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Chiishiarng Chen - One of the best experts on this subject based on the ideXlab platform.

  • Generation of clade- and symbiont-specific antibodies to characterize marker molecules during Cnidaria-Symbiodinium Endosymbiosis.
    Scientific Reports, 2017
    Co-Authors: Kao-jean Huang, Ziyu Huang, Lihsueh Wang, Ching-yen Lin, Pin-hsiang Chou, Chiishiarng Chen
    Abstract:

    The Endosymbiosis between cnidarians and dinoflagellates is responsible for the formation of coral reefs. Changes in molecules have been identified during the process of cnidaria-Symbiodinium Endosymbiosis. However, the complexity of the molecular interaction has prevented the establishment of a mechanistic explanation of cellular regulation in this mutualistic symbiosis. To date, no marker molecules have been identified to specifically represent the symbiotic status. Because the endosymbiotic association occurs in the symbiotic gastrodermal cells (SGCs), whole cells of isolated SGCs were used as an antigen to generate monoclonal antibodies (mAb) to screen possible molecular candidates of symbiotic markers. The results showed that one of the generated monoclonal antibodies, 2–6F, specifically recognized clade C symbiotic Symbiodinium but not its free-living counterpart or other Symbiodinium clades. The expression levels of 2–6F mAb-recognized proteins are highly correlated with the symbiotic status, and these proteins were characterized as N-linked glycoproteins via treatment with peptide N-glycosidase F. Furthermore, their glycan moieties were markedly different from those of free-living Symbiodinium, potentially suggesting host regulation of post-translational modification. Consequently, the 2–6F mAb can be used to detect the symbiotic state of corals and investigate the complex molecular interactions in cnidaria-Symbiodinium Endosymbiosis.

  • membrane labeling of coral gastrodermal cells by biotinylation the proteomic identification of surface proteins involving cnidaria dinoflagellate Endosymbiosis
    PLOS ONE, 2014
    Co-Authors: Ziyu Huang, Paichiao Cheng, Shuhwa Chen, Chiishiarng Chen
    Abstract:

    The cellular and molecular-scale processes underlying the stability of coral-Symbiodinium endosymbioses remain unclear despite decades of investigation. As the coral gastroderm is the only tissue layer characterized by this unique symbiotic association, the membranes of these symbiotic gastrodermal cells (SGCs) may play important roles in the initiation and maintenance of the Endosymbiosis. In order to elucidate the interactions between the endosymbiotic dinoflagellates and their coral hosts, a thorough characterization of SGC membranes is therefore required. Cell surface proteins of isolated SGCs were biotinylated herein by a cell impermeant agent, biotin-XX sulfosuccinimidyl ester. The in situ distribution of these biotinylated proteins was uncovered by both fluorescence and transmission electron microscopic imaging of proteins bound to Alexa Fluor® 488-conjugated streptavidin. The identity of these proteins was then determined by two-dimensional gel electrophoresis followed by liquid chromatography-tandem mass spectrometry. Nineteen (19) proteins were identified, and they are known to be involved in the molecular chaperone/stress response, cytoskeletal remodeling, and energy metabolism. These results not only reveal the molecular characters of the host SGC membrane, but also provide critical insight into understanding the possible role of host membranes in this ecologically important endosymbiotic association.

  • fatty acid and phospholipid syntheses are prerequisites for the cell cycle of symbiodinium and their Endosymbiosis within sea anemones
    PLOS ONE, 2013
    Co-Authors: Lihsueh Wang, Chiishiarng Chen, Hsiehhe Lee, Leeshing Fang, Anderson B Mayfield
    Abstract:

    Lipids are a source of metabolic energy, as well as essential components of cellular membranes. Although they have been shown to be key players in the regulation of cell proliferation in various eukaryotes, including microalgae, their role in the cell cycle of cnidarian-dinoflagellate (genus Symbiodinium) endosymbioses remains to be elucidated. The present study examined the effects of a lipid synthesis inhibitor, cerulenin, on the cell cycle of both cultured Symbiodinium (clade B) and those engaged in an endosymbiotic association with the sea anemone Aiptasia pulchella. In the former, cerulenin exposure was found to inhibit free fatty acid (FFA) synthesis, as it does in other organisms. Additionally, while it also significantly inhibited the synthesis of phosphatidylethanolamine (PE), it did not affect the production of sterol ester (SE) or phosphatidylcholine (PC). Interestingly, cerulenin also significantly retarded cell division by arresting the cell cycles at the G0/G1 phase. Cerulenin-treated Symbiodinium were found to be taken up by anemone hosts at a significantly depressed quantity in comparison with control Symbiodinium. Furthermore, the uptake of cerulenin-treated Symbiodinium in host tentacles occurred much more slowly than in untreated controls. These results indicate that FFA and PE may play critical roles in the recognition, proliferation, and ultimately the success of Endosymbiosis with anemones.

Rüdiger Cerff - One of the best experts on this subject based on the ideXlab platform.

  • Physiology, phylogeny, early evolution, and GAPDH
    Protoplasma, 2017
    Co-Authors: William F. Martin, Rüdiger Cerff
    Abstract:

    The chloroplast and cytosol of plant cells harbor a number of parallel biochemical reactions germane to the Calvin cycle and glycolysis, respectively. These reactions are catalyzed by nuclear encoded, compartment-specific isoenzymes that differ in their physiochemical properties. The chloroplast cytosol isoenzymes of d -glyceraldehyde-3-phosphate dehydrogenase (GAPDH) harbor evidence of major events in the history of life: the origin of the first genes, the bacterial-archaeal split, the origin of eukaryotes, the evolution of protein compartmentation during eukaryote evolution, the origin of plastids, and the secondary Endosymbiosis among the algae with complex plastids. The reaction mechanism of GAPDH entails phosphorolysis of a thioester to yield an energy-rich acyl phosphate bond, a chemistry that points to primitive pathways of energy conservation that existed even before the origin of the first free-living cells. Here, we recount the main insights that chloroplast and cytosolic GAPDH provided into Endosymbiosis and physiological evolution.

  • a green phosphoribulokinase in complex algae with red plastids evidence for a single secondary Endosymbiosis leading to haptophytes cryptophytes heterokonts and dinoflagellates
    Journal of Molecular Evolution, 2006
    Co-Authors: Jörn Petersen, Henner Brinkmann, Rene Teich, Rüdiger Cerff
    Abstract:

    Phosphoribulokinase (PRK) is an essential enzyme of photosynthetic eukaryotes which is active in the plastid-located Calvin cycle and regenerates the substrate for ribulose-bisphosphate carboxylase/oxygenase (Rubisco). Rhodophytes and chlorophytes (red and green algae) recruited their nuclear-encoded PRK from the cyanobacterial ancestor of plastids. The plastids of these organisms can be traced back to a single primary Endosymbiosis, whereas, for example, haptophytes, dinoflagellates, and euglenophytes obtained their “complex” plastids through secondary endosymbioses, comprising the engulfment of a unicellular red or green alga by a eukaryotic host cell. We have cloned eight new PRK sequences from complex algae as well as a rhodophyte in order to investigate their evolutionary origin. All available PRK sequences were used for phylogenetic analyses and the significance of alternative topologies was estimated by the approximately unbiased test. Our analyses led to several astonishing findings. First, the close relationship of PRK genes of haptophytes, heterokontophytes, cryptophytes, and dinophytes (complex red lineage) supports a monophyletic origin of their sequences and hence their plastids. Second, based on PRK genes the complex red lineage forms a highly supported assemblage together with chlorophytes and land plants, to the exclusion of the rhodophytes. This green affinity is in striking contrast to the expected red algal origin and our analyses suggest that the PRK gene was acquired once via lateral transfer from a green alga. Third, surprisingly the complex green lineages leading to Bigelowiella and Euglena probably also obtained their PRK genes via lateral gene transfers from a red alga and a complex alga with red plastids, respectively.

  • A “Green” Phosphoribulokinase in Complex Algae with Red Plastids: Evidence for a Single Secondary Endosymbiosis Leading to Haptophytes, Cryptophytes, Heterokonts, and Dinoflagellates
    Journal of Molecular Evolution, 2006
    Co-Authors: Jörn Petersen, Henner Brinkmann, Rene Teich, Rüdiger Cerff
    Abstract:

    Phosphoribulokinase (PRK) is an essential enzyme of photosynthetic eukaryotes which is active in the plastid-located Calvin cycle and regenerates the substrate for ribulose-bisphosphate carboxylase/oxygenase (Rubisco). Rhodophytes and chlorophytes (red and green algae) recruited their nuclear-encoded PRK from the cyanobacterial ancestor of plastids. The plastids of these organisms can be traced back to a single primary Endosymbiosis, whereas, for example, haptophytes, dinoflagellates, and euglenophytes obtained their “complex” plastids through secondary endosymbioses, comprising the engulfment of a unicellular red or green alga by a eukaryotic host cell. We have cloned eight new PRK sequences from complex algae as well as a rhodophyte in order to investigate their evolutionary origin. All available PRK sequences were used for phylogenetic analyses and the significance of alternative topologies was estimated by the approximately unbiased test. Our analyses led to several astonishing findings. First, the close relationship of PRK genes of haptophytes, heterokontophytes, cryptophytes, and dinophytes (complex red lineage) supports a monophyletic origin of their sequences and hence their plastids. Second, based on PRK genes the complex red lineage forms a highly supported assemblage together with chlorophytes and land plants, to the exclusion of the rhodophytes. This green affinity is in striking contrast to the expected red algal origin and our analyses suggest that the PRK gene was acquired once via lateral transfer from a green alga. Third, surprisingly the complex green lineages leading to Bigelowiella and Euglena probably also obtained their PRK genes via lateral gene transfers from a red alga and a complex alga with red plastids, respectively.

  • a nuclear gene of eubacterial origin in euglena gracilis reflects cryptic endosymbioses during protist evolution
    Proceedings of the National Academy of Sciences of the United States of America, 1995
    Co-Authors: Katrin Henze, Rüdiger Cerff, A Badr, Michael Wettern, William Martin
    Abstract:

    Genes for glycolytic and Calvin-cycle glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of higher eukaryotes derive from ancient gene duplications which occurred in eubacterial genomes; both were transferred to the nucleus during the course of Endosymbiosis. We have cloned cDNAs encoding chloroplast and cytosolic GAPDH from the early-branching photosynthetic protist Euglena gracilis and have determined the structure of its nuclear gene for cytosolic GAPDH. The gene contains four introns which possess unusual secondary structures, do not obey the GT-AG rule, and are flanked by 2- to 3-bp direct repeats. A gene phylogeny for these sequences in the context of eubacterial homologues indicates that euglenozoa, like higher eukaryotes, have obtained their GAPDH genes from eubacteria via endosymbiotic (organelle-to-nucleus) gene transfer. The data further suggest that the early-branching protists Giardia lamblia and Entamoeba histolytica--which lack mitochondria--and portions of the trypanosome lineage have acquired GAPDH genes from eubacterial donors which did not ultimately give rise to contemporary membrane-bound organelles. Evidence that "cryptic" (possibly ephemeral) endosymbioses during evolution may have entailed successful gene transfer is preserved in protist nuclear gene sequences.

Debashish Bhattacharya - One of the best experts on this subject based on the ideXlab platform.

  • Photosynthetic Paulinella : Recapitulation of Primary Plastid Establishment
    Endosymbiosis, 2013
    Co-Authors: Hwan Su Yoon, Eun Chan Yang, Debashish Bhattacharya
    Abstract:

    The origin of photosynthesis in eukaryotes stems from a single primary Endosymbiosis between a heterotrophic protist cell and a cyanobacterium that occurred more than 1.5 billion years ago. This proto-algal population gave rise to three lineages of the Plantae (Rhodophyta, Viridiplantae, and Glaucophyta). Rhodoplasts and chloroplasts were later spread horizontally into other eukaryotic lineages through secondary Endosymbiosis. Primary Endosymbiosis is therefore a critical feature of eukaryotic evolution; however, it is difficult to study because of the long evolutionary time span that has passed since primary plastid origin. The filose amoeba Paulinella chromatophora is an exceptional species that contains two plastids, referred to as “chromatophores,” that originated from a Synechococcus-like cyanobacterium. Photosynthetic Paulinella provides an ideal model to gain insights into the origin of photoautotrophy because its sister species are all heterotrophs that prey on cyanobacteria. Here, we review the evolutionary process that led to this second instance of primary Endosymbiosis based on recent studies that include biodiversity surveys and plastid and nuclear genome data. Draft genome data from heterotrophic Paulinella using the single-cell genomics approach demonstrate two cases of horizontal gene transfer (HGT) from cyanobacteria, demonstrating that prey items are potential sources of foreign DNA in these taxa. Genome data from photosynthetic Paulinella provide evidence of massive gene loss from the chromatophore genome, endosymbiotic gene transfer (EGT) to the host nucleus, and the potential establishment of a plastid protein import system that relies on the secretory pathway in the amoeba. We also present recent data regarding postendosymbiotic speciation in photosynthetic Paulinella and lineage specific differential gene loss and EGT.

  • Single cell genome analysis supports a link between phagotrophy and primary plastid Endosymbiosis
    Scientific Reports, 2012
    Co-Authors: Debashish Bhattacharya, Dana C. Price, Hwan Su Yoon, Nicole J. Poulton, Eun Chan Yang, Robert A Andersen
    Abstract:

    Two cases of primary plastid Endosymbiosis are known. The first occurred ca. 1.6 billion years ago and putatively gave rise to the canonical plastid in algae and plants. The second is restricted to a genus of rhizarian amoebae that includes Paulinella chromatophora . Photosynthetic Paulinella species gained their plastid from an α-cyanobacterial source and are sister to plastid-lacking phagotrophs such as Paulinella ovalis that ingest cyanobacteria. To study the role of feeding behavior in plastid origin, we analyzed single-cell genome assemblies from six P. ovalis -like cells isolated from Chesapeake Bay, USA. Dozens of contigs in these cell assemblies were derived from prey DNA of α-cyanobacterial origin and associated cyanophages. We found two examples of horizontal gene transfer (HGT) in P. ovalis -like nuclear DNA from cyanobacterial sources. This work suggests the first evidence of a link between feeding behavior in wild-caught cells, HGT and plastid primary Endosymbiosis in the monophyletic Paulinella lineage.

  • Secondary and Tertiary Endosymbiosis and Kleptoplasty
    Advances in Photosynthesis and Respiration, 2012
    Co-Authors: Jeferson Gross, Debashish Bhattacharya, Karen N. Pelletreau, Mary E. Rumpho, Adrian Reyes-prieto
    Abstract:

    Alga is an informal name that refers to a diverse group of photosynthetic eukaryotes that have a polyphyletic origin in the tree of life. Although genomics has provided powerful tools for understanding the evolution of algal photosynthesis many issues remain unresolved. These include explaining the intermingling of plastid-lacking taxa such as ciliates and oomycetes among plastid-containing groups of chromalveolates. Does this pattern reflect a single ancient Endosymbiosis in the chromalveolate ancestor followed by independent plastid losses or multiple secondary endosymbioses? Here we review current knowledge about chromalveolate evolution and phylogeny with a focus on secondary and tertiary Endosymbiosis and survey recent genome-wide analyses to assess the potentially broad and lasting impacts of plastid transfer on eukaryote evolution. We assess the evidence for ‘footprints’ of photosynthetic pasts that remain even when the plastid is lost. These data comprise remnant algal genes in the nucleus of plastid-lacking taxa that have putatively originated via intracellular gene transfer from the former endosymbiont. We also provide a survey of recent work done in the field of protein import (i.e., via translocons) into chromalveolate and other plastids derived from secondary endoysmbiosis. We contrast the similarities and differences between primary and secondary plastid protein import machineries and speculate on the key innovations that led to their establishment. And finally, we take a careful look at the remarkable case of sea slug (Elysia chlorotica) kleptoplasty and photosynthesis and review recent work aimed at explaining this phenomenon in different metazoa. In particular, we critically assess support for the hypothesis that sea slug photosynthesis is explained by massive horizontal gene transfer (HGT) from the genome of the captured alga.

  • Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms
    Science, 2009
    Co-Authors: Ahmed A. Moustafa, Bank Beszteri, Uwe G. Maier, Chris Bowler, Klaus Valentin, Debashish Bhattacharya
    Abstract:

    Diatoms and other chromalveolates are among the dominant phytoplankters in the world's oceans. Endosymbiosis was essential to the success of chromalveolates, and it appears that the ancestral plastid in this group had a red algal origin via an ancient secondary Endosymbiosis. However, recent analyses have turned up a handful of nuclear genes in chromalveolates that are of green algal derivation. Using a genome-wide approach to estimate the "green" contribution to diatoms, we identified >1700 green gene transfers, constituting 16% of the diatom nuclear coding potential. These genes were probably introduced into diatoms and other chromalveolates from a cryptic endosymbiont related to prasinophyte-like green algae. Chromalveolates appear to have recruited genes from the two major existing algal groups to forge a highly successful, species-rich protist lineage.

  • Plastid Endosymbiosis. Sources and Timing of the Major Events.
    Evolution of Primary Producers in the Sea, 2007
    Co-Authors: Jeremiah D. Hackett, Hwan Su Yoon, Nicholas J. Butterfield, Michael J. Sanderson, Debashish Bhattacharya
    Abstract:

    Publisher Summary This chapter reviews the current ideas regarding the origin of plastids in eukaryotes and the timing of these events, with particular emphasis on the initial source of eukaryotic photosynthesis. First, a general introduction is provided on plastid Endosymbiosis. The currently available evidence suggests that a single primary Endosymbiosis gave rise to the Plantae, comprising the glaucophytes, red algae, and Viridiplantae. The chapter looks in detail at the evidence regarding the source and timing of the plastids that have resulted from primary, secondary, and tertiary Endosymbiosis. The greatest attention is paid to the primary Endosymbiosis. Primary plastid's origin and Plantae monophyly are discussed in detail. The unique and relatively late appearance of photosynthetic eukaryotes has important implications for understanding the early biosphere and its fossil record. Nuclear phylogeny supports the monophyly of photosynthetic eukaryotes containing a primary plastid, and molecular clock estimates provide a timeline for reconstructing the early evolutionary history of the Plantae. Together with the fossil and geochemical records, these data provide an increasingly resolved view of early eukaryotic photosynthesis and, by extension, important features in evolutionary and Earth history. Plastid Endosymbiosis has clearly been a driving force in eukaryotic evolution and instrumental to the success of many eukaryotic groups and has influenced the evolution of other organisms that utilize these organisms for food or habitat. Ongoing studies of Paulinella may shed light on the early stages of primary Endosymbiosis, a process that has profoundly impacted evolution of life on Earth.

Geoffrey I Mcfadden - One of the best experts on this subject based on the ideXlab platform.

  • complete nucleotide sequence of the chlorarachniophyte nucleomorph nature s smallest nucleus
    Proceedings of the National Academy of Sciences of the United States of America, 2006
    Co-Authors: Paul R. Gilson, Claudio H. Slamovits, Vanessa Su, Michael Reith, Patrick J. Keeling, Geoffrey I Mcfadden
    Abstract:

    The introduction of plastids into different heterotrophic protists created lineages of algae that diversified explosively, proliferated in marine and freshwater environments, and radically altered the biosphere. The origins of these secondary plastids are usually inferred from the presence of additional plastid membranes. However, two examples provide unique snapshots of secondary-Endosymbiosis-in-action, because they retain a vestige of the endosymbiont nucleus known as the nucleomorph. These are chlorarachniophytes and cryptomonads, which acquired their plastids from a green and red alga respectively. To allow comparisons between them, we have sequenced the nucleomorph genome from the chlorarachniophyte Bigelowiella natans: at a mere 373,000 bp and with only 331 genes, the smallest nuclear genome known and a model for extreme reduction. The genome is eukaryotic in nature, with three linear chromosomes containing densely packed genes with numerous overlaps. The genome is replete with 852 introns, but these are the smallest introns known, being only 18, 19, 20, or 21 nt in length. These pygmy introns are shown to be miniaturized versions of normal-sized introns present in the endosymbiont at the time of capture. Seventeen nucleomorph genes encode proteins that function in the plastid. The other nucleomorph genes are housekeeping entities, presumably underpinning maintenance and expression of these plastid proteins. Chlorarachniophyte plastids are thus serviced by three different genomes (plastid, nucleomorph, and host nucleus) requiring remarkable coordination and targeting. Although originating by two independent endosymbioses, chlorarachniophyte and cryptomonad nucleomorph genomes have converged upon remarkably similar architectures but differ in many molecular details that reflect two distinct trajectories to hypercompaction and reduction.

  • Translocation of proteins across the multiple membranes of complex plastids.
    Biochimica et biophysica acta, 2001
    Co-Authors: Giel G. Van Dooren, Tatsuaki Osafune, Steven D Schwartzbach, Geoffrey I Mcfadden
    Abstract:

    Secondary Endosymbiosis describes the origin of plastids in several major algal groups such as dinoflagellates, euglenoids, heterokonts, haptophytes, cryptomonads, chlorarachniophytes and parasites such as apicomplexa. An integral part of secondary Endosymbiosis has been the transfer of genes for plastid proteins from the endosymbiont to the host nucleus. Targeting of the encoded proteins back to the plastid from their new site of synthesis in the host involves targeting across the multiple membranes surrounding these complex plastids. Although this process shows many overall similarities in the different algal groups, it is emerging that differences exist in the mechanisms adopted.

  • Primary and secondary Endosymbiosis and the origin of plastids
    Journal of Phycology, 2001
    Co-Authors: Geoffrey I Mcfadden
    Abstract:

    The theory of Endosymbiosis describes the origin of plastids from cyanobacterial-like prokaryotes living within eukaryotic host cells. The endosymbionts are much reduced, but morphological, biochemical, and molecular studies provide clear evidence of a prokaryotic ancestry for plastids. There appears to have been a single (primary) Endosymbiosis that produced plastids with two bounding membranes, such as those in green algae, plants, red algae, and glaucophytes. A subsequent round of endosymbioses, in which red or green algae were engulfed and retained by eukaryotic hosts, transferred photosynthesis into other eukaryotic lineages. These endosymbiotic plastid acquisitions from eukaryotic algae are referred to as secondary endosymbioses, and the resulting plastids classically have three or four bounding membranes. Secondary endosymbioses have been a potent factor in eukaryotic evolution, producing much of the modern diversity of life.

  • Plastids and protein targeting.
    Journal of Eukaryotic Microbiology, 1999
    Co-Authors: Geoffrey I Mcfadden
    Abstract:

    : Plastids with two bounding membranes--as exemplified by red algae, green algae, plants, and glaucophytes--derive from primary Endosymbiosis; a process involving engulfment and retention of a cyanobacterium by a phagotrophic eukaryote. Plastids with more than two bounding membranes (such as those of euglenoids, dinoflagellates, heterokonts, haptopytes, apicomplexa, cryptomonads, and chlorarachniophytes) probably arose by secondary Endosymbiosis, in which a eukaryotic alga (itself the product of primary Endosymbiosis) was engulfed and retained by a phagotroph. Secondary Endosymbiosis transfers photosynthetic capacity into heterotrophic lineages, has apparently occurred numerous times, and has created several major eukaryotic lineages comprising upwards of 42,600 species. Plastids acquired by secondary Endosymbiosis are sometimes referred to as "second-hand." Establishment of secondary endosymbioses has involved transfer of genes from the endosymbiont nucleus to the secondary host nucleus. Limited gene transfer could initially have served to stabilise the endosymbioses, but it is clear that the transfer process has been extensive, leading in many cases to the complete disappearance of the endosymbiont nucleus. One consequence of these gene transfers is that gene products required in the plastid must be targeted into the organelle across multiple membranes: at least three for stromal proteins in euglenoids and dinoflagellates, and across five membranes in the case of thylakoid lumen proteins in plastids with four bounding membranes. Evolution of such targeting mechanisms was obviously a key step in the successful establishment of each different secondary Endosymbiosis. Analysis of targeted proteins in the various organisms now suggests that a similar system is used by each group. However, rather than interpreting this similarity as evidence of an homologous origin, I believe that targeting has evolved convergently by combining and recycling existing protein trafficking mechanisms already existing in the endosymbiont and host. Indeed, by analyzing the multiple motifs in targeting sequences of some genes it is possible to infer that they originated in the plastid genome, transferred from there into the primary host nucleus, and subsequently moved into the secondary host nucleus. Thus, each step of the targeting process in "second-hand" plastids recapitulates the gene's previous intracellular transfers.

  • What’s Eating Eu? The Role of Eukaryote/Eukaryote Endosymbioses in Plastid Origins
    Eukaryotism and Symbiosis, 1997
    Co-Authors: Geoffrey I Mcfadden, Paul Gilson
    Abstract:

    The plastids of green algae, and their descendants the land plants, clearly arose from a cyanobacterium-like endocytobiont. An early eukaryote (thus far unidentified) is believed to have phagocytosed a photosynthetic prokaryote and retained it as an endocytobiont. Having relinquished its autonomy, the endocytobiont is now reduced to organelle status (exogenosome) within the former eukaryotic host. The two membranes surrounding the plastid probably represent the two membranes of the gram-negative endocytobiont. A third membrane (presumed to have been created from the host plasma membrane during the en-gulfment of the endocytobiont) is now apparently lost. This scenario for plastid origin in green algae is termed a primary Endosymbiosis. Plastids of red algae probably also derive from a primary Endosymbiosis, quite possibly the same one as led to green algal plastids. Origins of plastids in other algal groups are less clear. The three-membraned plastids of dinoflagellates and euglenoids could also have arisen from one or more primary endosymbioses but with the food vacuole membrane being retained. However, the paucity of molecular data, particularly from dinoflagellates, leaves the origin of their plastids open to several different interpretations. The origin of plastids surrounded by four membranes (as occur in heterokonts, haptophytes, cryptophytes, and chlorarachniophytes) is hypothesised to involve two sequential endocytobioses. First, a primary Endosymbiosis between a eukaryote and a prokaryote created a photosynthetic eukaryote analogous to, or perhaps even homologous to, the archetypal algal cell. This primary Endosymbiosis was then followed by secondary Endosymbiosis between a phagotrophic eukaryote and the product of the primary Endosymbiosis to create a eukaryote with a photosynthetic eukaryotic endocytobiont. Secondary Endosymbiosis produces plastids with four membranes: two from the original gram-negative prokaryote, a third from the plasma membrane of the primary host, and a fourth from the food vacuole of the secondary host. Initially, the nucleus and cytoplasm of the endocytobiont probably persisted, but in the case of heterokonts and haptophytes these structures have now apparently vanished leaving an essentially empty space between the endocytobiont’s plasma membrane and the two membranes of the plastid. In the case of cryptomonads and chlorarachniophytes, however, it has now been shown that vestiges of the endocytobiont’s nucleus and cytoplasm are retained. Now much reduced, these nucleocytoplasmic remnants are an invaluable key to unraveling the history of plastid origins through eukaryote/eukaryote en-docytobioses. The extra membranes surrounding the plastids pose novel challenges for understanding targeting of proteins into plastids and a hypothesis for targeting is presented. The extraordinarily compact nuclear genomes of the en-docytobionts are now being sequenced and could prove to be useful models for the coming wave of eukaryotic genome research.

Ken-ichiro Ishida - One of the best experts on this subject based on the ideXlab platform.

  • Polyploidy of Endosymbiotically Derived Genomes in Complex Algae
    Genome Biology and Evolution, 2014
    Co-Authors: Yoshihisa Hirakawa, Ken-ichiro Ishida
    Abstract:

    Chlorarachniophyte and cryptophyte algae have complex plastids that were acquired by the uptake of a green or red algal endosymbiont via secondary Endosymbiosis. The plastid is surrounded by four membranes, and a relict nucleus, called the nucleomorph, remains in the periplastidal compartment that is the remnant cytoplasm of the endosymbiont. Thus, these two algae possess four different genomes in a cell: Nuclear, nucleomorph, plastid, and mitochondrial. Recently, sequencing of the nuclear genomes of the chlorarachniophyte Bigelowiella natans and the cryptophyte Guillardia theta has been completed, and all four genomes have been made available. However, the copy number of each genome has never been investigated. It is important to know the actual DNA content of each genome, especially the highly reduced nucleomorph genome, for studies on genome evolution. In this study, we calculated genomic copy numbers in B. natans and G. theta using a real-time quantitative polymerase chain reaction approach. The nuclear genomes were haploid in both species, whereas the nucleomorph genomes were estimated to be diploid and tetraploid, respectively. Mitochondria and plastids contained a large copy number of genomic DNA in each cell. In the secondary endosymbioses of chlorarachniophytes and cryptophytes, the endosymbiont nuclear genomes were highly reduced in size and in the number of coding genes, whereas the chromosomal copy number was increased, as in bacterial endosymbiont genomes. This suggests that polyploidization is a general characteristic of highly reduced genomes in broad prokaryotic and eukaryotic endosymbionts.

  • internal plastid targeting signal found in a rubisco small subunit protein of a chlorarachniophyte alga
    Plant Journal, 2010
    Co-Authors: Yoshihisa Hirakawa, Ken-ichiro Ishida
    Abstract:

    SUMMARYInallplantsandalgae,mostplastidproteinsareencodedbythenucleargenomeand,consequently,needtobetransportedinto plastidsacross multiple membranes.In organismswith secondaryplastids, which evolved bysecondary endosymbioses, and are surrounded by three or four envelope membranes, precursors of nuclear-encoded plastid proteins generally have an N-terminal bipartite targeting sequence that consists of anendoplasmic reticulum (ER)-targeting signal peptide (SP) and a transit peptide-like (TPL) sequence. Thebipartite targeting sequences have been demonstrated to be necessary and sufficient for targeting proteinsinto the plastids of many algal groups, including chlorarachniophytes. Here, we report a new type of targetingsignal that is required for delivering a RubisCO small subunit (RbcS) protein into the secondary plastids ofchlorarachniophyte algae. In this study, we analyzed the plastid-targeting ability of an RbcS pre-protein, usinggreen fluorescent protein (GFP) as a reporter molecule in chlorarachniophyte cells. We demonstrate that theN-terminal bipartite targeting sequence of the RbcS pre-protein is not sufficient, and that a part of the matureprotein is also necessary for plastid targeting. By deletion analyses of amino acids, we determined theapproximate location of an internal plastid-targeting signal within the mature protein, which is involved intargeting the protein from the ER into the chlorarachniophyte plastids.Keywords: plastid targeting, RubisCO small subunit, chlorarachniophyte, secondary Endosymbiosis, bipartitetargeting sequence, transit peptide.INTRODUCTIONPlastids evolved by a single primary Endosymbiosis, andsubsequent lateral transfers to several different eukaryotelineages via multiple secondary endosymbioses (Martinet al., 1998; McFadden, 2001; Keeling et al., 2004). In the pri-mary Endosymbiosis, a cyanobacterium was incorporatedinto a non-photosynthetic eukaryote cell, and evolved intothe two-membrane-bound plastids (so-called primary plast-ids) of land plants, green algae, red algae and glaucophytes(Martin et al., 1998; Moreira et al., 2000; Rodri´guez-Ezpeletaet al., 2005). In the subsequent secondary endosymbioses,several different photosynthetic eukaryotes containingprimary plastids were engulfed and retained by eukaryoticcells in different lineages; these evolved into so-calledsecondary plastids that are surrounded by three or fourenvelope membranes (Cavalier-Smith, 2000; Keeling et al.,2004). The evolutionary lateral transfer of plastids resultedin a remarkable structural diversity of plastids and cellsamong photosynthetic eukaryotes, and had a significantimpact on the evolution and diversity of lives on earth(Ishida, 2005).In these endosymbiotic processes, a large number ofgenes were transferred from the endosymbionts to thehost’s nuclear genomes. Precursors of the nuclear-encodedplastid proteins must consequently be sent back to plastids(the endosymbionts) across several envelope membranes:two membranes in primary plastids and three or fourmembranesinsecondaryplastids.Systemsforthetransportof nuclear-encoded plastid proteins into plastids haveaccordingly developed in order to maintain the endos-ymbionts as photosynthetic organelles (Ishida, 2005;Nassoury and Morse, 2005; Bolte et al., 2009). The targetingsignals for pre-proteins targeted into primary plastids andtheir transport mechanisms have been well studied in landplants. In land plant cells, each precursor of the plastid-targeted proteins, which is post-translationally transportedinto the plastid, has a plastid-targeting sequence in itsN-terminal extension, referred to as the transit peptide (TP)(Bruce, 2000, 2001). This targeting signal is recognized byprotein translocator complexes called TOC and TIC (translo-consattheouter/innerenvelopemembraneofchloroplasts),

  • Internal plastid‐targeting signal found in a RubisCO small subunit protein of a chlorarachniophyte alga
    Plant Journal, 2010
    Co-Authors: Yoshihisa Hirakawa, Ken-ichiro Ishida
    Abstract:

    SUMMARYInallplantsandalgae,mostplastidproteinsareencodedbythenucleargenomeand,consequently,needtobetransportedinto plastidsacross multiple membranes.In organismswith secondaryplastids, which evolved bysecondary endosymbioses, and are surrounded by three or four envelope membranes, precursors of nuclear-encoded plastid proteins generally have an N-terminal bipartite targeting sequence that consists of anendoplasmic reticulum (ER)-targeting signal peptide (SP) and a transit peptide-like (TPL) sequence. Thebipartite targeting sequences have been demonstrated to be necessary and sufficient for targeting proteinsinto the plastids of many algal groups, including chlorarachniophytes. Here, we report a new type of targetingsignal that is required for delivering a RubisCO small subunit (RbcS) protein into the secondary plastids ofchlorarachniophyte algae. In this study, we analyzed the plastid-targeting ability of an RbcS pre-protein, usinggreen fluorescent protein (GFP) as a reporter molecule in chlorarachniophyte cells. We demonstrate that theN-terminal bipartite targeting sequence of the RbcS pre-protein is not sufficient, and that a part of the matureprotein is also necessary for plastid targeting. By deletion analyses of amino acids, we determined theapproximate location of an internal plastid-targeting signal within the mature protein, which is involved intargeting the protein from the ER into the chlorarachniophyte plastids.Keywords: plastid targeting, RubisCO small subunit, chlorarachniophyte, secondary Endosymbiosis, bipartitetargeting sequence, transit peptide.INTRODUCTIONPlastids evolved by a single primary Endosymbiosis, andsubsequent lateral transfers to several different eukaryotelineages via multiple secondary endosymbioses (Martinet al., 1998; McFadden, 2001; Keeling et al., 2004). In the pri-mary Endosymbiosis, a cyanobacterium was incorporatedinto a non-photosynthetic eukaryote cell, and evolved intothe two-membrane-bound plastids (so-called primary plast-ids) of land plants, green algae, red algae and glaucophytes(Martin et al., 1998; Moreira et al., 2000; Rodri´guez-Ezpeletaet al., 2005). In the subsequent secondary endosymbioses,several different photosynthetic eukaryotes containingprimary plastids were engulfed and retained by eukaryoticcells in different lineages; these evolved into so-calledsecondary plastids that are surrounded by three or fourenvelope membranes (Cavalier-Smith, 2000; Keeling et al.,2004). The evolutionary lateral transfer of plastids resultedin a remarkable structural diversity of plastids and cellsamong photosynthetic eukaryotes, and had a significantimpact on the evolution and diversity of lives on earth(Ishida, 2005).In these endosymbiotic processes, a large number ofgenes were transferred from the endosymbionts to thehost’s nuclear genomes. Precursors of the nuclear-encodedplastid proteins must consequently be sent back to plastids(the endosymbionts) across several envelope membranes:two membranes in primary plastids and three or fourmembranesinsecondaryplastids.Systemsforthetransportof nuclear-encoded plastid proteins into plastids haveaccordingly developed in order to maintain the endos-ymbionts as photosynthetic organelles (Ishida, 2005;Nassoury and Morse, 2005; Bolte et al., 2009). The targetingsignals for pre-proteins targeted into primary plastids andtheir transport mechanisms have been well studied in landplants. In land plant cells, each precursor of the plastid-targeted proteins, which is post-translationally transportedinto the plastid, has a plastid-targeting sequence in itsN-terminal extension, referred to as the transit peptide (TP)(Bruce, 2000, 2001). This targeting signal is recognized byprotein translocator complexes called TOC and TIC (translo-consattheouter/innerenvelopemembraneofchloroplasts),

  • Protein targeting into plastids: a key to understanding the symbiogenetic acquisitions of plastids
    Journal of Plant Research, 2005
    Co-Authors: Ken-ichiro Ishida
    Abstract:

    Recent progress in molecular phylogenetics has proven that photosynthetic eukaryotes acquired plastids via primary and secondary Endosymbiosis and has given us information about the origin of each plastid. How a photosynthetic endosymbiont became a plastid in each group is, however, poorly understood, especially for the organisms with secondary plastids. Investigating how a nuclear-encoded plastid protein is targeted into a plastid in each photosynthetic group is one of the most important keys to understanding the evolutionary process of symbiogenetic plastid acquisition and its diversity. For organisms which originated through primary Endosymbiosis, protein targeting into plastids has been well studied at the molecular level. For organisms which originated through secondary Endosymbiosis, molecular-level studies have just started on the plastid-targeted protein-precursor sequences and the targeting pathways of the precursors. However, little information is available about how the proteins get across the inner two or three envelope membranes in organisms with secondary plastids. A good in vitro protein-import system for isolated plastids and a cell transformation system must be established for each group of photosynthetic eukaryotes in order to understand the mechanisms, the evolutionary processes and the diversity of symbiogenetic plastid acquisitions in photosynthetic eukaryotes.