow electron donation from TyrD (compared with that from TyrZ) can be reassessed. At pH 6.5, TyrZ (t1/2 = 2-10 micros) donates much faster to P680+ than does TyrD (t1/2 > 150 micros). These different rates may reflect the different fates of the proton released from the respective tyrosines upon oxidation. The rapid rate of electron donation from TyrD requires at least partial localization of P680+ on the chlorophyll (PD2) that is located on the D2 side of the reaction center.

  11. Red chlorophylls in the exciton model of photosystem I.

    PubMed

    Vaitekonis, Sarunas; Trinkunas, Gediminas; Valkunas, Leonas

    2005-11-01

    Structural arrangement of pigment molecules of Photosystem I of photosynthetic cyanobacterium Synechococcus elongatus is used for theoretical modeling of the excitation energy spectrum. It is demonstrated that a straightforward application of the exciton theory with the assumption of the same molecular transition energy does not describe the red side of the absorption spectrum. Since the inhomogeneity in the molecular transition energies caused by a dispersive interaction with the molecular surrounding cannot be identified directly from the structural model, the evolutionary search procedure is used for fitting the low temperature absorption and circular dichroism spectra. As a result, one dimer, three trimers and one tetramer of chlorophyll molecules responsible for the red side of the absorption spectrum with their assignment to the spectroscopically established three bands at 708, 714 and 719 nm are determined. All of them are found to be situated not in the very close vicinity of the reaction center but are encircling it almost at the same distance. In order to explain the unusual broadening on the red side of the spectrum the exciton state mixing with the charge transfer (CT) states is considered. It is shown that two effects can be distinguished as caused by mixing of those states: (i) the oscillator strength borrowing by the CT state from the exciton transition and (ii) the borrowing of the high density of the CT state by the exciton state. The intermolecular vibrations between two counter-charged molecules determine the high density in the CT state. From the broad red absorption wing it is concluded that the CT state should be the lowest state in the complexes under consideration. Such mixing effect enables resolving the diversity in the molecular transition energies as determined by different theoretical approaches.

  12. Ultrafast infrared observation of exciton equilibration from oriented single crystals of photosystem II

    NASA Astrophysics Data System (ADS)

    Kaucikas, Marius; Maghlaoui, Karim; Barber, Jim; Renger, Thomas; van Thor, Jasper J.

    2016-12-01

    In oxygenic photosynthesis, two photosystems work in series. Each of them contains a reaction centre that is surrounded by light-harvesting antennae, which absorb the light and transfer the excitation energy to the reaction centre where electron transfer reactions are driven. Here we report a critical test for two contrasting models of light harvesting by photosystem II cores, known as the trap-limited and the transfer-to-the trap-limited model. Oriented single crystals of photosystem II core complexes of Synechococcus elongatus are excited by polarized visible light and the transient absorption is probed with polarized light in the infrared. The dichroic amplitudes resulting from photoselection are maintained on the 60 ps timescale that corresponds to the dominant energy transfer process providing compelling evidence for the transfer-to-the-trap limitation of the overall light-harvesting process. This finding has functional implications for the quenching of excited states allowing plants to survive under high light intensities.

  13. 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.

  14. 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

  15. 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.

  16. Evidence for the involvement of PSI-E subunit in the reduction of ferredoxin by photosystem I.

    PubMed

    Rousseau, F; Sétif, P; Lagoutte, B

    1993-05-01

    Of the stroma-accessible proteins of photosystem I (PSI) from Synechocystis sp. PCC 6803, the PSI-C, PSI-D and PSI-E subunits have already been characterized, and the corresponding genes isolated. PCR amplification and cassette mutagenesis were used in this work to delete the psaE gene. PSI particles were isolated from this mutant, which lacks subunit PSI-E, and the direct photoreduction of ferredoxin was investigated by flash absorption spectroscopy. The second order rate constant for reduction of ferredoxin by wild type PSI was estimated to be approximately 10(9) M-1s-1. Relative to the wild type, PSI lacking PSI-E exhibited a rate of ferredoxin reduction decreased by a factor of at least 25. After reassociation of the purified PSI-E polypeptide, the original rate of electron transfer was recovered. When a similar reconstitution was performed with a PSI-E polypeptide from spinach, an intermediate rate of reduction was observed. Membrane labeling of the native PSI with fluorescein isothiocyanate allowed the isolation of a fluorescent PSI-E subunit. Peptide analysis showed that some residues following the N-terminal sequence were labeled and thus probably accessible to the stroma, whereas both N- and C-terminal ends were probably buried in the photosystem I complex. Site-directed mutagenesis based on these observations confirmed that important changes in either of the two terminal sequences of the polypeptide impaired its correct integration in PSI, leading to phenotypes identical to the deleted mutant. Less drastic modifications in the predicted stroma exposed sequences did not impair PSI-E integration, and the ferredoxin photoreduction was not significantly affected. All these results lead us to propose a structural role for PSI-E in the correct organization of the site involved in ferredoxin photoreduction.

  17. Hydrogen production in Chlamydomonas: photosystem II-dependent and -independent pathways differ in their requirement for starch metabolism.

    PubMed

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

    2009-10-01

    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.

  18. Structure of the catalytic, inorganic core of oxygen-evolving photosystem II at 1.9 Å resolution.

    PubMed

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

    2011-01-01

    The catalytic center for photosynthetic water-splitting consists of 4 Mn atoms and 1 Ca atom and is located near the lumenal surface of photosystem II. So far the structure of the Mn(4)Ca-cluster has been studied by a variety of techniques including X-ray spectroscopy and diffraction, and various structural models have been proposed. However, its exact structure is still unknown due to the limited resolution of crystal structures of PSII achieved so far, as well as possible radiation damages that might have occurred. Very recently, we have succeeded in solving the structure of photosystem II at 1.9 Å, which yielded a detailed picture of the Mn(4)CaO(5)-cluster for the first time. In the high resolution structure, the Mn(4)CaO(5)-cluster is arranged in a distorted chair form, with a cubane-like structure formed by 3 Mn and 1 Ca, 4 oxygen atoms as the distorted base of the chair, and 1 Mn and 1 oxygen atom outside of the cubane as the back of the chair. In addition, four water molecules were associated with the cluster, among which, two are associated with the terminal Mn atom and two are associated with the Ca atom. Some of these water molecules may therefore serve as the substrates for water-splitting. The high resolution structure of the catalytic center provided a solid basis for elucidation of the mechanism of photosynthetic water splitting. We review here the structural features of the Mn(4)CaO(5)-cluster analyzed at 1.9 Å resolution, and compare them with the structures reported previously.

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

    PubMed

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

    2007-06-01

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

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

    PubMed

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

    2013-10-01

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

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

    SciTech Connect

    Michel, H.; Deisenhofer, J.

    1988-01-12

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

  2. Flash-induced structural dynamics in photosystem II membrane fragments of green plants.

    PubMed

    Pieper, Jörg; Renger, Gernot

    2009-07-07

    Time-resolved quasielastic neutron scattering with laser excitation is a promising novel pump-probe approach, which opens up new perspectives for the study of protein-membrane dynamics in specific functional states of even complex systems. This is demonstrated here for the case of photosystem II membrane fragments with inhibited electron transfer. In contrast to the case of the model system bacteriorhodopsin, a transient reduction of the dynamics is observed approximately 160 micros after the actinic laser flash. This effect is the first observation of a modulated structural dynamics in photosystem II membrane fragments.

  3. Energy transfer in photosystem I. Time resolved fluorescence of the native photosystem I complex and its core complex

    NASA Astrophysics Data System (ADS)

    Pålsson, Lars-Olof; Tjus, Staffan E.; Andersson, Bertil; Gillbro, Tomas

    1995-05-01

    Energy transfer within isolated spinach photosystem I (PS I) complexes with different antenna size were studied using time-resolved picosecond and steady-state fluorescence spectroscopy. In both the native PS I complexes and the PS I core complexes lacking the outer chlorophyll a/ b antenna we observed a fast dominating emission component ≈ 35 ps at room temperature which is associated with the trapping process by the reaction centre. In the native PS I complex there also appears a 120 ps component which was not observed in the PS I core complex. This component most likely represents an energy transfer from low energy pigments in the light-harvesting complex I antenna and into the core. Due to a very fast energy equilibration (< 10 ps) it was not possible to resolve the energy transfer at room temperature. At 77 K, however, it was possible to follow the energy transfer from F690 to F720 with a transfer time of ≈ 35 ps within the native PS I complex and slightly longer, 78 ps, in the PS I core complex. The native PS I complex also exhibited in the region 700-740 nm a 102 ps component which originates from F720 and represents energy transfer from F720 to P700 at 77 K. At low temperatures the PS I core complex exhibited a component of 161 ps which is associated with F720 and has the same function as the 102 ps component of the native PS I complex. We conclude that the F720 emission originates from pigments in the core antenna system. This emission also increases at low temperature. In the native PS I complex there is an initial increase in the F720 emission as the temperature is lowered but at 77 K the F735 emission originating from LHC I dominates.

  4. 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

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

    PubMed Central

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

    2016-01-01

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

  6. The vibrational spectrum of the secondary electron acceptor, A1, in photosystem I.

    PubMed

    Bender, Shana L; Keough, James M; Boesch, Scott E; Wheeler, Ralph A; Barry, Bridgette A

    2008-03-27

    Photosystem I (PSI) is a multisubunit protein complex which carries out light-induced, transmembrane charge separation in oxygenic photosynthesis. In PSI, the electron-transfer pathway consists of chlorophyll and phylloquinone molecules, as well as iron-sulfur clusters. There are two phylloquinone molecules, which are located in structurally symmetric positions in the reaction center. It has been proposed that both phylloquinone molecules are active as the A1 secondary electron acceptor in bidirectional electron-transfer reactions. The PSI A1 acceptors are of interest because they have the lowest reduction potential of any quinone found in nature. In this work using light-induced FT-IR spectroscopy, isotope-edited spectra are presented, which attribute vibrational bands to the carbonyl stretching vibrations of A1 and A1- and the quinoid ring stretching vibration of A1. Bands are assigned by comparison with hybrid Hartee-Fock density functional calculations, which predict vibrational frequencies, amplitudes, and isotope shifts for the phylloquinone singlet and radical anion states. The results are consistent with an environmental interaction increasing the frequency of the singlet CO vibration and decreasing the frequency of the anion radical CO vibration, relative to model compounds. This environmental interaction may be the asymmetric hydrogen bond to A1/A1-, electrostatic interactions with charged amino acid side chains, or a pi-pi interaction with the indole ring of a nearby tryptophan. Such differential effects on the structure of A1 and A1- may be associated with a destabilization of the anion radical. These studies give novel information concerning the effect of the protein matrix on the PSI electron-transfer cofactor.

  7. Structures and energetics for O2 formation in photosystem II.

    PubMed

    Siegbahn, Per E M

    2009-12-21

    Water oxidation, forming O(2) from water and sunlight, is a fundamental process for life on earth. In nature, the enzyme photosystem II (PSII) catalyzes this reaction. The oxygen evolving complex (OEC), the complex within PSII that catalyzes the actual formation of the O-O bond, contains four manganese atoms and one calcium atom connected by oxo bonds. Seven amino acid side chains in the structure, mostly carboxylates, are ligated to the metal atoms. In the study of many enzyme mechanisms, theoretical modeling using density functional theory has served as an indispensable tool. This Account summarizes theoretical research to elucidate the mechanism for water oxidation in photosynthesis, including the most recent findings. The development of successively larger models, ranging from 50 atoms in the active site up to the present model size of 170 atoms, has revealed the mechanism of O(2) formation with increasing detail. The X-ray crystal structures of PSII have provided a framework for optimizing the theoretical models. By constraint of the backbone atoms to be at the same positions as those in the X-ray structures, the theoretical structures are in good agreement with both the measured electron density and extended X-ray absorption fine structure (EXAFS) interpretations. By following the structural and energetic changes in those structures through the different steps in the catalytic process, we have modeled the oxidation of the catalytic complex, the binding of the two substrate water molecules, and the subsequent deprotonations of those substrate molecules. In these models, the OEC forms a basin into which the water molecules naturally fit. These findings demonstrate that the binding of the second water molecule causes a reconstruction, results that are consistent with earlier EXAFS measurements. Most importantly, this Account describes a low-barrier mechanism for formation of the O-O bond, involving an oxygen radical that reacts with a mu-oxo ligand of the OEC

  8. Chlorophyll Biosynthesis Gene Evolution Indicates Photosystem Gene Duplication, Not Photosystem Merger, at the Origin of Oxygenic Photosynthesis

    PubMed Central

    Sousa, Filipa L.; Shavit-Grievink, Liat; Allen, John F.; Martin, William F.

    2013-01-01

    An open question regarding the evolution of photosynthesis is how cyanobacteria came to possess the two reaction center (RC) types, Type I reaction center (RCI) and Type II reaction center (RCII). The two main competing theories in the foreground of current thinking on this issue are that either 1) RCI and RCII are related via lineage divergence among anoxygenic photosynthetic bacteria and became merged in cyanobacteria via an event of large-scale lateral gene transfer (also called "fusion" theories) or 2) the two RC types are related via gene duplication in an ancestral, anoxygenic but protocyanobacterial phototroph that possessed both RC types before making the transition to using water as an electron donor. To distinguish between these possibilities, we studied the evolution of the core (bacterio)chlorophyll biosynthetic pathway from protoporphyrin IX (Proto IX) up to (bacterio)chlorophyllide a. The results show no dichotomy of chlorophyll biosynthesis genes into RCI- and RCII-specific chlorophyll biosynthetic clades, thereby excluding models of fusion at the origin of cyanobacteria and supporting the selective-loss hypothesis. By considering the cofactor demands of the pathway and the source genes from which several steps in chlorophyll biosynthesis are derived, we infer that the cell that first synthesized chlorophyll was a cobalamin-dependent, heme-synthesizing, diazotrophic anaerobe. PMID:23258841

  9. Histology of “placoderm” dermal skeletons: Implications for the nature of the ancestral gnathostome

    PubMed Central

    Giles, Sam; Rücklin, Martin

    2013-01-01

    Abstract The vertebrate dermal skeleton has long been interpreted to have evolved from a primitive condition exemplified by chondrichthyans. However, chondrichthyans and osteichthyans evolved from an ancestral gnathostome stem‐lineage in which the dermal skeleton was more extensively developed. To elucidate the histology and skeletal structure of the gnathostome crown‐ancestor we conducted a histological survey of the diversity of the dermal skeleton among the placoderms, a diverse clade or grade of early jawed vertebrates. The dermal skeleton of all placoderms is composed largely of a cancellar architecture of cellular dermal bone, surmounted by dermal tubercles in the most ancestral clades, including antiarchs. Acanthothoracids retain an ancestral condition for the dermal skeleton, and we record its secondary reduction in antiarchs. We also find that mechanisms for remodeling bone and facilitating different growth rates between adjoining plates are widespread throughout the placoderms. J. Morphol., 2013. © 2013 Wiley Periodicals, Inc. PMID:23378262

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

    PubMed

    Elliot, Michael G

    2015-01-07

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

  11. 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.

  12. 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

  13. 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

  14. 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."

  15. 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.

  16. 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

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

    PubMed Central

    Chen, Hua; Chen, Kun

    2013-01-01

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

  18. Environmental enrichment mitigates the impact of ancestral stress on motor skill and corticospinal tract plasticity.

    PubMed

    McCreary, J Keiko; Erickson, Zachary T; Metz, Gerlinde A S

    2016-10-06

    An adverse fetal environment in utero has been associated with long-term alterations in brain structure and function, and a higher risk of neurological disorders in later life. A common consequence of early adverse experience is impaired motor system function. A causal relationship for stress-associated impairments and a suitable therapy, however, have not been determined yet. To investigate the impact of ancestral stress on corticospinal tract (CST) morphology and fine motor performance in rats, and to determine if adverse programming by ancestral stress can be mitigated by environmental enrichment therapy in rats. The study examined F3 offspring generated by three lineages; one with prenatal stress only in the F1 generation, one with compounding effects of multigenerational prenatal stress, and a non-stress control lineage. F3 offspring from each lineage were injected with biotinylated dextran amine (BDA) into the motor cortex for anterograde tracing of the CST. Examination of the CST revealed reduced axonal density in the ancestrally stressed lineages. These anatomical changes were associated with significant impairments in skilled walking, as indicated by reduced foot placement accuracy and disturbed inter-limb coordination. Therapeutic intervention by environmental enrichment reduced the neuromorphological consequences of ancestral stress and restored skilled walking ability. The data suggest a causal relationship between stress-induced abnormal CST function and loss of fine motor performance. Thus, ancestral stress may be a determinant of motor system development and motor skill. Environmental enrichment may represent an effective intervention for the adverse programming by ancestral stress and trauma. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Common 5' beta-globin RFLP haplotypes harbour a surprising level of ancestral sequence mosaicism.

    PubMed

    Webster, Matthew T; Clegg, John B; Harding, Rosalind M

    2003-07-01

    Blocks of linkage disequilibrium (LD) in the human genome represent segments of ancestral chromosomes. To investigate the relationship between LD and genealogy, we analysed diversity associated with restriction fragment length polymorphism (RFLP) haplotypes of the 5' beta-globin gene complex. Genealogical analyses were based on sequence alleles that spanned a 12.2-kb interval, covering 3.1 kb around the psibeta gene and 6.2 kb of the delta-globin gene and its 5' flanking sequence known as the R/T region. Diversity was sampled from a Kenyan Luo population where recent malarial selection has contributed to substantial LD. A single common sequence allele spanning the 12.2-kb interval exclusively identified the ancestral chromosome bearing the "Bantu" beta(s) (sickle-cell) RFLP haplotype. Other common 5' RFLP haplotypes comprised interspersed segments from multiple ancestral chromosomes. Nucleotide diversity was similar between psibeta and R/T-delta-globin but was non-uniformly distributed within the R/T-delta-globin region. High diversity associated with the 5' R/T identified two ancestral lineages that probably date back more than 2 million years. Within this genealogy, variation has been introduced into the 3' R/T by gene conversion from other ancestral chromosomes. Diversity in delta-globin was found to lead through parts of the main genealogy but to coalesce in a more recent ancestor. The well-known recombination hotspot is clearly restricted to the region 3' of delta-globin. Our analyses show that, whereas one common haplotype in a block of high LD represents a long segment from a single ancestral chromosome, others are mosaics of short segments from multiple ancestors related in genealogies of unsuspected complexity.

  20. Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size.

    PubMed

    Chen, Hua; Chen, Kun

    2013-07-01

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

  1. Multiple LHCII antennae can transfer energy efficiently to a single Photosystem I.

    PubMed

    Bos, Inge; Bland, Kaitlyn M; Tian, Lijin; Croce, Roberta; Frankel, Laurie K; van Amerongen, Herbert; Bricker, Terry M; Wientjes, Emilie

    2017-05-01

    Photosystems I and II (PSI and PSII) work in series to drive oxygenic photosynthesis. The two photosystems have different absorption spectra, therefore changes in light quality can lead to imbalanced excitation of the photosystems and a loss in photosynthetic efficiency. In a short-term adaptation response termed state transitions, excitation energy is directed to the light-limited photosystem. In higher plants a special pool of LHCII antennae, which can be associated with either PSI or PSII, participates in these state transitions. It is known that one LHCII antenna can associate with the PsaH site of PSI. However, membrane fractions were recently isolated in which multiple LHCII antennae appear to transfer energy to PSI. We have used time-resolved fluorescence-streak camera measurements to investigate the energy transfer rates and efficiency in these membrane fractions. Our data show that energy transfer from LHCII to PSI is relatively slow. Nevertheless, the trapping efficiency in supercomplexes of PSI with ~2.4 LHCIIs attached is 94%. The absorption cross section of PSI can thus be increased with ~65% without having significant loss in quantum efficiency. Comparison of the fluorescence dynamics of PSI-LHCII complexes, isolated in a detergent or located in their native membrane environment, indicates that the environment influences the excitation energy transfer rates in these complexes. This demonstrates the importance of studying membrane protein complexes in their natural environment. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    ERIC Educational Resources Information Center

    Muhoz, Romualdo; Quiles, Maria J.

    2003-01-01

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

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

    ERIC Educational Resources Information Center

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

    2005-01-01

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

  4. A synthetic model for the oxygen-evolving complex in Sr(2+)-containing photosystem II.

    PubMed

    Chen, Changhui; Zhang, Chunxi; Dong, Hongxing; Zhao, Jingquan

    2014-08-25

    A novel heterometallic MnSr complex containing the Mn3SrO4 cuboidal moiety and all types of μ-O(2-) moieties observed in the oxygen-evolving complex (OEC) in Sr(2+)-containing photosystem II (PSII) has been synthesized and characterized, which provides a new synthetic model of the OEC.

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

    PubMed

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

    2016-07-01

    Etioplasts lack thylakoid membranes and photosystem complexes. Light triggers differentiation of etioplasts into mature chloroplasts, and photosystem complexes assemble in parallel with thylakoid membrane development. Plastids isolated at various time points of de-etiolation are ideal to study the kinetic biogenesis of photosystem complexes during chloroplast development. Here, we investigated the chronology of photosystem II (PSII) biogenesis by monitoring assembly status of chlorophyll-binding protein complexes and development of water splitting via O2 production in plastids (etiochloroplasts) isolated during de-etiolation of barley (Hordeum vulgare L.). Assembly of PSII monomers, dimers and complexes binding outer light-harvesting antenna [PSII-light-harvesting complex II (LHCII) supercomplexes] was identified after 1, 2 and 4 h of de-etiolation, respectively. Water splitting was detected in parallel with assembly of PSII monomers, and its development correlated with an increase of bound Mn in the samples. After 4 h of de-etiolation, etiochloroplasts revealed the same water-splitting efficiency as mature chloroplasts. We conclude that the capability of PSII to split water during de-etiolation precedes assembly of the PSII-LHCII supercomplexes. Taken together, data show a rapid establishment of water-splitting activity during etioplast-to-chloroplast transition and emphasize that assembly of the functional water-splitting site of PSII is not the rate-limiting step in the formation of photoactive thylakoid membranes. © 2016 John Wiley & Sons Ltd.

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

    USDA-ARS?s Scientific Manuscript database

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

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

    ERIC Educational Resources Information Center

    Muhoz, Romualdo; Quiles, Maria J.

    2003-01-01

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

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

    ERIC Educational Resources Information Center

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

    2005-01-01

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

  9. Organization of transmembrane helices in photosystem II: comparison of plants and cyanobacteria.

    PubMed Central

    Barber, J; Nield, J

    2002-01-01

    Electron microscopy and X-ray crystallography are revealing the structure of photosystem II. Electron crystallography has yielded a 3D structure at sufficient resolution to identify subunit positioning and transmembrane organization of the reaction-centre core complex of spinach. Single-particle analyses are providing 3D structures of photosystem II-light-harvesting complex II supercomplexes that can be used to incorporate high-resolution structural data emerging from electron and X-ray crystallography. The positions of the chlorins and metal centres within photosystem II are now available. It can be concluded that photosystem II is a dimeric complex with the transmembrane helices of CP47/D2 proteins related to those of the CP43/D1 proteins by a twofold axis within each monomer. Further, both electron microscopy and X-ray analyses show that P(680) is not a 'special pair' and that cytochrome b559 is located on the D2 side of the reaction centres some distance from P(680). However, although comparison of the electron microscopy and X-ray models for spinach and Synechococcus elongatus show considerable similarities, there seem to be differences in the number and positioning of some small subunits. PMID:12437871

  10. Glutathione Facilitates Antibiotic Resistance and Photosystem I Stability during Exposure to Gentamicin in Cyanobacteria ▿

    PubMed Central

    Cameron, Jeffrey C.; Pakrasi, Himadri B.

    2011-01-01

    Understanding mechanisms of antibiotic resistance is important to the fields of biology and medicine. We find that glutathione contributes to antibiotic resistance in the cyanobacterium Synechocystis sp. PCC 6803. Our results also suggest that glutathione protects photosystem I from oxidative damage resulting from growth in the presence of gentamicin. PMID:21460113

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

    PubMed

    Jennings, Robert C; Zucchelli, Giuseppe

    2014-01-01

    We examine ergodicity and configurational entropy for a dilute pigment solution and for a suspension of plant photosystem particles in which both ground and excited state pigments are present. It is concluded that the pigment solution, due to the extreme brevity of the excited state lifetime, is non-ergodic and the configurational entropy approaches zero. Conversely, due to the rapid energy transfer among pigments, each photosystem is ergodic and the configurational entropy is positive. This decreases the free energy of the single photosystem pigment array by a small amount. On the other hand, the suspension of photosystems is non-ergodic and the configurational entropy approaches zero. The overall configurational entropy which, in principle, includes contributions from both the single excited photosystems and the suspension which contains excited photosystems, also approaches zero. Thus the configurational entropy upon photon absorption by either a pigment solution or a suspension of photosystem particles is approximately zero. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Arctic Micromonas uses protein pools and non-photochemical quenching to cope with temperature restrictions on Photosystem II protein turnover.

    PubMed

    Ni, Guangyan; Zimbalatti, Gabrielle; Murphy, Cole D; Barnett, Audrey B; Arsenault, Christopher M; Li, Gang; Cockshutt, Amanda M; Campbell, Douglas A

    2017-02-01

    Micromonas strains of small prasinophyte green algae are found throughout the world's oceans, exploiting widely different niches. We grew arctic and temperate strains of Micromonas and compared their susceptibilities to photoinactivation of Photosystem II, their counteracting Photosystem II repair capacities, their Photosystem II content, and their induction and relaxation of non-photochemical quenching. In the arctic strain Micromonas NCMA 2099, the cellular content of active Photosystem II represents only about 50 % of total Photosystem II protein, as a slow rate constant for clearance of PsbA protein limits instantaneous repair. In contrast, the temperate strain NCMA 1646 shows a faster clearance of PsbA protein which allows it to maintain active Photosystem II content equivalent to total Photosystem II protein. Under growth at 2 °C, the arctic Micromonas maintains a constitutive induction of xanthophyll deepoxidation, shown by second-derivative whole-cell spectra, which supports strong induction of non-photochemical quenching under low to moderate light, even if xanthophyll cycling is blocked. This non-photochemical quenching, however, relaxes during subsequent darkness with kinetics nearly comparable to the temperate Micromonas NCMA 1646, thereby limiting the opportunity cost of sustained downregulation of PSII function after a decrease in light.

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

    PubMed

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

    2015-09-01

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

  14. 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.

  15. 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.

  16. Cis-by-Trans Regulatory Divergence Causes the Asymmetric Lethal Effects of an Ancestral Hybrid Incompatibility Gene

    PubMed Central

    Maheshwari, Shamoni; Barbash, Daniel A.

    2012-01-01

    The Dobzhansky and Muller (D-M) model explains the evolution of hybrid incompatibility (HI) through the interaction between lineage-specific derived alleles at two or more loci. In agreement with the expectation that HI results from functional divergence, many protein-coding genes that contribute to incompatibilities between species show signatures of adaptive evolution, including Lhr, which encodes a heterochromatin protein whose amino acid sequence has diverged extensively between Drosophila melanogaster and D. simulans by natural selection. The lethality of D. melanogaster/D. simulans F1 hybrid sons is rescued by removing D. simulans Lhr, but not D. melanogaster Lhr, suggesting that the lethal effect results from adaptive evolution in the D. simulans lineage. It has been proposed that adaptive protein divergence in Lhr reflects antagonistic coevolution with species-specific heterochromatin sequences and that defects in LHR protein localization cause hybrid lethality. Here we present surprising results that are inconsistent with this coding-sequence-based model. Using Lhr transgenes expressed under native conditions, we find no evidence that LHR localization differs between D. melanogaster and D. simulans, nor do we find evidence that it mislocalizes in their interspecific hybrids. Rather, we demonstrate that Lhr orthologs are differentially expressed in the hybrid background, with the levels of D. simulans Lhr double that of D. melanogaster Lhr. We further show that this asymmetric expression is caused by cis-by-trans regulatory divergence of Lhr. Therefore, the non-equivalent hybrid lethal effects of Lhr orthologs can be explained by asymmetric expression of a molecular function that is shared by both orthologs and thus was presumably inherited from the ancestral allele of Lhr. We present a model whereby hybrid lethality occurs by the interaction between evolutionarily ancestral and derived alleles. PMID:22457639

  17. The physiological links of the increased photosystem II activity in moderately desiccated Porphyra haitanensis (Bangiales, Rhodophyta) to the cyclic electron flow during desiccation and re-hydration.

    PubMed

    Gao, Shan; Niu, Jianfeng; Chen, Weizhou; Wang, Guangce; Xie, Xiujun; Pan, Guanghua; Gu, Wenhui; Zhu, Daling

    2013-09-01

    Photosynthetic electron flow changed considerably during desiccation and re-hydration of the intertidal macroalgae Porphyra haitanensis. Activities of both photosystem (PSI) and photosystem (PSII) increased significantly at moderate desiccation levels. Whereas PSII activity was abolished at an absolute water content (AWC) <24 %, PSI remained active with progressive decreases in AWC to values as low as 16 %. This result suggested that cyclic electron flow around PSI was still active after inactivation of linear electron flow following severe desiccation. Moreover, the PSI activity was restored more rapidly than that of PSII upon re-hydration. Pretreatment of the blades with 3-(3',4'-dichlorophenyl)-1,1-dimethylurea (DCMU) suppressed PSII activity following desiccation to an AWC of ~16 % AWC. Cyclic electron flow around PSI decreased markedly in blades pretreated with DCMU than in blades without pretreatment of DCMU during re-hydration in seawater containing DCMU. All results suggested that the activity of PSII under desiccation conditions plays an important role in the operation of cyclic electron flow during desiccation and its recovery during re-hydration. Therefore, we proposed the PSII activity during desiccation could eventually lead to the accumulation of NADPH, which could serve as electron donor for P700(+) and promote its recovery during re-hydration, thereby favoring the operation of cyclic electron flow.

  18. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates.

    PubMed

    Nakatani, Yoichiro; Takeda, Hiroyuki; Kohara, Yuji; Morishita, Shinichi

    2007-09-01

    Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as the two rounds of whole-genome duplications (2R WGD) affected evolutionary complexity and novelty in vertebrates. Reconstructing the ancestral vertebrate genome is highly nontrivial because of the difficulty in identifying traces originating from the 2R WGD. To resolve this problem, we developed a novel method capable of pinning down remains of the 2R WGD in the human and medaka fish genomes using invertebrate tunicate and sea urchin genes to define ohnologs, i.e., paralogs produced by the 2R WGD. We validated the reconstruction using the chicken genome, which was not considered in the reconstruction step, and observed that many ancestral proto-chromosomes were retained in the chicken genome and had one-to-one correspondence to chicken microchromosomes, thereby confirming the reconstructed ancestral genomes. Our reconstruction revealed a contrast between the slow karyotype evolution after the second WGD and the rapid, lineage-specific genome reorganizations that occurred in the ancestral lineages of major taxonomic groups such as teleost fishes, amphibians, reptiles, and marsupials.

  19. 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.

  20. Patterns and mechanisms of ancestral histone protein inheritance in budding yeast.

    PubMed

    Radman-Livaja, Marta; Verzijlbergen, Kitty F; Weiner, Assaf; van Welsem, Tibor; Friedman, Nir; Rando, Oliver J; van Leeuwen, Fred

    2011-06-01

    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.

  1. Fish 'tails' result from outgrowth and reduction of two separate ancestral tails.

    PubMed

    Sallan, Lauren

    2016-12-05

    The symmetrical, flexible teleost fish 'tail' has been a prime example of recapitulation - evolutionary change (phylogeny) mirrored in development (ontogeny). Paleozoic ray-finned fishes (Actinopterygii), relatives of teleosts, exhibited ancestral scale-covered tails curved over their caudal fins. For over 150 years, this arrangement was thought to be retained in teleost larva and overgrown, mirroring an ancestral transformation series. New ontogenetic data for the 350-million-year-old teleost relative Aetheretmon overturns this long-held hypothesis. The ancestral state consists of two outgrowths with distinct organizers and growth trajectories; a lower median fin turned caudal fin, and an upper vertebrae-bearing tail, equivalent to that of tetrapods. These two tails appear at a shared developmental stage in Aetheretmon, teleosts and all living actinopterygians. Ontogeny does not recapitulate phylogeny; instead, differential outgrowth determines final morphology. In Aetheretmon and other Paleozoic fishes, the vertebrae-bearing tail continues to grow beyond the caudal fin. In teleosts, and some others, a stunted tail is eclipsed by the upward-expanding caudal fin, rendering a once ventral body margin as the terminus. The double tail likely reflects the ancestral state for bony fishes. Many tetrapods and non-teleost actinopterygians have undergone body elongation through tail outgrowth extension, by mechanisms likely shared with distal limbs. Teleosts have gone to the other extreme; losing tail outgrowth for functional reasons. Recognition of the tail as a limb-like outgrowth has important implications for the evolution of vertebrate form.

  2. Inferring ancestral distribution area and survival vegetation of Caragana (Fabaceae) in Tertiary

    Treesearch

    Mingli Zhang; Juanjuan Xue; Qiang Zhang; Stewart C. Sanderson

    2015-01-01

    Caragana, a leguminous genus mainly restricted to temperate Central and East Asia, occurs in arid, semiarid, and humid belts, and has forest, grassland, and desert ecotypes. Based on the previous molecular phylogenetic tree and dating, biogeographical analyses of extant species area and ecotype were conducted by means of four ancestral optimization approaches: S-DIVA,...

  3. 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…

  4. 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.

  5. Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes

    PubMed Central

    Wu, Yonghua; Wang, Haifeng; Hadly, Elizabeth A.

    2017-01-01

    Nocturnality is a key evolutionary innovation of mammals that enables mammals to occupy relatively empty nocturnal niches. Invasion of ancestral mammals into nocturnality has long been inferred from the phylogenetic relationships of crown Mammalia, which is primarily nocturnal, and crown Reptilia, which is primarily diurnal, although molecular evidence for this is lacking. Here we used phylogenetic analyses of the vision genes involved in the phototransduction pathway to predict the diel activity patterns of ancestral mammals and reptiles. Our results demonstrated that the common ancestor of the extant Mammalia was dominated by positive selection for dim-light vision, supporting the predominate nocturnality of the ancestral mammals. Further analyses showed that the nocturnality of the ancestral mammals was probably derived from the predominate diurnality of the ancestral amniotes, which featured strong positive selection for bright-light vision. Like the ancestral amniotes, the common ancestor of the extant reptiles and various taxa in Squamata, one of the main competitors of the temporal niches of the ancestral mammals, were found to be predominate diurnality as well. Despite this relatively apparent temporal niche partitioning between ancestral mammals and the relevant reptiles, our results suggested partial overlap of their temporal niches during crepuscular periods. PMID:28425474

  6. RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees.

    PubMed

    Kratsch, Christina; McHardy, Alice C

    2014-09-01

    Ancestral character state reconstruction describes a set of techniques for estimating phenotypic or genetic features of species or related individuals that are the predecessors of those present today. Such reconstructions can reach into the distant past and can provide insights into the history of a population or a set of species when fossil data are not available, or they can be used to test evolutionary hypotheses, e.g. on the co-evolution of traits. Typical methods for ancestral character state reconstruction of continuous characters consider the phylogeny of the underlying data and estimate the ancestral process along the branches of the tree. They usually assume a Brownian motion model of character evolution or extensions thereof, requiring specific assumptions on the rate of phenotypic evolution. We suggest using ridge regression to infer rates for each branch of the tree and the ancestral values at each inner node. We performed extensive simulations to evaluate the performance of this method and have shown that the accuracy of its reconstructed ancestral values is competitive to reconstructions using other state-of-the-art software. Using a hierarchical clustering of gene mutation profiles from an ovarian cancer dataset, we demonstrate the use of the method as a feature selection tool. The algorithm described here is implemented in C++ as a stand-alone program, and the source code is freely available at http://algbio.cs.uni-duesseldorf.de/software/RidgeRace.tar.gz. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  7. 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

  8. Inhibition of the oxygen-evolving complex of photosystem II and depletion of extrinsic polypeptides by nickel.

    PubMed

    Boisvert, Steve; Joly, David; Leclerc, Sébastien; Govindachary, Sridharan; Harnois, Johanne; Carpentier, Robert

    2007-12-01

    The toxic effect of Ni(2+) on photosynthetic electron transport was studied in a photosystem II submembrane fraction. It was shown that Ni(2+) strongly inhibits oxygen evolution in the millimolar range of concentration. The inhibition was insensitive to NaCl but significantly decreased in the presence of CaCl(2). Maximal chlorophyll fluorescence, together with variable fluorescence, maximal quantum yield of photosystem II, and flash-induced fluorescence decays were all significantly declined by Ni(2+). Further, the extrinsic polypeptides of 16 and 24 kDa associated with the oxygen-evolving complex of photosystem II were depleted following Ni(2+) treatment. It was deduced that interaction of Ni(2+) with these polypeptides caused a conformational change that induced their release together with Ca(2+) from the oxygen-evolving complex of photosystem II with consequent inhibition of the electron transport activity.

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

    SciTech Connect

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

    1995-09-01

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

  10. The Vitamin B12-Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters

    PubMed Central

    Fang, Mingxu

    2017-01-01

    ABSTRACT Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental conditions often through the control of transcription. One of the main transcription factors involved in controlling expression of the Rhodobacter capsulatus photosystem is CrtJ, which functions as an aerobic repressor of photosystem genes. Recently, we reported that a vitamin B12 binding antirepressor of CrtJ called AerR is required for anaerobic expression of the photosystem. However, the mechanism whereby AerR regulates CrtJ activity is unclear. In this study, we used a combination of next-generation sequencing and biochemical methods to globally identify genes under control of CrtJ and the role of AerR in controlling this regulation. Our results indicate that CrtJ has a much larger regulon than previously known, with a surprising regulatory function under both aerobic and anaerobic photosynthetic growth conditions. A combination of in vivo chromatin immunoprecipitation-DNA sequencing (ChIP-seq) and ChIP-seq and exonuclease digestion (ChIP-exo) studies and in vitro biochemical studies demonstrate that AerR forms a 1:2 complex with CrtJ (AerR-CrtJ2) and that this complex binds to many promoters under photosynthetic conditions. The results of in vitro and in vivo DNA binding studies indicate that AerR-CrtJ2 anaerobically forms an extended interaction with the bacteriochlorophyll bchC promoter to relieve repression by CrtJ. This is contrasted by aerobic growth conditions where CrtJ alone functions as an aerobic repressor of bchC expression. These results indicate that the DNA binding activity of CrtJ is modified by interacting with AerR in a redox-regulated manner and that this interaction alters CrtJ’s function. PMID:28325764

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

    PubMed

    Curnoe, D; Thorne, A

    2003-01-01

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

  12. Charge separation and energy transfer in the photosystem II core complex studied by femtosecond midinfrared spectroscopy.

    PubMed

    Pawlowicz, N P; Groot, M-L; van Stokkum, I H M; Breton, J; van Grondelle, R

    2007-10-15

    The core of photosystem II (PSII) of green plants contains the reaction center (RC) proteins D1D2-cytb559 and two core antennas CP43 and CP47. We have used time-resolved visible pump/midinfrared probe spectroscopy in the region between 1600 and 1800 cm(-1) to study the energy transfer and charge separation events within PSII cores. The absorption difference spectra in the region of the keto and ester chlorophyll modes show spectral evolution with time constants of 3 ps, 27 ps, 200 ps, and 2 ns. Comparison of infrared (IR) difference spectra obtained for the isolated antennas CP43 and CP47 and the D1D2-RC with those measured for the PSII core allowed us to identify the features specific for each of the PSII core components. From the presence of the CP43 and CP47 specific features in the spectra up to time delays of 20-30 ps, we conclude that the main part of the energy transfer from the antennas to the RC occurs on this timescale. Direct excitation of the pigments in the RC evolution associated difference spectra to radical pair formation of PD1+PheoD1- on the same timescale as multi-excitation annihilation and excited state equilibration within the antennas CP43 and CP47, which occur within approximately 1-3 ps. The formation of the earlier radical pair ChlD1+PheoD1-, as identified in isolated D1D2 complexes with time-resolved mid-IR spectroscopy is not observed in the current data, probably because of its relatively low concentration. Relaxation of the state PD1+PheoD1-, caused by a drop in free energy, occurs in 200 ps in closed cores. We conclude that the kinetic model proposed earlier for the energy and electron transfer dynamics within the D1D2-RC, plus two slowly energy-transferring antennas C43 and CP47 explain the complex excited state and charge separation dynamics in the PSII core very well. We further show that the time-resolved IR-difference spectrum of PD1+PheoD1- as observed in PSII cores is virtually identical to that observed in the isolated D1D2-RC

  13. Long-Wavelength Limit of Photochemical Energy Conversion in Photosystem I

    PubMed Central

    2014-01-01

    In Photosystem I (PS I) long-wavelength chlorophylls (LWC) of the core antenna are known to extend the spectral region up to 750 nm for absorbance of light that drives photochemistry. Here we present clear evidence that even far-red light with wavelengths beyond 800 nm, clearly outside the LWC absorption bands, can still induce photochemical charge separation in PS I throughout the full temperature range from 295 to 5 K. At room temperature, the photoaccumulation of P700+• was followed by the absorbance increase at 826 nm. At low temperatures (T < 100 K), the formation of P700+•FA/B–• was monitored by the characteristic EPR signals of P700+• and FA/B–• and by the characteristic light-minus-dark absorbance difference spectrum in the QY region. P700 oxidation was observed upon selective excitation at 754, 785, and 808 nm, using monomeric and trimeric PS I core complexes of Thermosynechococcus elongatus and Arthrospira platensis, which differ in the amount of LWC. The results show that the LWC cannot be responsible for the long-wavelength excitation-induced charge separation at low temperatures, where thermal uphill energy transfer is frozen out. Direct energy conversion of the excitation energy from the LWC to the primary radical pair, e.g., via a superexchange mechanism, is excluded, because no dependence on the content of LWC was observed. Therefore, it is concluded that electron transfer through PS I is induced by direct excitation of a proposed charge transfer (CT) state in the reaction center. A direct signature of this CT state is seen in absorbance spectra of concentrated PS I samples, which reveal a weak and featureless absorbance band extending beyond 800 nm, in addition to the well-known bands of LWC (C708, C719 and C740) in the range between 700 and 750 nm. The present findings suggest that nature can exploit CT states for extending the long wavelength limit in PSI even beyond that of LWC. Similar mechanisms may work in other photosynthetic

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

    SciTech Connect

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

    1991-05-01

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

  15. Thermostability of photosystem I trimers and monomers from the cyanobacterium Thermosynechococcus elongatus

    NASA Astrophysics Data System (ADS)

    Shubin, Vladimir V.; Terekhova, Irina V.; Bolychevtseva, Yulia V.; El-Mohsnawy, Eithar; Rögner, Matthias; Mäntele, Werner; Kopczak, Marta J.; Džafić, Enela

    2017-05-01

    The performance of solar energy conversion into alternative energy sources in artificial systems highly depends on the thermostability of photosystem I (PSI) complexes Terasaki et al. (2007), Iwuchukwu et al. (2010), Kothe et al. (2013) . To assess the thermostability of PSI complexes from the thermophilic cyanobacterium Thermosynechococcus elongatus heating induced perturbations on the level of secondary structure of the proteins were studied. Changes were monitored by Fourier transform infrared (FT-IR) spectra in the mid-IR region upon slow heating (1 °C per minute) of samples in D2O phosphate buffer (pD 7.4) from 20 °C to 100 °C. These spectra showed distinct changes in the Amide I region of PSI complexes as a function of the rising temperature. Absorbance at the Amide I maximum of PSI monomers (centered around 1653 cm- 1), gradually dropped in two temperature intervals, i.e. 60-75 and 80-90 °C. In contrast, absorbance at the Amide I maximum of PSI trimers (around 1656 cm- 1) dropped only in one temperature interval 80-95 °C. The thermal profile of the spectral shift of α-helices bands in the region 1656-1642 cm- 1 confirms the same two temperature intervals for PSI monomers and only one interval for trimers. Apparently, the observed absorbance changes at the Amide I maximum during heating of PSI monomers and trimers are caused by deformation and unfolding of α-helices. The absence of absorbance changes in the interval of 20-65 °C in PSI trimers is probably caused by a greater stability of protein secondary structure as compared to that in monomers. Upon heating above 80 °C a large part of α-helices both in trimers and monomers converts to unordered and aggregated structures. Spectral changes of PSI trimers and monomers heated up to 100 °C are irreversible due to protein denaturation and non-specific aggregation of complexes leading to new absorption bands at 1618-1620 cm- 1. We propose that monomers shield the denaturation sensitive sides at the

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

    NASA Technical Reports Server (NTRS)

    Miller, Scott R.; Bebout, Brad M.

    2004-01-01

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

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

    SciTech Connect

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

    1986-05-01

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

  18. Antimycin A-like molecules inhibit cyclic electron transport around photosystem I in ruptured chloroplasts.

    PubMed

    Taira, Yoshichika; Okegawa, Yuki; Sugimoto, Kazuhiko; Abe, Masato; Miyoshi, Hideto; Shikanai, Toshiharu

    2013-01-01

    Antimycin A3 (AA) is used as an inhibitor of cyclic electron transport around photosystem I. However, the high concentrations of AA that are needed for inhibition have secondary effects, even in chloroplasts. Here, we screened for chemicals that inhibited ferredoxin-dependent plastoquinone reduction in ruptured chloroplasts at lower concentrations than those required for AA. We identified two AA-like compounds: AAL1 and AAL2. AAL1 likely shares an inhibitory site with AA, most probably in the PGR5-PGRL1 protein complex, and enhances O2 evolution in photosystem II, most likely via an uncoupler-like effect. AAL1 and AAL2 are unlikely to penetrate intact leaves. In ruptured chloroplasts, AALs are superior to AA as inhibitors of cyclic electron transport.

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

    SciTech Connect

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

    2010-08-31

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

  20. Expected and actual adverse drug-drug interactions in elderly patients accessing the emergency department: data from the ANCESTRAL-ED study.

    PubMed

    Marino, A; Capogrosso-Sansone, A; Tuccori, M; Bini, G; Calsolaro, V; Mantarro, S; Convertino, I; Pasqualetti, G; Orsitto, E; Santini, M; Monzani, F; Blandizzi, C

    2016-12-01

    This study was aimed at evaluating the frequency and describing the adverse drug-drug interactions (DDIs) recorded among elderly patients accessing the emergency department (ED). Patients aged ≥65 years, accessing the ED of Pisa University Hospital (Italy) from 1 January 2015 to 31 December 2015 within the ANCESTRAL-ED program, were included in this study. 'Expected' DDIs were assessed using Thomson Micromedex®. Each ED admission (discharge diagnosis) consistent with the signs and symptoms of an expected DDI for each patient was classified as an 'actual' DDI. Throughout the study period, 3473 patients (3812 ED admissions, 58% females, mean age: 80.3) were recorded. The total number of expected DDIs was 12,578 (67 contraindicated; 3334 major; 8878 moderate; 299 minor) detected in 2147 (62%) patients. Overall 464 expected DDIs were found to be consistent with the ED admission in 194 patients (representing 9% of patients with expected DDIs). More than one half of elderly patients admitted to ED presented at least one expected DDI at the time of ED presentation. However, 9% of the expected DDIs were identified as actual DDIs, based on the consistency of the expected event with the ED discharge diagnosis.

  1. The Acceptor Side of Photosystem II Is the Initial Target of Nitrite Stress in Synechocystis sp. Strain PCC 6803.

    PubMed

    Zhang, Xin; Ma, Fei; Zhu, Xi; Zhu, Junying; Rong, Junfeng; Zhan, Jiao; Chen, Hui; He, Chenliu; Wang, Qiang

    2017-02-01

    Nitrite, a common form of inorganic nitrogen (N), can be used as a nitrogen source through N assimilation. However, high levels of nitrite depress photosynthesis in various organisms. In this study, we investigated which components of the photosynthetic electron transfer chain are targeted by nitrite stress in Synechocystis sp. strain PCC 6803 cells. Measurements of whole-chain and photosystem II (PSII)-mediated electron transport activities revealed that high levels of nitrite primarily impair electron flow in PSII. Changes in PSII activity in response to nitrite stress occurred in two distinct phases. During the first phase, which occurred in the first 3 h of nitrite treatment, electron transfer from the primary quinone acceptor (QA) to the secondary quinone acceptor (QB) was retarded, as indicated by chlorophyll (Chl) a fluorescence induction, S-state distribution, and QA(-) reoxidation tests. In the second phase, which occurred after 6 h of nitrite exposure, the reaction center was inactivated and the donor side of photosystem II was inhibited, as revealed by changes in Chl fluorescence parameters and thermoluminescence and by immunoblot analysis. Our data suggest that nitrite stress is highly damaging to PSII and disrupts PSII activity by a stepwise mechanism in which the acceptor side is the initial target. IMPORTANCE In our previous studies, an alga-based technology was proposed to fix the large amounts of nitrite that are released from NOX-rich flue gases and proved to be a promising industrial strategy for flue gas NOX bioremediation (W. Chen et al., Environ Sci Technol 50:1620-1627, 2016, https://doi.org/10.1021/acs.est.5b04696; X. Zhang et al., Environ Sci Technol 48:10497-10504, 2014, https://doi.org/10.1021/es5013824). However, the toxic effects of high concentrations of nitrite on algal cells remain obscure. The analysis of growth rates, photochemistry, and protein profiles in our study provides important evidence that the inhibition by nitrite occurs

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

    PubMed

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

    2016-01-01

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

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

    DOE PAGES

    Sierra, Raymond G.; Gati, Cornelius; Laksmono, Hartawan; ...

    2015-11-30

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

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

    SciTech Connect

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

    2015-11-30

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

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

    USGS Publications Warehouse

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

    2008-01-01

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

  6. The role of the individual Lhcas in photosystem I excitation energy trapping.

    PubMed

    Wientjes, Emilie; van Stokkum, Ivo H M; van Amerongen, Herbert; Croce, Roberta

    2011-08-03

    In this work, we have investigated the role of the individual antenna complexes and of the low-energy forms in excitation energy transfer and trapping in Photosystem I of higher plants. To this aim, a series of Photosystem I (sub)complexes with different antenna size/composition/absorption have been studied by picosecond fluorescence spectroscopy. The data show that Lhca3 and Lhca4, which harbor the most red forms, have similar emission spectra (λ(max) = 715-720 nm) and transfer excitation energy to the core with a relative slow rate of ∼25/ns. Differently, the energy transfer from Lhca1 and Lhca2, the "blue" antenna complexes, occurs about four times faster. In contrast to what is often assumed, it is shown that energy transfer from the Lhca1/4 and the Lhca2/3 dimer to the core occurs on a faster timescale than energy equilibration within these dimers. Furthermore, it is shown that all four monomers contribute almost equally to the transfer to the core and that the red forms slow down the overall trapping rate by about two times. Combining all the data allows the construction of a comprehensive picture of the excitation-energy transfer routes and rates in Photosystem I.

  7. Ultrafast infrared observation of exciton equilibration from oriented single crystals of photosystem II

    PubMed Central

    Kaucikas, Marius; Maghlaoui, Karim; Barber, Jim; Renger, Thomas; van Thor, Jasper J.

    2016-01-01

    In oxygenic photosynthesis, two photosystems work in series. Each of them contains a reaction centre that is surrounded by light-harvesting antennae, which absorb the light and transfer the excitation energy to the reaction centre where electron transfer reactions are driven. Here we report a critical test for two contrasting models of light harvesting by photosystem II cores, known as the trap-limited and the transfer-to-the trap-limited model. Oriented single crystals of photosystem II core complexes of Synechococcus elongatus are excited by polarized visible light and the transient absorption is probed with polarized light in the infrared. The dichroic amplitudes resulting from photoselection are maintained on the 60 ps timescale that corresponds to the dominant energy transfer process providing compelling evidence for the transfer-to-the-trap limitation of the overall light-harvesting process. This finding has functional implications for the quenching of excited states allowing plants to survive under high light intensities. PMID:28008915

  8. Substrate–water exchange in photosystem II is arrested before dioxygen formation

    PubMed Central

    Nilsson, Håkan; Rappaport, Fabrice; Boussac, Alain; Messinger, Johannes

    2014-01-01

    Light-driven oxidation of water into dioxygen, catalysed by the oxygen-evolving complex (OEC) in photosystem II, is essential for life on Earth and provides the blueprint for devices for producing fuel from sunlight. Although the structure of the OEC is known at atomic level for its dark-stable state, the mechanism by which water is oxidized remains unsettled. Important mechanistic information was gained in the past two decades by mass spectrometric studies of the H218O/H216O substrate–water exchange in the four (semi) stable redox states of the OEC. However, until now such data were not attainable in the transient states formed immediately before the O–O bond formation. Using modified photosystem II complexes displaying up to 40-fold slower O2 production rates, we show here that in the transient state the substrate–water exchange is dramatically slowed as compared with the earlier S states. This further constrains the possible sites for substrate–water binding in photosystem II. PMID:24993602

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

    PubMed

    Steinbach, Gábor; Schubert, Félix; Kaňa, Radek

    2015-11-01

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

  10. Dipolar Photosystems: Engineering Oriented Push-Pull Components into Double- and Triple-Channel Surface Architectures.

    PubMed

    Bolag, Altan; Sakai, Naomi; Matile, Stefan

    2016-06-20

    Push-pull aromatics are not popular as optoelectronic materials because their supramolecular organization is difficult to control. However, recent progress with synthetic methods has suggested that the directional integration of push-pull components into multicomponent photosystems should become possible. In this study, we report the design, synthesis, and evaluation of double- or triple-channel architectures that contain π stacks with push-pull components in parallel or mixed orientation. Moreover, the parallel push-pull stacks were uniformly oriented with regard to co-axial stacks, either with inward or outward oriented push-pull dipoles. Hole-transporting (p) aminoperylenemonoimides (APIs) and aminonaphthalimides (ANIs) are explored for ordered push-pull stacks. For the co-axial electron-transporting (n) stacks, naphthalenediimides (NDIs) are used. In double-channel photosystems, mixed push-pull stacks are overall less active than parallel push-pull stacks. The orientation of the parallel push-pull stacks with regard to the co-axial NDI stacks has little influence on activity. In triple-channel photosystems, outward-directed dipoles in bridging stacks between peripheral p and central n channels show higher activity than inward-directed dipolar stacks. Higher activities in response to direct irradiation of outward-directed parallel stacks reveal the occurrence of quite remarkable optical gating.

  11. Photoelectric response generated under non-heme iron reduction on the photosystem II acceptor side.

    PubMed

    Mamedov, M D; Beshta, O E; Shutilova, N I; Semenov, A Y; Samuilov, V D

    2000-06-01

    Proteoliposomes containing oxygen-evolving particles of Photosystem II and associated with a planar phospholipid membrane generate a transmembrane electric potential difference (DeltaPsi) induced by a laser flash. With direct electrometrical technique, it was shown that the direction of the electrical field ("minus" inside the proteoliposome) corresponds to acceptor side of the Photosystem II complex facing inside and donor side facing outside of the liposomes. In addition to the fast phase (tau < 0.1 microsec) of the DeltaPsi generation due to electron transfer between YZ of the water-oxidizing complex and the primary plastoquinone QA, a phase with tau approximately 120 microsec and maximum amplitude approximately 30% of the amplitude of the fast phase was observed under the first flash in proteoliposomes containing potassium ferricyanide, which is known as an oxidant of the non-heme iron (Fenh) on the acceptor side of Photosystem II. This additional phase was absent under the second laser flash but was completely restored after 5 min dark adaptation. The phase of the photoelectric response with tau approximately 120 microsec is probably due to electron transfer from QA to Fenh(III) and likely includes a component related to H+ transfer.

  12. Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II.

    PubMed

    Narzi, Daniele; Coccia, Emanuele; Manzoli, Marco; Guidoni, Leonardo

    2017-10-01

    Light harvesting from the Sun by antenna complexes surrounding the reaction center of Photosystem II represents the first step of the natural oxygenic photosynthesis performed by plants, algae and cyanobacteria. The excitation energy derived from the sunlight is absorbed by the chlorophylls of the antenna and subsequently conveyed to the reaction center of Photosystem II through resonant energy transfer mechanisms. In the special pair of chlorophylls of the reaction center the charge separation occurs, eventually leading to the oxidation of water molecules into protons, electrons and molecular oxygen. The adsorption properties of the antenna chlorophylls are ad hoc modulated by the protein environment to guarantee fast energy transfer and minimize side and back reactions. At the same time these properties are influenced by the molecular fluctuations occurring at physiological temperature. In the present work, combining classical molecular dynamics simulations with the Charge Density Coupling method, we estimated the impact of the thermal fluctuations on the site energy shift of the chlorophylls embedded in the Photosystem II complex. Our results show how the effect of the molecular fluctuations is not homogeneous throughout the complex, although the symmetry of the homodimer is maintained. Many peripheral chromophores undergo fluctuations larger then 10kJ/mol around the average values. Possible physiological roles of such fluctuations are discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  14. Molecular configuration of xanthophyll cycle carotenoids in photosystem II antenna complexes.

    PubMed

    Ruban, Alexander V; Pascal, Andy; Lee, Pamela J; Robert, Bruno; Horton, Peter

    2002-11-08

    The molecular configuration of the xanthophyll cycle carotenoids, violaxanthin and zeaxanthin, was studied in various isolated photosystem II antenna components in comparison to intact photosystem II membranes using resonance Raman combined with low-temperature absorption spectroscopy. The molecular configurations of zeaxanthin and violaxanthin in thylakoids and isolated photosystem II membranes were found to be the same within an isolated oligomeric LHCII antenna, confirming our recent conclusion that these molecules are not freely located in photosynthetic membranes (Ruban, A. V., Pascal, A. A., Robert, B., and Horton, P. (2001) J. Biol. Chem. 276, 24862-24870). In contrast, xanthophyll cycle carotenoids bound to LHCII trimers had largely lost their in vivo configuration, suggesting their partial dissociation from the binding locus. Violaxanthin and zeaxanthin associated with the minor antenna complexes, CP26 and CP29, were also found to be in a relaxed configuration, similar to that of free pigment. The origin of the characteristic C-H vibrational bands of violaxanthin and zeaxanthin in vivo is discussed by comparison with those of neoxanthin and lutein in oligomeric and trimeric LHCII respectively.

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

    PubMed

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

    2016-06-02

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  18. Far-red light-regulated efficient energy transfer from phycobilisomes to photosystem I in the red microalga Galdieria sulphuraria and photosystems-related heterogeneity of phycobilisome population.

    PubMed

    Stadnichuk, Igor N; Bulychev, Alexander A; Lukashev, Evgeni P; Sinetova, Mariya P; Khristin, Mikhail S; Johnson, Matthew P; Ruban, Alexander V

    2011-02-01

    Phycobilisomes (PBS) are the major photosynthetic antenna complexes in cyanobacteria and red algae. In the red microalga Galdieria sulphuraria, action spectra measured separately for photosynthetic activities of photosystem I (PSI) and photosystem II (PSII) demonstrate that PBS fraction attributed to PSI is more sensitive to stress conditions and upon nitrogen starvation disappears from the cell earlier than the fraction of PBS coupled to PSII. Preillumination of the cells by actinic far-red light primarily absorbed by PSI caused an increase in the amplitude of the PBS low-temperature fluorescence emission that was accompanied by the decrease in PBS region of the PSI 77 K fluorescence excitation spectrum. Under the same conditions, fluorescence excitation spectrum of PSII remained unchanged. The amplitude of P700 photooxidation in PBS-absorbed light at physiological temperature was found to match the fluorescence changes observed at 77 K. The far-red light adaptations were reversible within 2-5min. It is suggested that the short-term fluorescence alterations observed in far-red light are triggered by the redox state of P700 and correspond to the temporal detachment of the PBS antenna from the core complexes of PSI. Furthermore, the absence of any change in the 77 K fluorescence excitation cross-section of PSII suggests that light energy transfer from PBS to PSI in G. sulphuraria is direct and does not occur through PSII. Finally, a novel photoprotective role of PBS in red algae is discussed.

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

    PubMed Central

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

    1995-01-01

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

  20. Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets.

    PubMed

    Alperovitch-Lavy, Ariella; Sharon, Itai; Rohwer, Forest; Aro, Eva-Mari; Glaser, Fabian; Milo, Ron; Nelson, Nathan; Béjà, Oded

    2011-01-01

    Cyanobacteria play a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Genes encoding the photosystem-II (PSII) reaction centre are found in many cyanophage genomes, and it was suggested that the horizontal transfer of these genes might be involved in increasing phage fitness. Recently, evidence for the existence of phages carrying Photosystem-I (PSI) genes was also reported. Here, using a combination of different marine metagenomic datasets and a unique crossing of the datasets, we now describe the finding of phages that, as in plants and cyanobacteria, contain both PSII and PSI genes. In addition, these phages also contain NADH dehydrogenase genes. The presence of modified PSII and PSI genes in the same viral entities in combination with electron transfer proteins like NAD(P)H dehydrogenase (NDH-1) strongly points to a role in perturbation of the cyanobacterial host photosynthetic electron flow. We therefore suggest that, depending on the physiological condition of the infected cyanobacterial host, the viruses may use different options to maximize survival. The modified PSI may alternate between functioning with PSII in linear electron transfer and contributing to the production of both NADPH and ATP or functioning independently of PSII in cyclic mode via the NDH-1 complex and thus producing only ATP.

  1. Design of new strategy for green algal photo-hydrogen production: spectral-selective photosystem I activation and photosystem II deactivation.

    PubMed

    Hoshino, Takanori; Johnson, Daniel J; Cuello, Joel L

    2012-09-01

    A new strategy in photosynthetic hydrogen (photo-H(2)) production from green algae was developed based on theory and successfully demonstrated. The new strategy applied a spectral-selective photosystem I (PSI) activating/photosystem II (PSII) deactivating radiation (or PSI light) that would drive a steady flow of electrons in the electron transport chain for delivery to hydrogenase for photo-H(2) production, but would reduce oxygen production through water photolysis below the respiratory oxygen consumption so that an anoxic condition would be maintained as required by hydrogenase. Implementing the strategy by using a PSI light (692 nm peak, 680-700 nm) on Chlamydomonas reinhardtii cells resulted in relatively sustained photo-H(2) production (total of 0.108 mL H(2)mg(-1)Chl, exceeding 0.066 mL H(2)mg(-1)Chl under white light). The strategy also proved successful and convenient in allowing cells to alternately switch between photo-H(2) production and a recovery period by simply turning on or off the PSI light. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. MET1 Is a Thylakoid-Associated TPR Protein Involved in Photosystem II Supercomplex Formation and Repair in Arabidopsis

    PubMed Central

    Bhuiyan, Nazmul H.; Friso, Giulia; Poliakov, Anton; Ponnala, Lalit

    2015-01-01

    Photosystem II (PSII) requires constant disassembly and reassembly to accommodate replacement of the D1 protein. Here, we characterize Arabidopsis thaliana MET1, a PSII assembly factor with PDZ and TPR domains. The maize (Zea mays) MET1 homolog is enriched in mesophyll chloroplasts compared with bundle sheath chloroplasts, and MET1 mRNA and protein levels increase during leaf development concomitant with the thylakoid machinery. MET1 is conserved in C3 and C4 plants and green algae but is not found in prokaryotes. Arabidopsis MET1 is a peripheral thylakoid protein enriched in stroma lamellae and is also present in grana. Split-ubiquitin assays and coimmunoprecipitations showed interaction of MET1 with stromal loops of PSII core components CP43 and CP47. From native gels, we inferred that MET1 associates with PSII subcomplexes formed during the PSII repair cycle. When grown under fluctuating light intensities, the Arabidopsis MET1 null mutant (met1) showed conditional reduced growth, near complete blockage in PSII supercomplex formation, and concomitant increase of unassembled CP43. Growth of met1 in high light resulted in loss of PSII supercomplexes and accelerated D1 degradation. We propose that MET1 functions as a CP43/CP47 chaperone on the stromal side of the membrane during PSII assembly and repair. This function is consistent with the observed differential MET1 accumulation across dimorphic maize chloroplasts. PMID:25587003

  3. Insights into substrate binding to the oxygen-evolving complex of photosystem II from ammonia inhibition studies.

    PubMed

    Vinyard, David J; Brudvig, Gary W

    2015-01-20

    Water oxidation in Photosystem II occurs at the oxygen-evolving complex (OEC), which cycles through distinct intermediates, S0-S4. The inhibitor ammonia selectively binds to the S2 state at an unresolved site that is not competitive with substrate water. By monitoring the yields of flash-induced oxygen production, we show that ammonia decreases the net efficiency of OEC turnover and slows the decay kinetics of S2 to S1. The temperature dependence of biphasic S2 decay kinetics provides activation energies that do not vary in control and ammonia conditions. We interpret our data in the broader context of previous studies by introducing a kinetic model for both the formation and decay of ammonia-bound S2. The model predicts ammonia binds to S2 rapidly (t1/2 = 1 ms) with a large equilibrium constant. This finding implies that ammonia decreases the reduction potential of S2 by at least 2.7 kcal mol(-1) (>120 mV), which is not consistent with ammonia substitution of a terminal water ligand of Mn(IV). Instead, these data support the proposal that ammonia binds as a bridging ligand between two Mn atoms. Implications for the mechanism of O-O bond formation are discussed.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-01-01

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

  6. Evidence on the Formation of Singlet Oxygen in the Donor Side Photoinhibition of Photosystem II: EPR Spin-Trapping Study

    PubMed Central

    Yadav, Deepak Kumar; Pospíšil, Pavel

    2012-01-01

    When photosystem II (PSII) is exposed to excess light, singlet oxygen (1O2) formed by the interaction of molecular oxygen with triplet chlorophyll. Triplet chlorophyll is formed by the charge recombination of triplet radical pair 3[P680•+Pheo•−] in the acceptor-side photoinhibition of PSII. Here, we provide evidence on the formation of 1O2 in the donor side photoinhibition of PSII. Light-induced 1O2 production in Tris-treated PSII membranes was studied by electron paramagnetic resonance (EPR) spin-trapping spectroscopy, as monitored by TEMPONE EPR signal. Light-induced formation of carbon-centered radicals (R•) was observed by POBN-R adduct EPR signal. Increased oxidation of organic molecules at high pH enhanced the formation of TEMPONE and POBN-R adduct EPR signals in Tris-treated PSII membranes. Interestingly, the scavenging of R• by propyl gallate significantly suppressed 1O2. Based on our results, it is concluded that 1O2 formation correlates with R• formation on the donor side of PSII due to oxidation of organic molecules (lipids and proteins) by long-lived P680•+/TyrZ•. It is proposed here that the Russell mechanism for the recombination of two peroxyl radicals formed by the interaction of R• with molecular oxygen is a plausible mechanism for 1O2 formation in the donor side photoinhibition of PSII. PMID:23049883

  7. Zipper and layer-by-layer assemblies of artificial photosystems analyzed by combining optical and piezoelectric surface techniques.

    PubMed

    Porus, Mariya; Maroni, Plinio; Bhosale, Rajesh; Sakai, Naomi; Matile, Stefan; Borkovec, Michal

    2011-06-07

    Quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) were used to study zipper and layer-by-layer multilayer assemblies of artificial photosystems based on naphthalenediimides (NDIs) attached to an oligophenylethynyl (OPE-NDI) or p-oligophenyl (POP-NDI) backbone in dry and wet state. For the most interesting OPE-NDI zipper, one obtains for the dry film a monolayer thickness of 1.85 nm and a density of 1.58 g/cm(3), while the wet film has a larger monolayer thickness of 3.6 nm with a water content of 36%. The dry thickness of a monolayer in OPE-NDI zippers corresponds to about one-half of the length of the OPE scaffold in agreement with the proposed structure of the zipper. The low water content of the OPE-NDI films confirms their compact structure. The dry monolayer thickness of the POP-NDI films of 1.45 nm is smaller than that for the OPE-NDI films, which is probably related to a tilt of the POP scaffolds within the adsorbed layer. The POP-NDI films swell in water much more substantially, suggesting a much more open structure. These features are in excellent agreement with the better photophysical performance of the OPE-NDI assemblies when compared to the POP-NDI films.

  8. Origin of an ancient hormone/receptor couple revealed by resurrection of an ancestral estrogen.

    PubMed

    Markov, Gabriel V; Gutierrez-Mazariegos, Juliana; Pitrat, Delphine; Billas, Isabelle M L; Bonneton, François; Moras, Dino; Hasserodt, Jens; Lecointre, Guillaume; Laudet, Vincent

    2017-03-01

    The origin of ancient ligand/receptor couples is often analyzed via reconstruction of ancient receptors and, when ligands are products of metabolic pathways, they are not supposed to evolve. However, because metabolic pathways are inherited by descent with modification, their structure can be compared using cladistic analysis. Using this approach, we studied the evolution of steroid hormones. We show that side-chain cleavage is common to most vertebrate steroids, whereas aromatization was co-opted for estrogen synthesis from a more ancient pathway. The ancestral products of aromatic activity were aromatized steroids with a side chain, which we named "paraestrols." We synthesized paraestrol A and show that it effectively binds and activates the ancestral steroid receptor. Our study opens the way to comparative studies of biologically active small molecules.

  9. Ancestral Variation in Orbital Rim Shape: A Three-Dimensional Pilot Study.

    PubMed

    Rubin, Katie M; DeLeon, Valerie B

    2017-03-06

    Traditional nonmetric methods of ancestry assessment posit orbital rim shape varies among ancestral groups. This pilot study uses morphometric analysis of 3D orbital variation to test discrimination among individuals of primarily European, African, and Asian ancestry. Although the size and nature of the sample analyzed limit inferences for other samples, principal components analysis suggests ancestry has a significant effect on rim shape (p = 2.93e-04). European orbits display more marked folding of the orbit in the sagittal plane than either African or Asian orbits, while the lateral margin of African orbits lies further posterior relative to the medial margin when compared to Asian orbits. The findings suggest curviplanar relationships are the most ancestrally informative aspect of orbital rim shape; these relationships may be distorted by perspective based on orientation of the skull relative to the viewer in traditional nonmetric analyses. Additional studies on geometric morphometric approaches to ancestry assessment are therefore warranted.

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

    PubMed Central

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

    2016-01-01

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

  11. Origin of an ancient hormone/receptor couple revealed by resurrection of an ancestral estrogen

    PubMed Central

    Markov, Gabriel V.; Gutierrez-Mazariegos, Juliana; Pitrat, Delphine; Billas, Isabelle M. L.; Bonneton, François; Moras, Dino; Hasserodt, Jens; Lecointre, Guillaume; Laudet, Vincent

    2017-01-01

    The origin of ancient ligand/receptor couples is often analyzed via reconstruction of ancient receptors and, when ligands are products of metabolic pathways, they are not supposed to evolve. However, because metabolic pathways are inherited by descent with modification, their structure can be compared using cladistic analysis. Using this approach, we studied the evolution of steroid hormones. We show that side-chain cleavage is common to most vertebrate steroids, whereas aromatization was co-opted for estrogen synthesis from a more ancient pathway. The ancestral products of aromatic activity were aromatized steroids with a side chain, which we named “paraestrols.” We synthesized paraestrol A and show that it effectively binds and activates the ancestral steroid receptor. Our study opens the way to comparative studies of biologically active small molecules. PMID:28435861

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

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

    2012-03-16

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

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

    SciTech Connect

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

    1996-09-01

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

  15. Temperature-dependent respiration-growth relations in ancestral maize cultivars

    Treesearch

    Bruce N. Smith; Jillian L. Walker; Rebekka L. Stone; Angela R. Jones; Lee D. Hansen

    2001-01-01

    Shoots from 4- to 6-day old seedlings of seven ancestral or old cultivars of Zea mays L. were placed in a calorimeter. Dark metabolic heat rate (q) and CO2 production rate (RCO2) were measured at nine temperatures (5, 10, 15, 20, 25, 30, 35, 40, and 45 °C). Temperature dependencies of q and RCO2 were used to model response of both growth and substrate carbon conversion...

  16. Reconstructed ancestral enzymes suggest long-term cooling of Earth's photic zone since the Archean

    NASA Astrophysics Data System (ADS)

    Garcia, Amanda K.; Schopf, J. William; Yokobori, Shin-ichi; Akanuma, Satoshi; Yamagishi, Akihiko

    2017-05-01

    Paleotemperatures inferred from the isotopic compositions (δ18O and δ30Si) of marine cherts suggest that Earth’s oceans cooled from 70 ± 15 °C in the Archean to the present ˜15 °C. This interpretation, however, has been subject to question due to uncertainties regarding oceanic isotopic compositions, diagenetic or metamorphic resetting of the isotopic record, and depositional environments. Analyses of the thermostability of reconstructed ancestral enzymes provide an independent method by which to assess the temperature history inferred from the isotopic evidence. Although previous studies have demonstrated extreme thermostability in reconstructed archaeal and bacterial proteins compatible with a hot early Earth, taxa investigated may have inhabited local thermal environments that differed significantly from average surface conditions. We here present thermostability measurements of reconstructed ancestral enzymatically active nucleoside diphosphate kinases (NDKs) derived from light-requiring prokaryotic and eukaryotic phototrophs having widely separated fossil-based divergence ages. The ancestral environmental temperatures thereby determined for these photic-zone organisms--shown in modern taxa to correlate strongly with NDK thermostability--are inferred to reflect ancient surface-environment paleotemperatures. Our results suggest that Earth's surface temperature decreased over geological time from ˜65-80 °C in the Archean, a finding consistent both with previous isotope-based and protein reconstruction-based interpretations. Interdisciplinary studies such as those reported here integrating genomic, geologic, and paleontologic data hold promise for providing new insight into the coevolution of life and environment over Earth history.

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

    PubMed

    Keever, Carson C; Hart, Michael W

    2008-01-01

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

  18. Reconstructed ancestral enzymes suggest long-term cooling of Earth's photic zone since the Archean.

    PubMed

    Garcia, Amanda K; Schopf, J William; Yokobori, Shin-Ichi; Akanuma, Satoshi; Yamagishi, Akihiko

    2017-05-02

    Paleotemperatures inferred from the isotopic compositions (δ(18)O and δ(30)Si) of marine cherts suggest that Earth's oceans cooled from 70 ± 15 °C in the Archean to the present ∼15 °C. This interpretation, however, has been subject to question due to uncertainties regarding oceanic isotopic compositions, diagenetic or metamorphic resetting of the isotopic record, and depositional environments. Analyses of the thermostability of reconstructed ancestral enzymes provide an independent method by which to assess the temperature history inferred from the isotopic evidence. Although previous studies have demonstrated extreme thermostability in reconstructed archaeal and bacterial proteins compatible with a hot early Earth, taxa investigated may have inhabited local thermal environments that differed significantly from average surface conditions. We here present thermostability measurements of reconstructed ancestral enzymatically active nucleoside diphosphate kinases (NDKs) derived from light-requiring prokaryotic and eukaryotic phototrophs having widely separated fossil-based divergence ages. The ancestral environmental temperatures thereby determined for these photic-zone organisms--shown in modern taxa to correlate strongly with NDK thermostability--are inferred to reflect ancient surface-environment paleotemperatures. Our results suggest that Earth's surface temperature decreased over geological time from ∼65-80 °C in the Archean, a finding consistent both with previous isotope-based and protein reconstruction-based interpretations. Interdisciplinary studies such as those reported here integrating genomic, geologic, and paleontologic data hold promise for providing new insight into the coevolution of life and environment over Earth history.

  19. Potential of ancestral sylvatic dengue-2 viruses to re-emerge.

    PubMed

    Vasilakis, Nikos; Shell, Elisabeth J; Fokam, Eric B; Mason, Peter W; Hanley, Kathryn A; Estes, D Mark; Weaver, Scott C

    2007-02-20

    Dengue viruses (DENV) are the most important arboviral pathogens in tropical and subtropical regions throughout the world. DENV transmission includes both a sylvatic, enzootic cycle between nonhuman primates and arboreal mosquitoes of the genus Aedes, and an urban, endemic/epidemic cycle between Aedes aegypti, a mosquito with larval development in peridomestic water containers, and human reservoir hosts. All 4 serotypes of endemic DENV evolved independently from ancestral sylvatic viruses and have become both ecologically and evolutionarily distinct; this process may have involved adaptation to (i) peridomestic mosquito vectors and/or (ii) human reservoir hosts. To test the latter hypothesis, we assessed the ability of sylvatic and endemic DENV-2 strains, representing major genotypes from Southeast Asia, West Africa and the Americas, to replicate in two surrogate human model hosts: monocyte-derived, human dendritic cells (moDCs), and mice engrafted with human hepatoma cells. Although the various DENV-2 strains showed significant inter-strain variation in mean replication titers in both models, no overall difference between sylvatic and endemic strains was detected in either model. Our findings suggest that emergence of endemic DENV strains from ancestral sylvatic strains may not have required adaptation to replicate more efficiently in human reservoir hosts, implying that the potential for re-emergence of sylvatic dengue strains into the endemic cycle is high. The shared replication profiles of the American endemic and sylvatic strains suggest that American strains have maintained or regained the ancestral phenotype.

  20. Environmental Intervention as a Therapy for Adverse Programming by Ancestral Stress

    PubMed Central

    McCreary, J. Keiko; Erickson, Zachary T.; Hao, YongXin; Ilnytskyy, Yaroslav; Kovalchuk, Igor; Metz, Gerlinde A. S.

    2016-01-01

    Ancestral stress can program stress sensitivity and health trajectories across multiple generations. While ancestral stress is uncontrollable to the filial generations, it is critical to identify therapies that overcome transgenerational programming. Here we report that prenatal stress in rats generates a transgenerationally heritable endocrine and epigenetic footprint and elevated stress sensitivity which can be alleviated by beneficial experiences in later life. Ancestral stress led to downregulated glucocorticoid receptor and prefrontal cortex neuronal densities along with precocious development of anxiety-like behaviours. Environmental enrichment (EE) during adolescence mitigated endocrine and neuronal markers of stress and improved miR-182 expression linked to brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) regulation in stressed lineages. Thus, EE may serve as a powerful intervention for adverse transgenerational programming through microRNA-mediated regulation of BDNF and NT-3 pathways. The identification of microRNAs that mediate the actions of EE highlights new therapeutic strategies for mental health conditions and psychiatric disease. PMID:27883060

  1. AAV ANCESTRAL RECONSTRUCTION LIBRARY ENABLES SELECTION OF BROADLY INFECTIOUS VIRAL VARIANTS

    PubMed Central

    Santiago-Ortiz, Jorge; Ojala, David S.; Westesson, Oscar; Weinstein, John R.; Wong, Sophie Y.; Steinsapir, Andrew; Kumar, Sanjay; Holmes, Ian; Schaffer, David V.

    2015-01-01

    Adeno-associated virus (AAV) vectors have achieved clinical efficacy in treating several diseases. Enhanced vectors are required to extend these landmark successes to other indications, however, and protein engineering approaches may provide the necessary vector improvements to address such unmet medical needs. To generate new capsid variants with potentially enhanced infectious properties, and to gain insights into AAV’s evolutionary history, we computationally designed and experimentally constructed a putative ancestral AAV library. Combinatorial variations at 32 amino acid sites were introduced to account for uncertainty in their identities. We then analyzed the evolutionary flexibility of these residues, the majority of which have not been previously studied, by subjecting the library to iterative selection on a representative cell line panel. The resulting variants exhibited transduction efficiencies comparable to the most efficient extant serotypes, and in general ancestral libraries were broadly infectious across the cell line panel, indicating that they favored promiscuity over specificity. Interestingly, putative ancestral AAVs were more thermostable than modern serotypes and did not utilize sialic acids, galactose, or heparan sulfate proteoglycans for cellular entry. Finally, variants mediated 19–31 fold higher gene expression in muscle compared to AAV1, a clinically utilized serotype for muscle delivery, highlighting their promise for gene therapy. PMID:26186661

  2. Distinct actions of ancestral vinclozolin and juvenile stress on neural gene expression in the male rat

    PubMed Central

    Gillette, Ross; Miller-Crews, Isaac; Skinner, Michael K.; Crews, David

    2015-01-01

    Exposure to the endocrine disrupting chemical vinclozolin during gestation of an F0 generation and/or chronic restraint stress during adolescence of the F3 descendants affects behavior, physiology, and gene expression in the brain. Genes related to the networks of growth factors, signaling peptides, and receptors, steroid hormone receptors and enzymes, and epigenetic related factors were measured using quantitative polymerase chain reaction via Taqman low density arrays targeting 48 genes in the central amygdaloid nucleus, medial amygdaloid nucleus, medial preoptic area (mPOA), lateral hypothalamus (LH), and the ventromedial nucleus of the hypothalamus. We found that growth factors are particularly vulnerable to ancestral exposure in the central and medial amygdala; restraint stress during adolescence affected neural growth factors in the medial amygdala. Signaling peptides were affected by both ancestral exposure and stress during adolescence primarily in hypothalamic nuclei. Steroid hormone receptors and enzymes were strongly affected by restraint stress in the mPOA. Epigenetic related genes were affected by stress in the ventromedial nucleus and by both ancestral exposure and stress during adolescence independently in the central amygdala. It is noteworthy that the LH showed no effects of either manipulation. Gene expression is discussed in the context of behavioral and physiological measures previously published. PMID:25784924

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

    USGS Publications Warehouse

    Levings, G.W.

    1986-01-01

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

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

    PubMed

    King, Benedict; Lee, Michael S Y

    2015-05-01

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

  5. Ancestral sleep.

    PubMed

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

    2016-04-04

    While we do not yet understand all the functions of sleep, its critical role for normal physiology and behaviour is evident. Its amount and temporal pattern depend on species and condition. Humans sleep about a third of the day with the longest, consolidated episode during the night. The change in lifestyle from hunter-gatherers via agricultural communities to densely populated industrialized centres has certainly affected sleep, and a major concern in the medical community is the impact of insufficient sleep on health [1,2]. One of the causal mechanisms leading to insufficient sleep is altered exposure to the natural light-dark cycle. This includes the wide availability of electric light, attenuated exposure to daylight within buildings, and evening use of light-emitting devices, all of which decrease the strength of natural light-dark signals that entrain circadian systems [3]. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. A clustered set of three Sp-family genes is ancestral in the Metazoa: evidence from sequence analysis, protein domain structure, developmental expression patterns and chromosomal location

    PubMed Central

    2010-01-01

    Background The Sp-family of transcription factors are evolutionarily conserved zinc finger proteins present in many animal species. The orthology of the Sp genes in different animals is unclear and their evolutionary history is therefore controversially discussed. This is especially the case for the Sp gene buttonhead (btd) which plays a key role in head development in Drosophila melanogaster, and has been proposed to have originated by a recent gene duplication. The purpose of the presented study was to trace orthologs of btd in other insects and reconstruct the evolutionary history of the Sp genes within the metazoa. Results We isolated Sp genes from representatives of a holometabolous insect (Tribolium castaneum), a hemimetabolous insect (Oncopeltus fasciatus), primitively wingless hexapods (Folsomia candida and Thermobia domestica), and an amphipod crustacean (Parhyale hawaienis). We supplemented this data set with data from fully sequenced animal genomes. We performed phylogenetic sequence analysis with the result that all Sp factors fall into three monophyletic clades. These clades are also supported by protein domain structure, gene expression, and chromosomal location. We show that clear orthologs of the D. melanogaster btd gene are present even in the basal insects, and that the Sp5-related genes in the genome sequence of several deuterostomes and the basal metazoans Trichoplax adhaerens and Nematostella vectensis are also orthologs of btd. Conclusions All available data provide strong evidence for an ancestral cluster of three Sp-family genes as well as synteny of this Sp cluster and the Hox cluster. The ancestral Sp gene cluster already contained a Sp5/btd ortholog, which strongly suggests that btd is not the result of a recent gene duplication, but directly traces back to an ancestral gene already present in the metazoan ancestor. PMID:20353601

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    PubMed

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

    2014-09-01

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

  10. Facial anatomy of Victoriapithecus and its relevance to the ancestral cranial morphology of Old World monkeys and apes.

    PubMed

    Benefit, B R; McCrossin, M L

    1993-11-01

    Recently discovered craniofacial fossils of the middle Miocene cercopithecoid Victoriapithecus are described. The frontal, zygomatic, maxilla, and premaxilla anatomy differ from the previously proposed colobine-like ancestral cercopithecoid morphotype in several significant respects. This morphotype was based on the assumption that features held in common by subordinate hominoid and cercopithecoid morphotypes (Colobinae and Hylobatidae) are primitive for Old World monkeys. Cranial similarities between Victoriapithecus, which represents the sister-group of both colobine and cercopithecine monkeys, and the shorter-snouted Cercopithecinae (Macaca and Cercopithecus) indicate that the last common ancestor of Old World monkeys possessed the following features: a narrow interorbital septum, moderately long snout, moderately long and anteriorly tapering premaxilla, large procumbent upper central incisors set anterior to and with longer roots than lateral incisors, moderately tall face below the orbits, teardrop-shaped nasal aperture of low height and moderate width, and probably long and narrow nasal bones. The Victoriapithecus cranium is also characterized by features not present in modern cercopithecids. These include a deep malar region of the zygomatic and the presence of a frontal trigon due to the occurrence of temporal lines that merge with supraorbital costae close to the midline of each orbit and converge anterior to bregma. These features are interpreted as primitive retentions from the basal catarrhine condition as indicated by the occurrence of these features among primitive catarrhines (Aegyptopithecus) and Miocene hominoids (Afropithecus).

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

    PubMed

    Moreau, Corrie S; Bell, Charles D

    2013-08-01

    Ants are one of the most ecologically and numerically dominant group of terrestrial organisms with most species diversity currently found in tropical climates. Several explanations for the disparity of biological diversity in the tropics compared to temperate regions have been proposed including that the tropics may act as a "museum" where older lineages persist through evolutionary time or as a "cradle" where new species continue to be generated. We infer the molecular phylogenetic relationships of 295 ant specimens including members of all 21 extant subfamilies to explore the evolutionary diversification and biogeography of the ants. By constraining the topology and age of the root node while using 45 fossils as minimum constraints, we converge on an age of 139-158 Mya for the modern ants. Further diversification analyses identified 10 periods with a significant change in the tempo of diversification of the ants, although these shifts did not appear to correspond to ancestral biogeographic range shifts. Likelihood-based historical biogeographic reconstructions suggest that the Neotropics were important in early ant diversification (e.g., Cretaceous). This finding coupled with the extremely high-current species diversity suggests that the Neotropics have acted as both a museum and cradle for ant diversity. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

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

    PubMed Central

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

    2015-01-01

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

  13. Unique scorpion toxin with a putative ancestral fold provides insight into evolution of the inhibitor cystine knot motif

    PubMed Central

    Smith, Jennifer J.; Hill, Justine M.; Little, Michelle J.; Nicholson, Graham M.; King, Glenn F.; Alewood, Paul F.

    2011-01-01

    The three-disulfide inhibitor cystine knot (ICK) motif is a fold common to venom peptides from spiders, scorpions, and aquatic cone snails. Over a decade ago it was proposed that the ICK motif is an elaboration of an ancestral two-disulfide fold coined the disulfide-directed β-hairpin (DDH). Here we report the isolation, characterization, and structure of a novel toxin [U1-liotoxin-Lw1a (U1-LITX-Lw1a)] from the venom of the scorpion Liocheles waigiensis that is the first example of a native peptide that adopts the DDH fold. U1-LITX-Lw1a not only represents the discovery of a missing link in venom protein evolution, it is the first member of a fourth structural fold to be adopted by scorpion-venom peptides. Additionally, we show that U1-LITX-Lw1a has potent insecticidal activity across a broad range of insect pest species, thereby providing a unique structural scaffold for bioinsecticide development. PMID:21670253

  14. Unique scorpion toxin with a putative ancestral fold provides insight into evolution of the inhibitor cystine knot motif.

    PubMed

    Smith, Jennifer J; Hill, Justine M; Little, Michelle J; Nicholson, Graham M; King, Glenn F; Alewood, Paul F

    2011-06-28

    The three-disulfide inhibitor cystine knot (ICK) motif is a fold common to venom peptides from spiders, scorpions, and aquatic cone snails. Over a decade ago it was proposed that the ICK motif is an elaboration of an ancestral two-disulfide fold coined the disulfide-directed β-hairpin (DDH). Here we report the isolation, characterization, and structure of a novel toxin [U(1)-liotoxin-Lw1a (U(1)-LITX-Lw1a)] from the venom of the scorpion Liocheles waigiensis that is the first example of a native peptide that adopts the DDH fold. U(1)-LITX-Lw1a not only represents the discovery of a missing link in venom protein evolution, it is the first member of a fourth structural fold to be adopted by scorpion-venom peptides. Additionally, we show that U(1)-LITX-Lw1a has potent insecticidal activity across a broad range of insect pest species, thereby providing a unique structural scaffold for bioinsecticide development.

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

    PubMed

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

    2016-04-01

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

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

    PubMed Central

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

    2016-01-01

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

  17. Evidence that the ancestral haplotype in Australian hemochromatosis patients may be associated with a common mutation in the gene

    SciTech Connect

    Crawford, D.H.G.; Powell, L.W.; Leggett, B.A.

    1995-08-01

    Hemochromatosis (HC) is a common inherited disorder of iron metabolism for which neither the gene nor biochemical defect have yet been identified. The aim of this study was to look for clinical evidence that the predominant ancestral haplotype in Australian patients is associated with a common mutation in the gene. We compared indices of iron metabolism and storage in three groups of HC patients categorized according to the presence of the ancestral haplotype (i.e., patients with two copies, one copy, and no copies of the ancestral haplotype). We also examined iron indices in two groups of HC heterozygotes (those with the ancestral haplotype and those without) and in age-matched controls. These analyses indicate that (i) HC patients with two copies of the ancestral haplotype show significantly more severe expression of the disorder than those with one copy or those without, (ii) HC heterozygotes have partial clinical expression, which may be influenced by the presence of the ancestral haplotype in females but not in males, and (iii) the high population frequency of the HC gene may be the result of the selective advantage conferred by protecting heterozygotes against iron deficiency. 18 refs., 3 tabs.

  18. Role of Carotenoids in Photosystem II (PSII) Reaction Centers

    NASA Astrophysics Data System (ADS)

    Braslavsky, Silvia E.; Holzwarth, Alfred R.

    2012-11-01

    A photoprotection mechanism operative in closed reaction centers (RCs) is proposed, where-as a consequence of the negative charge on the quinone QA-triplet 3Chl is formed by the radical pair mechanism on the accessory Chl of the normally inactive D2 branch where it can be subsequently quenched by the spatially close β-carotene in the D2 branch. Whereas β-carotene in the D1 branch is more than 17 Å away from the accessory D1-chlorophyll ({Chl_accD_1)} and, therefore, cannot quench the Chl triplet, the D2-carotene is only 13.2 Å away from {Chl_accD_2} . We propose that the D2 branch becomes active in electron transfer and thus plays a photoprotective role when the intact RCs are closed under high photon fluence conditions. This interpretation allows combining many seemingly inconsistent observations in the literature and reveals the so far "elusive" RC triplet quenching mechanism in PSII. Based on laser-induced optoacoustic studies, an important structural role is assigned to the β-carotene in the D1 branch, i.e., this carotene ensures a rigid structure.

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

    PubMed

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

    2014-10-01

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

  20. Deactivation processes in PsbA1-Photosystem II and PsbA3-Photosystem II under photoinhibitory conditions in the cyanobacterium Thermosynechococcus elongatus.

    PubMed

    Ogami, Shogo; Boussac, Alain; Sugiura, Miwa

    2012-08-01

    The sensitivity to high light conditions of Photosystem II with either PsbA1 (WT*1) or PsbA3 (WT*3) as the D1 protein was studied in whole cells of the thermophilic cyanobacterium Thermosynechococcus elongatus. When the cells are cultivated under high light conditions the following results were found: (i) The O(2) evolution activity decreases faster in WT*1 cells than in WT*3 cells both in the absence and in the presence of lincomycin, a protein synthesis inhibitor; (ii) In WT*1 cells, the rate constant for the decrease of the O(2) evolution activity is comparable in the presence and in the absence of lincomycin; (iii) The D1 content revealed by western blot analysis decays similarly in both WT*1 and WT*3 cells and much slowly than O(2) evolution; (iv) The faster decrease in O(2) evolution in WT*1 than in WT*3 cells correlates with a much faster inhibition of the S(2)-state formation; (v) The shape of the WT*1 cells is altered. All these results are in agreement with a photo-inhibition process resulting in the loss of the O(2) activity much faster than the D1 turnover in PsbA1-PSII and likely to a greater production of reactive oxygen species under high light conditions in WT*1 than in WT*3. This latter result is discussed in view of the known effects of the PsbA1 to PsbA3 substitution on the redox properties of the Photosystem II cofactors. The observation that under low light conditions WT*3 cells are able to express the psbA(3) gene, whereas under similar conditions wild type cells are expressing mainly the psbA(1) gene is also discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. A single origin of Batesian mimicry among hybridizing populations of admiral butterflies (Limenitis arthemis) rejects an evolutionary reversion to the ancestral phenotype.

    PubMed

    Savage, Wesley K; Mullen, Sean P

    2009-07-22

    Batesian mimicry is a fundamental example of adaptive phenotypic evolution driven by strong natural selection. Given the potentially dramatic impacts of selection on individual fitness, it is important to understand the conditions under which mimicry is maintained versus lost. Although much empirical and theoretical work has been devoted to the maintenance of Batesian mimicry, there are no conclusive examples of its loss in natural populations. Recently, it has been proposed that non-mimetic populations of the polytypic Limenitis arthemis species complex represent an evolutionary loss of Batesian mimicry, and a reversion to the ancestral phenotype. Here, we evaluate this conclusion using segregating amplified fragment length polymorphism markers to investigate the history and fate of mimicry among forms of the L. arthemis complex and closely related Nearctic Limenitis species. In contrast to the previous finding, our results support a single origin of mimicry within the L. arthemis complex and the retention of the ancestral white-banded form in non-mimetic populations. Our finding is based on a genome-wide sampling approach to phylogeny reconstruction that highlights the challenges associated with inferring the evolutionary relationships among recently diverged species or populations (i.e. incomplete lineage sorting, introgressive hybridization and/or selection).

  2. A single origin of Batesian mimicry among hybridizing populations of admiral butterflies (Limenitis arthemis) rejects an evolutionary reversion to the ancestral phenotype

    PubMed Central

    Savage, Wesley K.; Mullen, Sean P.

    2009-01-01

    Batesian mimicry is a fundamental example of adaptive phenotypic evolution driven by strong natural selection. Given the potentially dramatic impacts of selection on individual fitness, it is important to understand the conditions under which mimicry is maintained versus lost. Although much empirical and theoretical work has been devoted to the maintenance of Batesian mimicry, there are no conclusive examples of its loss in natural populations. Recently, it has been proposed that non-mimetic populations of the polytypic Limenitis arthemis species complex represent an evolutionary loss of Batesian mimicry, and a reversion to the ancestral phenotype. Here, we evaluate this conclusion using segregating amplified fragment length polymorphism markers to investigate the history and fate of mimicry among forms of the L. arthemis complex and closely related Nearctic Limenitis species. In contrast to the previous finding, our results support a single origin of mimicry within the L. arthemis complex and the retention of the ancestral white-banded form in non-mimetic populations. Our finding is based on a genome-wide sampling approach to phylogeny reconstruction that highlights the challenges associated with inferring the evolutionary relationships among recently diverged species or populations (i.e. incomplete lineage sorting, introgressive hybridization and/or selection). PMID:19369265

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

    USDA-ARS?s Scientific Manuscript database

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

  4. Isolation of a photosystem II reaction center consisting of D-1 and D-2 polypeptides and cytochrome b-559

    SciTech Connect

    Nanba, O.; Satoh, K.

    1987-01-01

    A photosystem II reaction center complex consisting of D-1 and D-2 polypeptides and cytochrome b-559 was isolated from spinach grana thylakoids, treated with 4% (wt/vol) Triton X-100, by ion-exchange chromatography using DEAE-Toyopearl 650S. The isolated complex appears to contain five chlorophyll a, two pheophytin a, one ..beta..-carotene, and one or two cytochrome b-559 heme(s) (molar ratio) and exhibits a reversible absorbance change attributable to the photochemical accumulation of reduced pheophytin typical for the intermediary electron acceptor of photosystem II reaction center. These results strongly suggest that the site of primary charge separation in photosystem II is located on the heterodimer composed of D-1 and D-2 subunits.

  5. Variety in excitation energy transfer processes from phycobilisomes to photosystems I and II.

    PubMed

    Ueno, Yoshifumi; Aikawa, Shimpei; Niwa, Kyosuke; Abe, Tomoko; Murakami, Akio; Kondo, Akihiko; Akimoto, Seiji

    2017-02-09

    The light-harvesting antennas of oxygenic photosynthetic organisms capture light energy and transfer it to the reaction centers of their photosystems. The light-harvesting antennas of cyanobacteria and red algae, called phycobilisomes (PBSs), supply light energy to both photosystem I (PSI) and photosystem II (PSII). However, the excitation energy transfer processes from PBS to PSI and PSII are not understood in detail. In the present study, the energy transfer processes from PBS to PSs in various cyanobacteria and red algae were examined in vivo by selectively exciting their PSs or PBSs, and measuring the resulting picosecond to nanosecond time-resolved fluorescences. By observing the delayed fluorescence spectrum of PBS-selective excitation in Arthrospira platensis, we demonstrated that energy transfer from PBS to PSI via PSII (PBS→PSII→PSI transfer) occurs even for PSI trimers. The contribution of PBS→PSII→PSI transfer was species dependent, being largest in the wild-type of red alga Pyropia yezoensis (formerly Porphyra yezoensis) and smallest in Synechococcus sp. PCC 7002. Comparing the time-resolved fluorescence after PSs- and PBS-selective excitation, we revealed that light energy flows from CP43 to CP47 by energy transfer between the neighboring PSII monomers in PBS-PSII supercomplexes. We also suggest two pathways of energy transfer: direct energy transfer from PBS to PSI (PBS→PSI transfer) and indirect transfer through PSII (PBS→PSII→PSI transfer). We also infer that PBS→PSI transfer conveys light energy to a lower-energy red chlorophyll than PBS→PSII→PSI transfer.

  6. Heat- and light-induced detachment of the light harvesting complex from isolated photosystem I supercomplexes.

    PubMed

    Nellaepalli, Sreedhar; Zsiros, Ottó; Tóth, Tünde; Yadavalli, Venkateswarlu; Garab, Győző; Subramanyam, Rajagopal; Kovács, László

    2014-08-01

    In a previous study, using photosystem I enriched stroma thylakoid membrane vesicles, we have shown that the light harvesting complexes of this photosystem are prone to heat- and light-induced, thermo-optically driven detachment from the supercomplex [43]. We have also shown that the splitting of the supercomplex occurs in a gradual and specific manner, selectively affecting the different constituents of the antenna complexes. Here we further analyse these heat- and light-induced processes in isolated Photosystem I supercomplex using circular dichroism and 77K fluorescence emission spectroscopy and immuno blotting, and obtain further details on the sequence of events of the dissociation process as well as on the thermal stability of the different components. Our absorption and circular dichroism spectroscopy and immuno blotting data show that the dissociation of LHCI from PSI-LHCI supercomplex starts above 50°C. Also, the low temperature fluorescence emission spectra depicts decrease of maximum fluorescence emission at 730nm and an increase of the intensity at 685nm, and about 10nm blue-shifts, from 730 to 720nm and from 685 to 676nm, respectively, indicating the heat (50°C) induced detachment of LHCI from PSI core complexes. The reaction centre proteins are highly stable even at high temperatures. Lhca2 is more heat stable than the other light harvesting protein complexes of PSI, whereas Lhca4 and Lhca3 are rather labile. Combined heat and light treatments significantly enhances the disorganization of PSI-LHCI supercomplexes, indicating a thermo-optic mechanism, which might have significant role under combined heat and light stress conditions. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Cytochrome b559 content in isolated photosystem II reaction center preparations.

    PubMed

    Yruela, Inmaculada; Miota, Francisca; Torrado, Elena; Seibert, Michael; Picorel, Rafael

    2003-05-01

    The cytochrome b559 content was examined in five types of isolated photosystem II D1-D2-cytochrome b559 reaction center preparations containing either five or six chlorophylls per reaction center. The reaction center complexes were obtained following isolation procedures that differed in chromatographic column material, washing buffer composition and detergent concentration. Two different types of cytochrome b559 assays were performed. The absolute heme content in each preparation was obtained using the oxidized-minus-reduced difference extinction coefficient of cytochrome b559 at 559 nm. The relative amount of D1 and cytochrome b559alpha-subunit polypeptide was also calculated for each preparation from immunoblots obtained using antibodies raised against the two polypeptides. The results indicate that the cytochrome b559 heme content in photosystem II reaction center complexes can vary with the isolation procedure, but the variation of the cytochrome b559alpha-subunit/D1 polypeptide ratio was even greater. This variation was not found in the PSII-enriched membrane fragments used as the RC-isolation starting material, as different batches of membranes obtained from spinach harvested at different seasons of the year or those from sugar beets grown in a chamber under controlled environmental conditions lack variation in their alpha-subunit/D1 polypeptide ratio. A precise determination of the ratio using an RC1-control sample calibration curve gave a ratio of 1.25 cytochrome b559alpha-subunit per 1.0 D1 polypeptide in photosystem II membranes. We conclude that the variations found in the reaction center preparations were due to the different procedures used to isolate and purify the different reaction center complexes.

  8. Quantitative Targeted Proteomics and Electrochromic Shift for Measuring Photosystem Content of Marine Phytoplankton

    NASA Astrophysics Data System (ADS)

    Brown, C. M.; Bailleul, B.; Melanson, J. R.; Campbell, D. A.; Cockshutt, A. M.; Cardol, P.

    2016-02-01

    Abundance and stoichiometry data for the photosystems, the intersystem electron transport complexes and the Calvin cycle enzymes are rich in information about light and nutrient acclimation. Quantifying these complexes is essential for understanding limitations on and capacities for photosynthesis. Targeted quantitative immunodetections of conserved subunits (eg. PsbA for PSII; PsaC for PSI) are becoming an established method for absolute measurement of these complexes. An advantage of protein measurements is that they can be done with non-living flash-frozen samples and processed post-field. A pitfall of physical versus functional measures is that in some scenarios, such as during photoinhibition of photosystem II (PSII), physical and functional measures give different values, but such disparities are often meaningful, informing targeted studies of regulation, repair and enzyme kinetics. Electrochromic Shift (ECS) is an alternative, fast and noninvasive method which can be exploited to determine functional PSI:PSII ratios in living cells. The basis for ECS is that pigments in the photosynthetic membrane exhibit a shift in their absorption spectra when the electric component of the proton motive force is generated across the membrane in the light. Cross-validation of methods by independent measures builds confidence in results from both approaches and can be useful for ground truthing of underway or high-throughput optical measurements or functional measurements from bioassays. We present comparative data from immunoquantitation and ECS for an array of diatom taxa. The physical data fall within established ranges. The basis for similarities and disparities in the photosystem stoichiometries between the methods are discussed.

  9. Light-induced gradual activation of photosystem II in dark-grown Norway spruce seedlings.

    PubMed

    Pavlovič, Andrej; Stolárik, Tibor; Nosek, Lukáš; Kouřil, Roman; Ilík, Petr

    2016-06-01

    Gymnosperms, unlike angiosperms, are able to synthesize chlorophyll and form photosystems in complete darkness. Photosystem I (PSI) formed under such conditions is fully active, but photosystem II (PSII) is present in its latent form with inactive oxygen evolving complex (OEC). In this work we have studied light-induced gradual changes in PSII function in dark-grown cotyledons of Norway spruce (Picea abies) via the measurement of chlorophyll a fluorescence rise, absorption changes at 830 nm, thermoluminescence glow curves (TL) and protein analysis. The results indicate that in dark-grown cotyledons, alternative reductants were able to act as electron donors to PSII with inactive OEC. Illumination of cotyledons for 5 min led to partial activation of PSII, which was accompanied by detectable oxygen evolution, but still a substantial number of PSII centers remained in the so called PSII-Q(B)-non-reducing form. Interestingly, even 24 h long illumination was not sufficient for the full activation of PSII centers. This was evidenced by a weak attachment of PsbP protein and the absence of PsbQ protein in PSII particles, the absence of PSII supercomplexes, the suboptimal maximum yield of PSII photochemistry, the presence of C band in TL curve and also the presence of up-shifted Q band in TL in DCMU-treated cotyledons. This slow light-induced activation of PSII in dark-grown cotyledons could contribute to the prevention of PSII overexcitation before the light-induced increase in PSI/PSII ratio allows effective operation of linear electron flow.

  10. Ancestral Plasticity and Allometry in Threespine Stickleback Fish Reveal Phenotypes Associated with Derived, Freshwater Ecotypes

    PubMed Central

    Valena, Sophie; Wood, Susan; Baker, John A.

    2011-01-01

    For over a century, evolutionary biologists have debated whether and how phenotypic plasticity impacts the processes of adaptation and diversification. The empirical tests required to resolve these issues have proven elusive, mainly because it requires documentation of ancestral reaction norms, a difficult prospect where many ancestors are either extinct or have evolved. The threespine stickleback radiation is not limited in this regard, making it an ideal system in which to address general questions regarding the role of plasticity in adaptive evolution. As retreating ice sheets have exposed new habitats, oceanic stickleback founded innumerable freshwater populations, many of which have evolved parallel adaptations to their new environments. Because the founding oceanic population is extant, we can directly evaluate whether specific patterns of ancestral phenotypic expression in the context of novel environments (plasticity), or over ontogeny, predisposed the repeated evolution of “benthic” and “limnetic” ecotypes in shallow and deep lakes, respectively. Consistent with this hypothesis, we found that oceanic stickleback raised in a complex habitat and fed a macroinvertebrate diet expressed traits resembling derived, benthic fish. Alternatively, when reared in a simple environment on a diet of zooplankton, oceanic stickleback developed phenotypes resembling derived, limnetic fish. As fish in both treatments grew, their body depths increased allometrically, as did the size of their mouths, while their eyes became relatively smaller. Allometric trajectories were subtly but significantly impacted by rearing environment. Thus, both environmental and allometric influences on development, along with their interactive effects, produced variation in phenotypes consistent with derived benthic and limnetic fish, which may have predisposed the repeated genetic accommodation of this specific suite of traits. We also found significant shape differences between marine

  11. Contrasting determinants of abundance in ancestral and colonized ranges of an invasive brood parasite

    USGS Publications Warehouse

    Hahn, D.C.; O'Connor, R.J.; Scott, J. Michael; Heglund, Patricia J.; Morrison, Michael L.; Haufler, Jonathan B.; Wall, William A.

    2002-01-01

    Avian species distributions are typically regarded as constrained by spatially extensive variables such as climate, habitat, spatial patchiness, and microhabitat attributes. We hypothesized that the distribution of a brood parasite depends as strongly on host distribution patterns as on biophysical factors and examined this hypothesis with respect to the national distribution of the Brown-headed Cowbird (Molothrus ater). We applied a classification and regression (CART) analysis to data from the Breeding Bird Survey (BBS) and the Christmas Bird Count (CBC) and derived hierarchically organized statistical models of the influence of climate and weather, cropping and land use, and host abundance and distribution on the distribution of the Brown-headed Cowbird within the conterminous United States. The model accounted for 47.2% of the variation in cowbird incidence, and host abundance was the top predictor with an R2 of 18.9%. The other predictors identified by the model (crops 15.7%, weather and climate 14.3%, and region 9.6%) fit the ecological profile of this cowbird. We showed that host abundance was independent of these environmental predictors of cowbird distribution. At the regional scale host abundance played a very strong role in determining cowbird abundance in the cowbird?s colonized range east and west of their ancestral range in the Great Plains (26.6%). Crops were not a major predictor for cowbirds in their ancestral range, although they are the most important predictive factor (33%) for the grassland passerines that are the cowbird?s ancestral hosts. Consequently our findings suggest that the distribution of hosts does indeed take precedence over habitat attributes in shaping the cowbird?s distribution at a national scale, within an envelope of constraint set by biophysical factors.

  12. What was the ancestral sex-determining mechanism in amniote vertebrates?

    PubMed

    Johnson Pokorná, Martina; Kratochvíl, Lukáš

    2016-02-01

    Amniote vertebrates, the group consisting of mammals and reptiles including birds, possess various mechanisms of sex determination. Under environmental sex determination (ESD), the sex of individuals depends on the environmental conditions occurring during their development and therefore there are no sexual differences present in their genotypes. Alternatively, through the mode of genotypic sex determination (GSD), sex is determined by a sex-specific genotype, i.e. by the combination of sex chromosomes at various stages of differentiation at conception. As well as influencing sex determination, sex-specific parts of genomes may, and often do, develop specific reproductive or ecological roles in their bearers. Accordingly, an individual with a mismatch between phenotypic (gonadal) and genotypic sex, for example an individual sex-reversed by environmental effects, should have a lower fitness due to the lack of specialized, sex-specific parts of their genome. In this case, evolutionary transitions from GSD to ESD should be less likely than transitions in the opposite direction. This prediction contrasts with the view that GSD was the ancestral sex-determining mechanism for amniote vertebrates. Ancestral GSD would require several transitions from GSD to ESD associated with an independent dedifferentiation of sex chromosomes, at least in the ancestors of crocodiles, turtles, and lepidosaurs (tuataras and squamate reptiles). In this review, we argue that the alternative theory postulating ESD as ancestral in amniotes is more parsimonious and is largely concordant with the theoretical expectations and current knowledge of the phylogenetic distribution and homology of sex-determining mechanisms. © 2014 Cambridge Philosophical Society.

  13. Clumped isotope paleothermometry of the Mio-Pliocene freshwater Lake Mohave. Lower ancestral Colorado River, USA

    NASA Astrophysics Data System (ADS)

    Lang, K. A.; Huntington, K. W.

    2015-12-01

    The fluvio-lacustrine deposits of the Bouse Formation are an archive of ancestral Colorado River integration in the Late Miocene and Early Pliocene. In Mohave Valley along the California-Arizona-Nevada border, exposures of the Bouse Formation are observed ~400 m above the modern river elevation, which has been interpreted as evidence of tectonic uplift following a regionally extensive marine incursion and integration of the ancestral Colorado River by capture. However, recent investigations instead favor a "top-down" process of river integration by sequential infilling of freshwater lakes that does not require subsequent tectonic uplift. Accurate interpretation of the Bouse Formation's depositional environment is needed to test these models and ultimately, constrain the timing and mechanism of southwestern Colorado Plateau uplift. To further constrain interpretations of depositional environment, we present new clumped isotope analyses with major and trace element geochemistry and scanning electron microscopy of carbonate samples from the Bouse Formation in Mohave Valley. Here the Bouse Formation contains three distinct facies: basal marl and limestone overlain by thick beds of calcareous claystone interbedded with siltstone and sandstone and locally overlain by tufa. Bulk geochemistry of all facies is consistent with a similar freshwater source yet each facies is isotopically distinct, potentially indicating a strong influence of facies-specific fractionation processes. Carbonate formation temperatures measured in tufa samples are variable, suggesting multiple generations of calcite precipitation. Formation temperatures from basal marl and claystone samples are generally consistent with near-surface lake temperatures, broadly supporting a lacustrine depositional environment and "top-down" process of ancestral Colorado River integration. More broadly, our results quantify the variability in carbonate formation temperatures with different lacustrine facies and

  14. Sex, Ancestral, and pattern type variation of fingerprint minutiae: A forensic perspective on anthropological dermatoglyphics.

    PubMed

    Fournier, Nichole A; Ross, Ann H

    2016-08-01

    The majority of anthropological studies on dermatoglyphics examine the heritability and inter-population variation of Level 1 detail (e.g., pattern type, total ridge count), while forensic scientists concentrate on individual uniqueness of Level 2 and 3 detail (e.g., minutiae and pores, respectively) used for positive identification. The present study bridges the gap between researcher-practitioner by examining sex, ancestral, and pattern type variation of Level 2 detail (e.g., minutiae). Bifurcations, ending ridges, short ridges, dots, and enclosures on the right index finger of 243 individuals (n = 61 African American ♀; n = 61 African American ♂; n = 61 European American ♀; n = 60 European American ♂) were analyzed. The overall effect of sex, ancestry, and pattern type on minutiae variation was assessed using a MANCOVA. ANOVA was used to identify Level 2 detail variables responsible for the variation. Logistic regression was used to classify individuals into groups. The effect of sex is insignificant. Ancestry is significant (Wilks' λ = 0.053 F value = 2.98, DF = 4,224, P value = 0.02), as is pattern type (Wilks' λ = 0.874 F value = 2.57, DF = 12,592.94, P value = 0.003). The ANOVA reveals that bifurcations are responsible for the variation between ancestral groups, while bifurcations and ending ridges vary between patterns. Logistic regression results suggest that total bifurcations can predict the ancestry of an individual (ChiSq = 6.55, df = 1, Prob > ChiSq = 0.01). Significant minutiae variation between ancestral groups yields information that is valuable in both a forensic and anthropological setting. Am J Phys Anthropol 160:625-632, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  15. Ancestral resurrection of anthropoid estrogen receptor β demonstrates functional consequences of positive selection.

    PubMed

    Weckle, Amy; McGowen, Michael R; Xing, Jun; Chen, Caoyi; Sterner, Kirstin N; Hou, Zhuo-Cheng; Romero, Roberto; Wildman, Derek E

    2017-09-13

    Anthropoid primates arose during the Eocene approximately 55 million years ago (mya), and extant anthropoids share a most recent common ancestor ∼40mya. Paleontology has been very successful at describing the morphological phenotypes of extinct anthropoids. Less well understood is the molecular biology of these extinct species as well as the phenotypic consequences of evolutionary variation in their genomes. Here we resurrect the most recent common ancestral anthropoid estrogen receptor β gene (ESR2) and demonstrate that the function of this ancestral estrogen receptor has been maintained during human descent but was altered during early New World monkey (NWM) evolution by becoming a more potent transcriptional activator. We tested hypotheses of adaptive evolution in the protein coding sequences of ESR2, and determined that ESR2 evolved via episodic positive selection on the NWM stem lineage. We separately co-transfected ESR2 constructs for human, NWM, and the anthropoid ancestor along with reporter gene vectors and performed hormone binding dose response experiments that measure transactivation activity. We found the transactivation potentials of the ancestral and human sequences to be significantly lower (p<0.0001 in each comparison) than that of the NWM when treated with estradiol, the most prevalent estrogen. We conclude the difference in fold activation is due to positive selection in the NWM ERβ ligand binding domain. Our study validates inferential methods for detecting adaptive evolution that predict functional consequences of nucleotide substitutions and points a way toward examining the functional consequences of positive Darwinian selection. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes

    PubMed Central

    Bourlat, Sarah J; Rota-Stabelli, Omar; Lanfear, Robert; Telford, Maximilian J

    2009-01-01

    Background Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups. Results The complete mitochondrial genome sequence of Xenoturbella bocki was determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement of Xenoturbella and find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication of Xenoturbella with those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias. Conclusion The mitochondrial genome of Xenoturbella bocki has a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the mitochondrial sequences support a

  17. Analysis of Ancestral and Functionally Relevant CD5 Variants in Systemic Lupus Erythematosus Patients

    PubMed Central

    Consuegra, Marta; Bonet, Lizette; Carnero-Montoro, Elena; Armiger, Noelia; Caballero-Baños, Miguel; Arias, Maria Teresa; Benitez, Daniel; Ortego-Centeno, Norberto; de Ramón, Enrique; Sabio, José Mario; García–Hernández, Francisco J.; Tolosa, Carles; Suárez, Ana; González-Gay, Miguel A.; Bosch, Elena; Martín, Javier; Lozano, Francisco

    2014-01-01

    Objective CD5 plays a crucial role in autoimmunity and is a well-established genetic risk factor of developing RA. Recently, evidence of positive selection has been provided for the CD5 Pro224-Val471 haplotype in East Asian populations. The aim of the present work was to further analyze the functional relevance of non-synonymous CD5 polymorphisms conforming the ancestral and the newly derived haplotypes (Pro224-Ala471 and Pro224-Val471, respectively) as well as to investigate the potential role of CD5 on the development of SLE and/or SLE nephritis. Methods The CD5 SNPs rs2241002 (C/T; Pro224Leu) and rs2229177 (C/T; Ala471Val) were genotyped using TaqMan allelic discrimination assays in a total of 1,324 controls and 681 SLE patients of Spanish origin. In vitro analysis of CD3-mediated T cell proliferative and cytokine response profiles of healthy volunteers homozygous for the above mentioned CD5 haplotypes were also analyzed. Results T-cell proliferation and cytokine release were significantly increased showing a bias towards to a Th2 profile after CD3 cross-linking of peripheral mononuclear cells from healthy individuals homozygous for the ancestral Pro224-Ala471 (CC) haplotype, compared to the more recently derived Pro224-Val471 (CT). The same allelic combination was statistically associated with Lupus nephritis. Conclusion The ancestral Ala471 CD5 allele confers lymphocyte hyper-responsiveness to TCR/CD3 cross-linking and is associated with nephritis in SLE patients. PMID:25402503

  18. Evolution of sexes from an ancestral mating-type specification pathway.

    PubMed

    Geng, Sa; De Hoff, Peter; Umen, James G

    2014-07-01

    Male and female sexes have evolved repeatedly in eukaryotes but the origins of dimorphic sexes and their relationship to mating types in unicellular species are not understood. Volvocine algae include isogamous species such as Chlamydomonas reinhardtii, with two equal-sized mating types, and oogamous multicellular species such as Volvox carteri with sperm-producing males and egg-producing females. Theoretical work predicts genetic linkage of a gamete cell-size regulatory gene(s) to an ancestral mating-type locus as a possible step in the evolution of dimorphic gametes, but this idea has not been tested. Here we show that, contrary to predictions, a single conserved mating locus (MT) gene in volvocine algae-MID, which encodes a RWP-RK domain transcription factor-evolved from its ancestral role in C. reinhardtii as a mating-type specifier, to become a determinant of sperm and egg development in V. carteri. Transgenic female V. carteri expressing male MID produced functional sperm packets during sexual development. Transgenic male V. carteri with RNA interference (RNAi)-mediated knockdowns of VcMID produced functional eggs, or self-fertile hermaphrodites. Post-transcriptional controls were found to regulate cell-type-limited expression and nuclear localization of VcMid protein that restricted its activity to nuclei of developing male germ cells and sperm. Crosses with sex-reversed strains uncoupled sex determination from sex chromosome identity and revealed gender-specific roles for male and female mating locus genes in sexual development, gamete fitness and reproductive success. Our data show genetic continuity between the mating-type specification and sex determination pathways of volvocine algae, and reveal evidence for gender-specific adaptations in the male and female mating locus haplotypes of Volvox. These findings will enable a deeper understanding of how a master regulator of mating-type determination in an ancestral unicellular species was reprogrammed to

  19. Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms.

    PubMed

    Lowery, Robert K; Uribe, Gabriel; Jimenez, Eric B; Weiss, Mark A; Herrera, Kristian J; Regueiro, Maria; Herrera, Rene J

    2013-11-01

    Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1-4% of the non-Sub-Saharan African gene pool may be Neanderthal derived, while 6-8% of the Melanesian gene pool may be the product of admixture between the Denisovans and the direct ancestors of Melanesians. In the present study, we analyzed single nucleotide polymorphism (SNP) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee). We partitioned SNPs into subsets, including those that are derived in both archaic lineages, those that are ancestral in both archaic lineages and those that are only derived in one archaic lineage. By doing this, we have conducted separate examinations of subsets of mutations with higher probabilities of divergent phylogenetic origins. While previous investigations have excluded SNPs from common ancestors in principal component analyses, we included common ancestral SNPs in our analyses to visualize the relative placement of the Neanderthal and Denisova among human populations. To assess the genetic similarities among the various hominin lineages, we performed genetic structure analyses to provide a comparison of genetic patterns found within contemporary human genomes that may have archaic or common ancestral roots. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Our results suggest that Neanderthal genetic associations with contemporary non-Sub-Saharan African populations, as well as the genetic affinities observed between Denisovans and Melanesians most likely result from the retention of ancient mutations in these populations.

  20. Do Père David's Deer Lose Memories of Their Ancestral Predators?

    PubMed Central

    Ding, Yuhua; Zhang, Linyuan; Fang, Hongxia; Tang, Songhua; Jiang, Zhigang

    2011-01-01

    Whether prey retains antipredator behavior after a long period of predator relaxation is an important question in predator-prey evolution. Père David's deer have been raised in enclosures for more than 1200 years and this isolation provides an opportunity to study whether Père David's deer still respond to the cues of their ancestral predators or to novel predators. We played back the sounds of crows (familiar sound) and domestic dogs (familiar non-predators), of tigers and wolves (ancestral predators), and of lions (potential naïve predator) to Père David's deer in paddocks, and blank sounds to the control group, and videoed the behavior of the deer during the experiment. We also showed life-size photo models of dog, leopard, bear, tiger, wolf, and lion to the deer and video taped their responses after seeing these models. Père David's deer stared at and approached the hidden loudspeaker when they heard the roars of tiger or lion. The deer listened to tiger roars longer, approached to tiger roars more and spent more time staring at the tiger model. The stags were also found to forage less in the trials of tiger roars than that of other sound playbacks. Additionally, it took longer for the deer to restore their normal behavior after they heard tiger roars, which was longer than that after the trial of other sound playbacks. Moreover, the deer were only found to walk away after hearing the sounds of tiger and wolf. Therefore, the tiger was probably the main predator for Père David's deer in ancient time. Our study implies that Père David's deer still retain the memories of the acoustic and visual cues of their ancestral predators in spite of the long term isolation from natural habitat. PMID:21887286

  1. Do Père David's deer lose memories of their ancestral predators?

    PubMed

    Li, Chunwang; Yang, Xiaobo; Ding, Yuhua; Zhang, Linyuan; Fang, Hongxia; Tang, Songhua; Jiang, Zhigang

    2011-01-01

    Whether prey retains antipredator behavior after a long period of predator relaxation is an important question in predator-prey evolution. Père David's deer have been raised in enclosures for more than 1200 years and this isolation provides an opportunity to study whether Père David's deer still respond to the cues of their ancestral predators or to novel predators. We played back the sounds of crows (familiar sound) and domestic dogs (familiar non-predators), of tigers and wolves (ancestral predators), and of lions (potential naïve predator) to Père David's deer in paddocks, and blank sounds to the control group, and videoed the behavior of the deer during the experiment. We also showed life-size photo models of dog, leopard, bear, tiger, wolf, and lion to the deer and video taped their responses after seeing these models. Père David's deer stared at and approached the hidden loudspeaker when they heard the roars of tiger or lion. The deer listened to tiger roars longer, approached to tiger roars more and spent more time staring at the tiger model. The stags were also found to forage less in the trials of tiger roars than that of other sound playbacks. Additionally, it took longer for the deer to restore their normal behavior after they heard tiger roars, which was longer than that after the trial of other sound playbacks. Moreover, the deer were only found to walk away after hearing the sounds of tiger and wolf. Therefore, the tiger was probably the main predator for Père David's deer in ancient time. Our study implies that Père David's deer still retain the memories of the acoustic and visual cues of their ancestral predators in spite of the long term isolation from natural habitat.

  2. Arbuscular mycorrhizal symbiosis ameliorates the optimum quantum yield of photosystem II and reduces non-photochemical quenching in rice plants subjected to salt stress.

    PubMed

    Porcel, Rosa; Redondo-Gómez, Susana; Mateos-Naranjo, Enrique; Aroca, Ricardo; Garcia, Rosalva; Ruiz-Lozano, Juan Manuel

    2015-08-01

    Rice is the most important food crop in the world and is a primary source of food for more than half of the world population. However, salinity is considered the most common abiotic stress reducing its productivity. Soil salinity inhibits photosynthetic processes, which can induce an over-reduction of the reaction centres in photosystem II (PSII), damaging the photosynthetic machinery. The arbuscular mycorrhizal (AM) symbiosis may improve host plant tolerance to salinity, but it is not clear how the AM symbiosis affects the plant photosynthetic capacity, particularly the efficiency of PSII. This study aimed at determining the influence of the AM symbiosis on the performance of PSII in rice plants subjected to salinity. Photosynthetic activity, plant gas-exchange parameters, accumulation of photosynthetic pigments and rubisco activity and gene expression were also measured in order to analyse comprehensively the response of the photosynthetic processes to AM symbiosis and salinity. Results showed that the AM symbiosis enhanced the actual quantum yield of PSII photochemistry and reduced the quantum yield of non-photochemical quenching in rice plants subjected to salinity. AM rice plants maintained higher net photosynthetic rate, stomatal conductance and transpiration rate than nonAM plants. Thus, we propose that AM rice plants had a higher photochemical efficiency for CO2 fixation and solar energy utilization and this increases plant salt tolerance by preventing the injury to the photosystems reaction centres and by allowing a better utilization of light energy in photochemical processes. All these processes translated into higher photosynthetic and rubisco activities in AM rice plants and improved plant biomass production under salinity.

  3. Induction of efficient energy dissipation in the isolated light-harvesting complex of Photosystem II in the absence of protein aggregation.

    PubMed

    Ilioaia, Cristian; Johnson, Matthew P; Horton, Peter; Ruban, Alexander V

    2008-10-24

    Under excess illumination, the Photosystem II light-harvesting antenna of higher plants has the ability to switch into an efficient photoprotective mode, allowing safe dissipation of excitation energy into heat. In this study, we show induction of the energy dissipation state, monitored by chlorophyll fluorescence quenching, in the isolated major light-harvesting complex (LHCII) incorporated into a solid gel system. Removal of detergent caused strong fluorescence quenching, which was totally reversible. Singlet-singlet annihilation and gel electrophoresis experiments suggested that the quenched complexes were in the trimeric not aggregated state. Both the formation and recovery of this quenching state were inhibited by a cross-linker, implying involvement of conformational changes. Absorption and CD measurements performed on the samples in the quenched state revealed specific alterations in the spectral bands assigned to the red forms of chlorophyll a, neoxanthin, and lutein 1 molecules. The majority of these alterations were similar to those observed during LHCII aggregation. This suggests that not the aggregation process as such but rather an intrinsic conformational transition in the complex is responsible for establishment of quenching. 77 K fluorescence measurements showed red-shifted chlorophyll a fluorescence in the 690-705 nm region, previously observed in aggregated LHCII. The fact that all spectral changes associated with the dissipative mode observed in the gel were different from those of the partially denatured complex strongly argues against the involvement of protein denaturation in the observed quenching. The implications of these findings for proposed mechanisms of energy dissipation in the Photosystem II antenna are discussed.