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ARTHOFER WOLFGANG, SCHÜLER SILVIO, STEINER FLORIANM, SCHLICK-STEINER BIRGITC. Chloroplast DNA-based studies in molecular ecology may be compromised by nuclear-encoded plastid sequence. Mol Ecol 2010; 19:3853-6. [DOI: 10.1111/j.1365-294x.2010.04787.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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202
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Nowack ECM, Vogel H, Groth M, Grossman AR, Melkonian M, Glockner G. Endosymbiotic Gene Transfer and Transcriptional Regulation of Transferred Genes in Paulinella chromatophora. Mol Biol Evol 2010; 28:407-22. [DOI: 10.1093/molbev/msq209] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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203
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Martín M, Sabater B. Plastid ndh genes in plant evolution. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2010; 48:636-45. [PMID: 20493721 DOI: 10.1016/j.plaphy.2010.04.009] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 04/15/2010] [Accepted: 04/24/2010] [Indexed: 05/02/2023]
Abstract
The plastid ndh genes encode components of the thylakoid Ndh complex which purportedly acts as an electron feeding valve to adjust the redox level of the cyclic photosynthetic electron transporters. During the process of evolution from endosymbiosis to modern chloroplast, most cyanobacterial genes were lost or transferred to nucleus. Eleven ndh genes are among the 150-200 genes remaining in higher plant chloroplast DNA, out of some 3000 genes in the original prokaryotic Cyanobacteria in which homologues to ndh genes encode components of the respiratory Complex I and probably other complexes. The ndh genes are absent in all sequenced plastid DNAs of algae except for the Charophyceae and some Prasinophyceae. With the possible exclusion of some Conifers and Gnetales, the plastid DNA of all photosynthetic land plants contains the ndh genes, whereas they are absent in epiphytic plants that have also lost genes for the photosynthetic machinery. Therefore, the functional role of the ndh genes seems closely related to the land adaptation of photosynthesis. Transcripts of several plastid genes require C to U editing. The ndh genes concentrate about 50% of the editing sites of angiosperm plastid transcripts. Editing sites may be remnants from an ancestor in which a number of T to C inactivating mutations took place in the ndh genes which, during evolution, are being corrected back to T. The comparison of homologous editing sites in the mRNAs of angiosperm ndh genes provides a tool to investigate selective and permissive environmental conditions of past evolutionary events.
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Affiliation(s)
- Mercedes Martín
- Department of Plant Biology, University of Alcalá, Alcalá de Henares, 28871 Madrid, Spain
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204
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Chou JY, Hung YS, Lin KH, Lee HY, Leu JY. Multiple molecular mechanisms cause reproductive isolation between three yeast species. PLoS Biol 2010; 8:e1000432. [PMID: 20652018 PMCID: PMC2907292 DOI: 10.1371/journal.pbio.1000432] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 06/10/2010] [Indexed: 11/30/2022] Open
Abstract
Incompatibility between nuclear and mitochondrial genomes in yeast species may represent a general mechanism of reproductive isolation during yeast evolution. Nuclear-mitochondrial conflict (cytonuclear incompatibility) is a specific form of Dobzhansky-Muller incompatibility previously shown to cause reproductive isolation in two yeast species. Here, we identified two new incompatible genes, MRS1 and AIM22, through a systematic study of F2 hybrid sterility caused by cytonuclear incompatibility in three closely related Saccharomyces species (S. cerevisiae, S. paradoxus, and S. bayanus). Mrs1 is a nuclear gene product required for splicing specific introns in the mitochondrial COX1, and Aim22 is a ligase encoded in the nucleus that is required for mitochondrial protein lipoylation. By comparing different species, our result suggests that the functional changes in MRS1 are a result of coevolution with changes in the COX1 introns. Further molecular analyses demonstrate that three nonsynonymous mutations are responsible for the functional differences of Mrs1 between these species. Functional complementation assays to determine when these incompatible genes altered their functions show a strong correlation between the sequence-based phylogeny and the evolution of cytonuclear incompatibility. Our results suggest that nuclear-mitochondrial incompatibility may represent a general mechanism of reproductive isolation during yeast evolution. Hybrids between species are usually inviable or sterile, possibly due to functional incompatibility between genes from the different species. Incompatible genes are hypothesized to encode interacting components that cannot function properly when paired with alleles from another species. To understand how incompatible gene pairs result in hybrid sterility or inviability, it is important to identify these genes and reconstruct their evolutionary history. A previous study has shown that incompatibility between nuclear and mitochondrial genomes (cytonuclear incompatibility) causes hybrid sterility between two yeast species. To expand on these findings, we screened three yeast species for genes involved in cytonuclear incompatibility, discovering two nuclear genes, MRS1 and AIM22, which encode proteins that are unable to support full mitochondrial function in the hybrids. Of these two genes, Mrs1 is required for removing a specific intron in the mitochondrial COX1 gene. By comparing different yeast species, we find a clear coevolutionary relationship between Mrs1 function and the COX1 intron pattern. We also show that changes in three amino acids in the Mrs1 RNA-binding domain are sufficient to make Mrs1 incompatible in hybrids. Our results suggest that cytonuclear incompatibility may represent a general mechanism of reproductive isolation during yeast evolution.
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Affiliation(s)
- Jui-Yu Chou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yin-Shan Hung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kuan-Huei Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hsin-Yi Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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205
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Reyes-Prieto A, Yoon HS, Moustafa A, Yang EC, Andersen RA, Boo SM, Nakayama T, Ishida KI, Bhattacharya D. Differential gene retention in plastids of common recent origin. Mol Biol Evol 2010; 27:1530-7. [PMID: 20123796 PMCID: PMC2912470 DOI: 10.1093/molbev/msq032] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The cyanobacterium-derived plastids of algae and plants have supported the diversification of much of extant eukaryotic life. Inferences about early events in plastid evolution must rely on reconstructing events that occurred over a billion years ago. In contrast, the photosynthetic amoeba Paulinella chromatophora provides an exceptional model to study organelle evolution in a prokaryote-eukaryote (primary) endosymbiosis that occurred approximately 60 mya. Here we sequenced the plastid genome (0.977 Mb) from the recently described Paulinella FK01 and compared the sequence with the existing data from the sister taxon Paulinella M0880/a. Alignment of the two plastid genomes shows significant conservation of gene order and only a handful of minor gene rearrangements. Analysis of gene content reveals 66 differential gene losses that appear to be outright gene deletions rather than endosymbiotic gene transfers to the host nuclear genome. Phylogenomic analysis validates the plastid ancestor as a member of the Synechococcus-Prochlorococcus group, and the cyanobacterial provenance of all plastid genes suggests that these organelles were not targets of interphylum gene transfers after endosymbiosis. Inspection of 681 DNA alignments of protein-encoding genes shows that the vast majority have dN/dS ratios <<1, providing evidence for purifying selection. Our study demonstrates that plastid genomes in sister taxa are strongly constrained by selection but follow distinct trajectories during the earlier phases of organelle evolution.
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Affiliation(s)
- Adrian Reyes-Prieto
- Department of Ecology, Evolution and Natural Resources, Rutgers University
- Institute of Marine and Coastal Sciences, Rutgers University
| | - Hwan Su Yoon
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME
| | - Ahmed Moustafa
- Department of Ecology, Evolution and Natural Resources, Rutgers University
- Institute of Marine and Coastal Sciences, Rutgers University
| | - Eun Chan Yang
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME
| | | | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Takuro Nakayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Ken-ichiro Ishida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University
- Institute of Marine and Coastal Sciences, Rutgers University
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206
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A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum. BMC Evol Biol 2010; 10:191. [PMID: 20565933 PMCID: PMC3055265 DOI: 10.1186/1471-2148-10-191] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 06/21/2010] [Indexed: 11/30/2022] Open
Abstract
Background Plastid replacements through secondary endosymbioses include massive transfer of genes from the endosymbiont to the host nucleus and require a new targeting system to enable transport of the plastid-targeted proteins across 3-4 plastid membranes. The dinoflagellates are the only eukaryotic lineage that has been shown to have undergone several plastid replacement events, and this group is thus highly relevant for studying the processes involved in plastid evolution. In this study, we analyzed the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastid rather than the red algal-derived, peridinin-containing plastid usually found in photosynthetic dinoflagellates. Results We sequenced 4,746 randomly picked clones from a L. chlorophorum cDNA library. 22 of the assembled genes were identified as genes encoding proteins functioning in plastids. Some of these were of green algal origin. This confirms that genes have been transferred from the plastid to the host nucleus of L. chlorophorum and indicates that the plastid is fully integrated as an organelle in the host. Other nuclear-encoded plastid-targeted protein genes, however, are clearly not of green algal origin, but have been derived from a number of different algal groups, including dinoflagellates, streptophytes, heterokonts, and red algae. The characteristics of N-terminal plastid-targeting peptides of all of these genes are substantially different from those found in peridinin-containing dinoflagellates and green algae. Conclusions L. chlorophorum expresses plastid-targeted proteins with a range of different origins, which probably arose through endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT). The N-terminal extension of the genes is different from the extensions found in green alga and other dinoflagellates (peridinin- and haptophyte plastids). These modifications have likely enabled the mosaic proteome of L. chlorophorum.
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207
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Allen JF. Why chloroplasts and mitochondria contain genomes. Comp Funct Genomics 2010; 4:31-6. [PMID: 18629105 PMCID: PMC2447392 DOI: 10.1002/cfg.245] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2002] [Accepted: 11/25/2002] [Indexed: 11/05/2022] Open
Abstract
Chloroplasts and mitochondria originated as bacterial symbionts. The larger, host
cells acquired genetic information from their prokaryotic guests by lateral gene
transfer. The prokaryotically-derived genes of the eukaryotic cell nucleus now
function to encode the great majority of chloroplast and mitochondrial proteins,
as well as many proteins of the nucleus and cytosol. Genes are copied and moved
between cellular compartments with relative ease, and there is no established obstacle
to successful import of any protein precursor from the cytosol. Yet chloroplasts and
mitochondria have not abdicated all genes and gene expression to the nucleus and
to cytosolic translation. What, then, do chloroplast- and mitochondrially-encoded
proteins have in common that confers a selective advantage on the cytoplasmic
location of their genes? The proposal advanced here is that co-location of chloroplast
and mitochondrial genes with their gene products is required for rapid and direct
regulatory coupling. Redox control of gene expression is suggested as the common
feature of those chloroplast and mitochondrial proteins that are encoded in situ.
Recent evidence is consistent with this hypothesis, and its underlying assumptions
and predictions are described.
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Affiliation(s)
- John F Allen
- Plant Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund SE-221 00, Sweden.
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208
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Chou JY, Leu JY. Speciation through cytonuclear incompatibility: Insights from yeast and implications for higher eukaryotes. Bioessays 2010; 32:401-11. [DOI: 10.1002/bies.200900162] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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209
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Bacterial infections associated with cancer: possible implication in etiology with special reference to lateral gene transfer. Cancer Metastasis Rev 2010; 29:331-7. [DOI: 10.1007/s10555-010-9217-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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210
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Lim L, McFadden GI. The evolution, metabolism and functions of the apicoplast. Philos Trans R Soc Lond B Biol Sci 2010; 365:749-63. [PMID: 20124342 PMCID: PMC2817234 DOI: 10.1098/rstb.2009.0273] [Citation(s) in RCA: 205] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The malaria parasite, Plasmodium falciparum, harbours a relict plastid known as the ‘apicoplast’. The discovery of the apicoplast ushered in an exciting new prospect for drug development against the parasite. The eubacterial ancestry of the organelle offers a wealth of opportunities for the development of therapeutic interventions. Morphological, biochemical and bioinformatic studies of the apicoplast have further reinforced its ‘plant-like’ characteristics and potential as a drug target. However, we are still not sure why the apicoplast is essential for the parasite's survival. This review explores the origins and metabolic functions of the apicoplast. In an attempt to decipher the role of the organelle within the parasite we also take a closer look at the transporters decorating the plastid to better understand the metabolic exchanges between the apicoplast and the rest of the parasite cell.
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Affiliation(s)
- Liting Lim
- School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia
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211
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Martin W. Evolutionary origins of metabolic compartmentalization in eukaryotes. Philos Trans R Soc Lond B Biol Sci 2010; 365:847-55. [PMID: 20124349 PMCID: PMC2817231 DOI: 10.1098/rstb.2009.0252] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Many genes in eukaryotes are acquisitions from the free-living antecedents of chloroplasts and mitochondria. But there is no evolutionary 'homing device' that automatically directs the protein product of a transferred gene back to the organelle of its provenance. Instead, the products of genes acquired from endosymbionts can explore all targeting possibilities within the cell. They often replace pre-existing host genes, or even whole pathways. But the transfer of an enzymatic pathway from one compartment to another poses severe problems: over evolutionary time, the enzymes of the pathway acquire their targeting signals for the new compartment individually, not in unison. Until the whole pathway is established in the new compartment, newly routed individual enzymes are useless, and their genes will be lost through mutation. Here it is suggested that pathways attain novel compartmentation variants via a 'minor mistargeting' mechanism. If protein targeting in eukaryotic cells possesses enough imperfection such that small amounts of entire pathways continuously enter novel compartments, selectable units of biochemical function would exist in new compartments, and the genes could become selected. Dual-targeting of proteins is indeed very common within eukaryotic cells, suggesting that targeting variation required for this minor mistargeting mechanism to operate exists in nature.
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Affiliation(s)
- William Martin
- Institute of Botany III, University of Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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212
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Bilateral communication between plastid and the nucleus: plastid protein import and plastid-to-nucleus retrograde signaling. Biosci Biotechnol Biochem 2010; 74:471-6. [PMID: 20208345 DOI: 10.1271/bbb.90842] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Plastids are a diverse group of organelles found in plants and some parasites. Chloroplasts are the archetypical plastids and are present in photosynthetic plant cells. Because most plastid proteins are encoded by the nuclear genome, plastid biogenesis relies on importing these proteins into the plastid. On the other hand, changes in functional or metabolic states of plastids have been known to affect the expression of nuclear genes encoding plastid proteins, and are collectively called "plastid signals." This regulation is also important for maintaining plastid function. This review focuses on the roles of these anterograde and retrograde pathways in plastid biogenesis and environmental adaptation.
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213
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Zhang Q. Why does biparental plastid inheritance revive in angiosperms? JOURNAL OF PLANT RESEARCH 2010; 123:201-6. [PMID: 20052516 DOI: 10.1007/s10265-009-0291-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 11/10/2009] [Indexed: 05/07/2023]
Abstract
It is widely believed that plastid and mitochondrial genomes are inherited through the maternal parent. In plants, however, paternal transmission of these genomes is frequently observed, especially for the plastid genome. A male gametic trait, called potential biparental plastid inheritance (PBPI), occurs in up to 20% of angiosperm genera, implying a strong tendency for plastid transmission from the male lineage. Why do plants receive organelles from the male parents? Are there clues in plastids that will help to elucidate the evolution of plants? Reconstruction of the ancestral state of plastid inheritance patterns in a phylogenetic context provides insights into these questions. In particular, a recent report demonstrated the unilateral occurrence of PBPI in angiosperms. This result implies that nuclear cytoplasmic conflicts, a basic driving force for altering the mode of organelle inheritance, might have arisen specifically in angiosperms. Based on existing evidence, it is likely that biparental inheritance may have occurred to rescue angiosperm species with defective plastids.
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Affiliation(s)
- Quan Zhang
- Key Laboratory of Cell Proliferation and Differentiation (Ministry of Education), College of Life Science, Peking University, 100871 Beijing, China
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214
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Yuan HM, Li KL, Ni RJ, Guo WD, Shen Z, Yang CP, Wang BC, Liu GF, Guo CH, Jiang J. A systemic proteomic analysis of Populus chloroplast by using shotgun method. Mol Biol Rep 2010; 38:3045-54. [DOI: 10.1007/s11033-010-9971-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
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215
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Smith AG, Johnson CB, Vitha S, Holzenburg A. Plant FtsZ1 and FtsZ2 expressed in a eukaryotic host: GTPase activity and self-assembly. FEBS Lett 2010; 584:166-72. [PMID: 19925792 DOI: 10.1016/j.febslet.2009.11.044] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/06/2009] [Accepted: 11/11/2009] [Indexed: 11/19/2022]
Abstract
Plants and algae contain the FtsZ1 and FtsZ2 protein families that perform specific, non-redundant functions in plastid division. In vitro studies of chloroplast division have been hampered by the lack of a suitable expression system. Here we report the expression and purification of FtsZ1-1 and FtsZ2-1 from Arabidopsis thaliana using a eukaryotic host. Specific GTPase activities were determined and found to be different for FtsZ1-1 vs. FtsZ2-1. The purified proteins readily assembled into previously unreported assembly products named type-I and -II filaments. In contrast to bacterial FtsZ, the Arabidopsis proteins do not form bundled sheets in the presence of Ca(2+).
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Affiliation(s)
- Aaron G Smith
- Microscopy and Imaging Center, Texas A&M University, College Station, TX 77843-2257, USA
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216
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Rauwolf U, Golczyk H, Greiner S, Herrmann RG. Variable amounts of DNA related to the size of chloroplasts III. Biochemical determinations of DNA amounts per organelle. Mol Genet Genomics 2010; 283:35-47. [PMID: 19911199 PMCID: PMC2799680 DOI: 10.1007/s00438-009-0491-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 09/28/2009] [Indexed: 11/30/2022]
Abstract
Plastid genomes (plastomes) are part of the integrated compartmentalised genetic system of photoautotrophic eukaryotes. They are highly redundant and generally dispersed in several regions (nucleoids) within organelles. DNA quantities and number of DNA-containing regions per plastid vary and are developmentally regulated in a way not yet understood. Reliable quantitative data describing these patterns are scarce. We present a protocol to isolate fractions of pure plastids with varying average sizes from leaflets (8 microm average diameter, corresponding from approximately a dozen to 330 genome equivalents per organelle and on average four to seven copies per nucleoid. The ratio of plastid/nuclear DNA changed continuously during leaf development from as little as 0.4% to about 20% in fully developed leaves. On the other hand, mesophyll cells of mature leaves differing in ploidy (di-, tri- and tetraploid) appeared to maintain a relatively constant nuclear genome/plastome ratio, equivalent to about 1,700 copies per C-value.
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Affiliation(s)
- Uwe Rauwolf
- Department für Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität München, Menzinger Straße 67, 80638 Munich, Germany
| | - Hieronim Golczyk
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Grodzka 52, 31-044 Kraków, Poland
| | - Stephan Greiner
- Department für Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität München, Menzinger Straße 67, 80638 Munich, Germany
- Present Address: Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Reinhold G. Herrmann
- Department für Biologie I, Bereich Botanik, Ludwig-Maximilians-Universität München, Menzinger Straße 67, 80638 Munich, Germany
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217
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Nishikawa T, Kajitani H, Sato M, Mogi Y, Moriyama Y, Kawano S. Isolation of chloroplast FtsZ and AtpC, and analysis of protein targeting into the complex chloroplast of the haptophyte Pavlova pinguis. CYTOLOGIA 2010. [DOI: 10.1508/cytologia.75.203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Toshikazu Nishikawa
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Hiroyuki Kajitani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Mayuko Sato
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Yuko Mogi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Yohsuke Moriyama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Shigeyuki Kawano
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
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218
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Abstract
Nucleomorphs are the remnant nuclei of algal endosymbionts in cryptophytes and chlorarachniophytes, two evolutionarily distinct unicellular eukaryotic lineages that acquired photosynthesis secondarily by the engulfment of red and green algae, respectively. At less than one million base pairs in size, nucleomorph genomes are the most highly reduced nuclear genomes known, with three small linear chromosomes and a gene density similar to that seen in prokaryotes. The independent origin of nucleomorphs in cryptophytes and chlorarachniophytes presents an interesting opportunity to study the reductive evolutionary forces that have led to their remarkable convergence upon similar genome architectures and coding capacities. In this article, we review the current state of knowledge with respect to the structure, function, origin, and evolution of nucleomorph genomes across the known diversity of cryptophyte and chlorarachniophyte algae.
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Affiliation(s)
- Christa E Moore
- The Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5, Canada
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219
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Koonin EV, Wolf YI, Puigbò P. The phylogenetic forest and the quest for the elusive tree of life. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2009; 74:205-13. [PMID: 19687142 PMCID: PMC3380366 DOI: 10.1101/sqb.2009.74.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Extensive horizontal gene transfer (HGT) among prokaryotes seems to undermine the tree of life (TOL) concept. However, the possibility remains that the TOL can be salvaged as a statistical central trend in the phylogenetic "forest of life" (FOL). A comprehensive comparative analysis of 6901 phylogenetic trees for prokaryotic genes revealed a signal of vertical inheritance that was particularly strong among the 102 nearly universal trees (NUTs), despite the high topological inconsistency among the trees in the FOL, most likely, caused by HGT. The topologies of the NUTs are similar to the topologies of numerous other trees in the FOL; although the NUTs cannot represent the FOL completely, they reflect a significant central trend. Thus, the original TOL concept becomes obsolete but the idea of a "weak" TOL as the dominant trend in the FOL merits further investigation. The totality of gene trees comprising the FOL appears to be a natural representation of the history of life given the inherent tree-like character of the replication process.
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Affiliation(s)
- E V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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220
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Puigbò P, Wolf YI, Koonin EV. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol 2009; 8:59. [PMID: 19594957 PMCID: PMC2737373 DOI: 10.1186/jbiol159] [Citation(s) in RCA: 191] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2009] [Revised: 05/19/2009] [Accepted: 06/12/2009] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Comparative genomics has revealed extensive horizontal gene transfer among prokaryotes, a development that is often considered to undermine the 'tree of life' concept. However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'. RESULTS A comprehensive comparative analysis of a 'forest' of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus, the nearly universal trees might reflect a significant central tendency, although they cannot represent the forest completely. However, topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla, suggesting that early phases of evolution could be non-tree-like (Biological Big Bang). Simulations of evolution under compressed cladogenesis or Biological Big Bang yielded a better fit to the observed dependence between tree inconsistency and phylogenetic depth for the compressed cladogenesis model. CONCLUSIONS Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.
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Affiliation(s)
- Pere Puigbò
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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221
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Gross J, Bhattacharya D. Mitochondrial and plastid evolution in eukaryotes: an outsiders' perspective. Nat Rev Genet 2009; 10:495-505. [PMID: 19506574 DOI: 10.1038/nrg2610] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The eukaryotic organelles mitochondrion and plastid originated from eubacterial endosymbionts. Here we propose that, in both cases, prokaryote-to-organelle conversion was driven by the internalization of host-encoded factors progressing from the outer membrane of the endosymbionts towards the intermembrane space, inner membrane and finally the organelle interior. This was made possible by an outside-to-inside establishment in the endosymbionts of host-controlled protein-sorting components, which enabled the gradual integration of organelle functions into the nuclear genome. Such a convergent trajectory for mitochondrion and plastid establishment suggests a novel paradigm for organelle evolution that affects theories of eukaryogenesis.
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Affiliation(s)
- Jeferson Gross
- Department of Biology, Roy J. Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, Iowa 52242, USA
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222
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Characterization of two putative protein translocation components in the apicoplast of Plasmodium falciparum. EUKARYOTIC CELL 2009; 8:1146-54. [PMID: 19502580 DOI: 10.1128/ec.00061-09] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein trafficking to the stroma of the apicoplast of Plasmodium falciparum requires translocation across several membranes. To further elucidate the mechanisms responsible, we investigated two proteins: P. falciparum Tic22 (PfTic22), a putative component of the translocon of the inner chloroplast membrane; and PfsDer1-1, one of two homologues of the P. falciparum symbiont-derived Der1 (sDer1) protein, a putative component of an endoplasmic reticulum-associated degradation (ERAD) complex in the periplastid membrane. We constructed parasites expressing hemagglutinin (HA)-tagged PfTic22 and PfsDer1-1 under the control of their endogenous promoters using the 3' replacement strategy. We show that both PfTic22-HA and PfsDer1-1-HA are expressed predominantly during the trophozoite stage of the asexual replication cycle, which corresponds to the most dynamic stages of apicoplast activity. Although both proteins localize to the periphery of the apicoplast, PfTic22-HA is a membrane-associated protein while PfsDer1-1-HA is an integral membrane protein. Phylogenetic analysis indicates that PfsDer1-1 is one of two Der1 paralogues predicted to localize to the apicoplast in P. falciparum and that it has orthologues in diatom algae, supporting the chromalveolate hypothesis. These observations are consistent with putative roles for PfTic22 and PfsDer1-1 in protein translocation into the apicoplast of P. falciparum.
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Sun CW, Huang YC, Chang HY. CIA2 coordinately up-regulates protein import and synthesis in leaf chloroplasts. PLANT PHYSIOLOGY 2009; 150:879-88. [PMID: 19386807 PMCID: PMC2689949 DOI: 10.1104/pp.109.137240] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 04/14/2009] [Indexed: 05/21/2023]
Abstract
Plastid biogenesis and maintenance depend on the coordinated assembly of proteins imported from the cytosol with proteins translated within plastids. Chloroplasts in leaf cells have a greater need for protein import and protein synthesis than plastids in other organs due to the large amount of proteins required for photosynthesis. We previously reported that the Arabidopsis (Arabidopsis thaliana) transcription factor CIA2 specifically up-regulates leaf expression of genes encoding protein translocons Toc33 and Toc75, which are essential for protein import into chloroplasts. Protein import efficiency was therefore reduced in cia2 mutant chloroplasts. To further understand the function of CIA2, gene expression profiles of the wild type and a cia2 mutant were compared by microarray analysis. Interestingly, in addition to genes encoding protein translocon components, other genes down-regulated in cia2 almost exclusively encode chloroplast ribosomal proteins. Isolated cia2 mutant chloroplasts showed reduced translation efficiency and steady-state accumulation of plastid-encoded proteins. When CIA2 was ectopically expressed in roots, expression of both the protein translocon and ribosomal protein genes increased. Further analyses in vivo revealed that CIA2 up-regulated these genes by binding directly to their promoter regions. We propose that CIA2 is an important factor responsible for fulfilling the higher protein demands of leaf chloroplasts by coordinately increasing both protein import and protein translation efficiencies.
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Affiliation(s)
- Chih-Wen Sun
- Department of Life Sciences, National Taiwan Normal University, Taipei 116, Taiwan.
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224
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Yoon HS, Nakayama T, Reyes-Prieto A, Andersen RA, Boo SM, Ishida KI, Bhattacharya D. A single origin of the photosynthetic organelle in different Paulinella lineages. BMC Evol Biol 2009; 9:98. [PMID: 19439085 PMCID: PMC2685391 DOI: 10.1186/1471-2148-9-98] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 05/13/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gaining the ability to photosynthesize was a key event in eukaryotic evolution because algae and plants form the base of the food chain on our planet. The eukaryotic machines of photosynthesis are plastids (e.g., chloroplast in plants) that evolved from cyanobacteria through primary endosymbiosis. Our knowledge of plastid evolution, however, remains limited because the primary endosymbiosis occurred more than a billion years ago. In this context, the thecate "green amoeba" Paulinella chromatophora is remarkable because it very recently (i.e., minimum age of approximately 60 million years ago) acquired a photosynthetic organelle (termed a "chromatophore"; i.e., plastid) via an independent primary endosymbiosis involving a Prochlorococcus or Synechococcus-like cyanobacterium. All data regarding P. chromatophora stem from a single isolate from Germany (strain M0880/a). Here we brought into culture a novel photosynthetic Paulinella strain (FK01) and generated molecular sequence data from these cells and from four different cell samples, all isolated from freshwater habitats in Japan. Our study had two aims. The first was to compare and contrast cell ultrastructure of the M0880/a and FK01 strains using scanning electron microscopy. The second was to assess the phylogenetic diversity of photosynthetic Paulinella to test the hypothesis they share a vertically inherited plastid that originated in their common ancestor. RESULTS Comparative morphological analyses show that Paulinella FK01 cells are smaller than M0880/a and differ with respect to the number of scales per column. There are more distinctive, multiple fine pores on the external surface of FK01 than in M0880/a. Molecular phylogenetic analyses using multiple gene markers demonstrate these strains are genetically distinct and likely comprise separate species. The well-supported monophyly of the Paulinella chromatophora strains analyzed here using plastid-encoded 16S rRNA suggests strongly that they all share a common photosynthetic ancestor. The strain M0880/a is most closely related to Japanese isolates (Kanazawa-1, -2, and Kaga), whereas FK01 groups closely with a Kawaguchi isolate. CONCLUSION Our results indicate that Paulinella chromatophora comprises at least two distinct evolutionary lineages and likely encompasses a broader taxonomic diversity than previously thought. The finding of a single plastid origin for both lineages shows these taxa to be valuable models for studying post-endosymbiotic cell and genome evolution.
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Affiliation(s)
- Hwan Su Yoon
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, USA.
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225
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Zhu J, Liu W, Zhou W, Hu Y, He Y. A Nucleus-encoded topological specificity factor PpMinE in Physcomitrella patens has conserved function similar to its chloroplast-encoded ancestor. J Genet Genomics 2009; 34:229-38. [PMID: 17498620 DOI: 10.1016/s1673-8527(07)60024-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 07/28/2006] [Indexed: 11/16/2022]
Abstract
A nucleus-encoded MinE gene, designated PpMinE, from Physcomitrella patens was identified using RT-PCR. The presence of both N- and C-terminal extensions in PpMinE protein suggested its cyanobacterial origin. The transient expression of PpMinE using green fluorescent protein fusion in tobacco (Nicotiana tabacum L.) indicated that the PpMinE was a chloroplast-targeted protein. Overexpression of PpMinE in Escherichia coli caused division site misplacement and minicell formation, suggesting evolutionary functional conservation of MinE during plant phylogenesis. According to the phylogenetic tree, PpMinE protein has a close relationship with the highland plants, which suggests that the transfer events of MinE gene from plastid to nucleus might have occurred before the origin of the land plants.
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Affiliation(s)
- Jiaying Zhu
- College of Life Science, Capital Normal University, Beijing 100037, China
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226
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Waller RF, Jackson CJ. Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology. Bioessays 2009; 31:237-45. [PMID: 19204978 DOI: 10.1002/bies.200800164] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mitochondrial genomes represent relict bacterial genomes derived from a progenitor alpha-proteobacterium that gave rise to all mitochondria through an ancient endosymbiosis. Evolution has massively reduced these genomes, yet despite relative simplicity their organization and expression has developed considerable novelty throughout eukaryotic evolution. Few organisms have reengineered their mitochondrial genomes as thoroughly as the protist lineage of dinoflagellates. Recent work reveals dinoflagellate mitochondrial genomes as likely the most gene-impoverished of any free-living eukaryote, encoding only two to three proteins. The organization and expression of these genomes, however, is far from the simplicity their gene content would suggest. Gene duplication, fragmentation, and scrambling have resulted in an inflated and complex genome organization. Extensive RNA editing then recodes gene transcripts, and trans-splicing is required to assemble full-length transcripts for at least one fragmented gene. Even after these processes, messenger RNAs (mRNAs) lack canonical start codons and most transcripts have abandoned stop codons altogether.
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Affiliation(s)
- Ross F Waller
- School of Botany, University of Melbourne, Melbourne, Victoria, Australia.
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227
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Gruber A, Weber T, Bártulos CR, Vugrinec S, Kroth PG. Intracellular distribution of the reductive and oxidative pentose phosphate pathways in two diatoms. J Basic Microbiol 2009; 49:58-72. [PMID: 19206144 DOI: 10.1002/jobm.200800339] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Diatoms contribute a large proportion to the worldwide primary production and are particularly effective in fixing carbon dioxide. Possibly because diatom plastids originate from a secondary endocytobiosis, their cellular structure is more complex and metabolic pathways are rearranged within diatom cells compared to cells containing primary plastids. We annotated genes encoding isozymes of the reductive and oxidative pentose phosphate pathways in the genomes of the centric diatom Thalassiosira pseudonana and the pennate diatom Phaeodactylum tricornutum and bioinformatically inferred their intracellular distribution. Prediction results were confirmed by fusion of selected presequences to Green Fluorescent Protein and expression of these constructs in P. tricornutum. Calvin cycle enzymes for the carbon fixation and reduction of 3-phosphoglycerate are present in single isoforms, while we found multiple isoenzymes involved in the regeneration of ribulose-1,5-bisphosphate. We only identified one cytosolic sedoheptulose-1,7-bisphosphatase in both investigated diatoms. The oxidative pentose phosphate pathway seems to be restricted to the cytosol in diatoms, since we did not find stromal glucose-6-phosphate dehydrogenase and 6-phosphogluconolactone dehydrogenase isoforms. However, the two species apparently possess a plastidic phosphogluconolactonase. A 6-phosphogluconolactone dehydrogenase is apparently plastid associated in P. tricornutum and might be active in the periplastidic compartment, suggesting that this compartment might be involved in metabolic processes in diatoms.
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Affiliation(s)
- Ansgar Gruber
- Pflanzliche Okophysiologie, Universität Konstanz, Konstanz, Germany.
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228
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Abstract
Marine eukaryotic photosynthesis is dominated by a diverse group of unicellular organisms collectively called microalgae. Microalgae include cells derived from a primary endosymbiotic event (similar to land plants) and cells derived from subsequent secondary and/or tertiary endosymbiotic events. These latter cells are chimeras of several genomes and dominate primary production in the marine environment. Two consequences of multiple endosymbiotic events include complex targeting mechanisms to allow nuclear-encoded proteins to be imported into the plastid and coordination of enzymes, potentially from disparate originator cells, to form complete metabolic pathways. In this review, we discuss the forces that shaped the genomes of marine microalgae and then discuss some of the metabolic consequences of such a complex evolutionary history. We focus our metabolic discussion on carbon, nitrogen, and iron. We then discuss biomineralization and new evidence for programmed cell death in microalgae. We conclude with a short summary on advances in genetic manipulation of microalgae and thoughts on the future directions of marine algal genomics.
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Affiliation(s)
- Micaela S Parker
- School of Oceanography, University of Washington, Seattle, Washington 98195, USA.
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229
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Abstract
Mitochondrial DNA (mtDNA) is a pivotal tool in molecular ecology, evolutionary and population genetics. The power of mtDNA analyses derives from a relatively high mutation rate and the apparent simplicity of mitochondrial inheritance (maternal, without recombination), which has simplified modelling population history compared to the analysis of nuclear DNA. However, in biology things are seldom simple, and advances in DNA sequencing and polymorphism detection technology have documented a growing list of exceptions to the central tenets of mitochondrial inheritance, with paternal leakage, heteroplasmy and recombination now all documented in multiple systems. The presence of paternal leakage, recombination and heteroplasmy can have substantial impact on analyses based on mtDNA, affecting phylogenetic and population genetic analyses, estimates of the coalescent and the myriad of other parameters that are dependent on such estimates. Here, we review our understanding of mtDNA inheritance, discuss how recent findings mean that established ideas may need to be re-evaluated, and we assess the implications of these new-found complications for molecular ecologists who have relied for decades on the assumption of a simpler mode of inheritance. We show how it is possible to account for recombination and heteroplasmy in evolutionary and population analyses, but that accurate estimates of the frequencies of biparental inheritance and recombination are needed. We also suggest how nonclonal inheritance of mtDNA could be exploited, to increase the ways in which mtDNA can be used in analyses.
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Affiliation(s)
- Daniel James White
- Department of Anatomy & Structural Biology University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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230
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Rowan BA, Oldenburg DJ, Bendich AJ. A multiple-method approach reveals a declining amount of chloroplast DNA during development in Arabidopsis. BMC PLANT BIOLOGY 2009; 9:3. [PMID: 19128504 PMCID: PMC2632658 DOI: 10.1186/1471-2229-9-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2008] [Accepted: 01/07/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND A decline in chloroplast DNA (cpDNA) during leaf maturity has been reported previously for eight plant species, including Arabidopsis thaliana. Recent studies, however, concluded that the amount of cpDNA during leaf development in Arabidopsis remained constant. RESULTS To evaluate alternative hypotheses for these two contradictory observations, we examined cpDNA in Arabidopsis shoot tissues at different times during development using several methods: staining leaf sections as well as individual isolated chloroplasts with 4',6-diamidino-2-phenylindole (DAPI), real-time quantitative PCR with DNA prepared from total tissue as well as from isolated chloroplasts, fluorescence microscopy of ethidium-stained DNA molecules prepared in gel from isolated plastids, and blot-hybridization of restriction-digested total tissue DNA. We observed a developmental decline of about two- to three-fold in mean DNA per chloroplast and two- to five-fold in the fraction of cellular DNA represented by chloroplast DNA. CONCLUSION Since the two- to five-fold reduction in cpDNA content could not be attributed to an artifact of chloroplast isolation, we conclude that DNA within Arabidopsis chloroplasts is degraded in vivo as leaves mature.
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Affiliation(s)
- Beth A Rowan
- Department of Biology, University of Washington, Seattle, WA 91895, USA
| | | | - Arnold J Bendich
- Department of Biology, University of Washington, Seattle, WA 91895, USA
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Oborník M, Janouškovec J, Chrudimský T, Lukeš J. Evolution of the apicoplast and its hosts: From heterotrophy to autotrophy and back again. Int J Parasitol 2009; 39:1-12. [DOI: 10.1016/j.ijpara.2008.07.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 07/23/2008] [Accepted: 07/25/2008] [Indexed: 10/21/2022]
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232
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Kleine T, Maier UG, Leister D. DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. ANNUAL REVIEW OF PLANT BIOLOGY 2009; 60:115-38. [PMID: 19014347 DOI: 10.1146/annurev.arplant.043008.092119] [Citation(s) in RCA: 243] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In eukaryotes, DNA is exchanged between endosymbiosis-derived compartments (mitochondria and chloroplasts) and the nucleus. Organelle-to-nucleus DNA transfer involves repair of double-stranded breaks by nonhomologous end-joining, and resulted during early organelle evolution in massive relocation of organelle genes to the nucleus. A large fraction of the products of the nuclear genes so acquired are retargeted to their ancestral compartment; many others now function in new subcellular locations. Almost all present-day nuclear transfers of mitochondrial or plastid DNA give rise to noncoding sequences, dubbed nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs). Some of these sequences were recruited as exons, thus introducing new coding sequences into preexisting nuclear genes by a novel mechanism. In organisms derived from secondary or tertiary endosymbiosis, serial gene transfers involving nucleus-to-nucleus migration of DNA have also occurred. Intercompartmental DNA transfer therefore represents a significant driving force for gene and genome evolution, relocating and refashioning genes and contributing to genetic diversity.
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Affiliation(s)
- Tatjana Kleine
- Lehrstuhl für Botanik, Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
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233
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A type II NAD(P)H dehydrogenase mediates light-independent plastoquinone reduction in the chloroplast of Chlamydomonas. Proc Natl Acad Sci U S A 2008; 105:20546-51. [PMID: 19074271 DOI: 10.1073/pnas.0806896105] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In photosynthetic eukaryotes, nonphotochemical plastoquinone (PQ) reduction is important for the regulation of photosynthetic electron flow. In green microalgae where this process has been demonstrated, the chloroplastic enzyme that catalyses nonphotochemical PQ reduction has not been identified yet. Here, we show by an RNA interference (RNAi) approach that the NDA2 gene, belonging to a type II NAD(P)H dehydrogenases family in the green microalga Chlamydomonas reinhardtii, encodes a chloroplastic dehydrogenase that functions to reduce PQ nonphotochemically in this alga. Using a specific antibody, we show that the Nda2 protein is localized in chloroplasts of wild-type cells and is absent in two Nda2-RNAi cell lines. In both mutant cell lines, nonphotochemical PQ reduction is severely affected, as indicated by altered chlorophyll fluorescence transients after saturating illumination. Compared with wild type, change in light excitation distribution between photosystems ('state transition') upon inhibition of mitochondrial electron transport is strongly impaired in transformed cells because of inefficient PQ reduction. Furthermore, the amount of hydrogen produced by Nda2-RNAi cells under sulfur deprivation is substantially decreased compared with wild type, which supports previous assumptions that endogenous substrates serve as source of electrons for hydrogen formation. These results demonstrate the importance of Nda2 for nonphotochemical PQ reduction and associated processes in C. reinhardtii.
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234
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Aronsson H, Jarvis P. The Chloroplast Protein Import Apparatus, Its Components, and Their Roles. PLANT CELL MONOGRAPHS 2008. [DOI: 10.1007/978-3-540-68696-5_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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235
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Reyes-Prieto A, Moustafa A, Bhattacharya D. Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. Curr Biol 2008; 18:956-62. [PMID: 18595706 DOI: 10.1016/j.cub.2008.05.042] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 05/20/2008] [Accepted: 05/22/2008] [Indexed: 11/25/2022]
Abstract
Plantae (as defined by Cavalier-Smith, 1981) plastids evolved via primary endosymbiosis whereby a heterotrophic protist enslaved a photosynthetic cyanobacterium. This "primary" plastid spread into other eukaryotes via secondary endosymbiosis. An important but contentious theory in algal evolution is the chromalveolate hypothesis that posits chromists (cryptophytes, haptophytes, and stramenopiles) and alveolates (ciliates, apicomplexans, and dinoflagellates) share a common ancestor that contained a red-algal-derived "secondary" plastid. Under this view, the existence of several later-diverging plastid-lacking chromalveolates such as ciliates and oomycetes would be explained by plastid loss in these lineages. To test the idea of a photosynthetic ancestry for ciliates, we used the 27,446 predicted proteins from the macronuclear genome of Tetrahymena thermophila to query prokaryotic and eukaryotic genomes. We identified 16 proteins of possible algal origin in the ciliates Tetrahymena and Paramecium tetraurelia. Fourteen of these are present in other chromalveolates. Here we compare and contrast the likely scenarios for algal-gene origin in ciliates either via multiple rounds of horizontal gene transfer (HGT) from algal prey or symbionts, or through endosymbiotic gene transfer (EGT) during a putative photosynthetic phase in their evolution.
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Affiliation(s)
- Adrian Reyes-Prieto
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa 52242-1324, USA
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236
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The chloroplast protein translocation complexes of Chlamydomonas reinhardtii: a bioinformatic comparison of Toc and Tic components in plants, green algae and red algae. Genetics 2008; 179:95-112. [PMID: 18493043 DOI: 10.1534/genetics.107.085704] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recently completed genome of Chlamydomonas reinhardtii was surveyed for components of the chloroplast protein translocation complexes. Putative components were identified using reciprocal BlastP searches with the protein sequences of Arabidopsis thaliana as queries. As a comparison, we also surveyed the new genomes of the bryophyte Physcomitrella patens, two prasinophyte green algae (Ostreococcus lucimarinus and Ostreococcus tauri), the red alga Cyanidioschizon merolae, and several cyanobacteria. Overall, we found that the components of the import pathway are remarkably well conserved, particularly among the Viridiplantae lineages. Specifically, C. reinhardtii contained almost all the components found in A. thaliana, with two exceptions. Missing from C. reinhardtii are the C-terminal ferredoxin-NADPH-reductase (FNR) binding domain of Tic62 and a full-length, TPR-bearing Toc64. Further, the N-terminal domain of C. reinhardtii Toc34 is highly acidic, whereas the analogous region in C. reinhardtii Toc159 is not. This reversal of the vascular plant model may explain the similarity of C. reinhardtii chloroplast transit peptides to mitochondrial-targeting peptides. Other findings from our genome survey include the absence of Tic22 in both Ostreococcus genomes; the presence of only one Toc75 homolog in C. merolae; and, finally, a distinctive propensity for gene duplication in P. patens.
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237
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Carter DR. Plastocyanin-ferredoxin oxidoreduction and endosymbiotic gene transfer. PHOTOSYNTHESIS RESEARCH 2008; 97:245-253. [PMID: 18661249 DOI: 10.1007/s11120-008-9333-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2008] [Accepted: 07/10/2008] [Indexed: 05/26/2023]
Abstract
Sequence similarities of proteins associated with plastocyanin-ferredoxin oxidoreduction (PcFdOR) activity of Photosystem I (PSI) were grouped and compared. PsaA, psaB, psaC, and petG represent genes that have been retained in the chloroplasts of both green- and red-lineage species. PsaD, psaE, psaF, and petF represent genes that have been retained in the chloroplast of red-lineage species, but have been transferred to the nuclear genome of green-lineage species. Translated sequences from red- and green-lineage proteins were compared to that of contemporary cyanobacteria, Synechocystis PCC 6803, and Gloeobacter violaceus PCC 7421. Within the green lineage, a lower level of sequence conservation coincided with gene transfer to the nuclear genome. Surprisingly, a similar pattern of sequence conservation existed for the same set of genes found in the red lineage even though all those genes were retained in their chloroplast genomes. This discrepancy between green and red lineage is discussed in terms of endosymbiotic gene transfer.
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Affiliation(s)
- Douglas R Carter
- Department of Biology, Central Connecticut State University, 1615 Stanley St., New Britain, CT, 06050, USA.
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238
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Kwon KC, Cho MH. Deletion of the chloroplast-localized AtTerC gene product in Arabidopsis thaliana leads to loss of the thylakoid membrane and to seedling lethality. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 55:428-42. [PMID: 18429937 DOI: 10.1111/j.1365-313x.2008.03523.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Early seedling development in plants depends on the biogenesis of chloroplasts from proplastids, accompanied by the formation of thylakoid membranes. An Arabidopsis thaliana gene, AtTerC, whose gene product shares sequence similarity with bacterial tellurite resistance C (TerC), is shown to be involved in a critical step required for the normal organization of prothylakoids and transition into mature thylakoid stacks. The AtTerC gene encodes an integral membrane protein, which contains eight putative transmembrane helices, localized in the thylakoid of the chloroplast, as shown by localization of an AtTerC-GFP fusion product in protoplasts and by immunoblot analysis of subfractions of chloroplasts. T-DNA insertional mutation of AtTerC resulted in a pigment-deficient and seedling-lethal phenotype under normal light conditions. Transmission electron microscopic analysis revealed that mutant etioplasts had normal prolamellar bodies (PLBs), although the prothylakoids had ring-like shapes surrounding the PLBs. In addition, the ultrastructures of mutant chloroplasts lacked thylakoids, did not have grana stacks, and showed numerous globular structures of varying sizes. Also, the accumulation of thylakoid membrane proteins was severely defective in this mutant. These results suggest that the AtTerC protein plays a crucial role in prothylakoid membrane biogenesis and thylakoid formation in early chloroplast development.
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Affiliation(s)
- Kwang-Chul Kwon
- Department of Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
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239
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Abstract
Plastids are a diverse group of essential organelles in plants that include chloroplasts. The biogenesis and maintenance of these organelles relies on the import of thousands of nucleus-encoded proteins. The complexity of plastid structure has resulted in the evolution of at least four general import pathways that target proteins into and across the double membrane of the plastid envelope. Several of these pathways can be further divided into specialty pathways that mediate and regulate the import of specific classes of proteins. The co-ordination of import by these specialized pathways with changes in gene expression is critical for plastid and plant development. Moreover, protein import is acutely regulated in response to physiological and metabolic changes within the cell. In the present review we summarize the current knowledge of the mechanism of import via these pathways and highlight the regulatory mechanisms that integrate the plastid protein-trafficking pathways with the developmental and metabolic state of the plant.
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240
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Bock R, Timmis JN. Reconstructing evolution: gene transfer from plastids to the nucleus. Bioessays 2008; 30:556-66. [PMID: 18478535 DOI: 10.1002/bies.20761] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
During evolution, the genomes of eukaryotic cells have undergone major restructuring to meet the new regulatory challenges associated with compartmentalization of the genetic material in the nucleus and the organelles acquired by endosymbiosis (mitochondria and plastids). Restructuring involved the loss of dispensable or redundant genes and the massive translocation of genes from the ancestral organelles to the nucleus. Genomics and bioinformatic data suggest that the process of DNA transfer from organelles to the nucleus still continues, providing raw material for evolutionary tinkering in the nuclear genome. Recent reconstruction of these events in the laboratory has provided a unique tool to observe genome evolution in real time and to study the molecular mechanisms by which plastid genes are converted into functional nuclear genes. Here, we summarize current knowledge about plastid-to-nuclear gene transfer in the context of genome evolution and discuss new insights gained from experiments that recapitulate endosymbiotic gene transfer in the laboratory.
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Affiliation(s)
- Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.
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241
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Abstract
The establishment of the photosynthetic organelle (plastid) in eukaryotes and the diversification of algae and plants were landmark evolutionary events because these taxa form the base of the food chain for many ecosystems on our planet. The plastid originated via a putative single, ancient primary endosymbiosis in which a heterotrophic protist engulfed and retained a cyanobacterium in its cytoplasm. Once successfully established, this plastid spread into other protist lineages through eukaryote-eukaryote (secondary and tertiary) endosymbioses. This process of serial cell capture and enslavement explains the diversity of photosynthetic eukaryotes. Recent genomic and phylogenomic approaches have significantly clarified plastid genome evolution, the movement of endosymbiont genes to the "host" nuclear genome (endosymbiotic gene transfer), and plastid spread throughout the eukaryotic tree of life. Here we review these aspects of plastid evolution with a focus on understanding early events in plastid endosymbiosis.
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Affiliation(s)
- Adrian Reyes-Prieto
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242-1324, USA.
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242
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Moustafa A, Reyes-Prieto A, Bhattacharya D. Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions. PLoS One 2008; 3:e2205. [PMID: 18493612 PMCID: PMC2376095 DOI: 10.1371/journal.pone.0002205] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 04/07/2008] [Indexed: 11/19/2022] Open
Abstract
Background The photosynthetic organelle (plastid) originated via primary endosymbiosis in which a phagotrophic protist captured and harnessed a cyanobacterium. The plastid was inherited by the common ancestor of the red, green (including land plants), and glaucophyte algae (together, the Plantae). Despite the critical importance of primary plastid endosymbiosis, its ancient derivation has left behind very few “footprints” of early key events in organelle genesis. Methodology/Principal Findings To gain insights into this process, we conducted an in-depth phylogenomic analysis of genomic data (nuclear proteins) from 17 Plantae species to identify genes of a surprising provenance in these taxa, Chlamydiae bacteria. Previous studies show that Chlamydiae contributed many genes (at least 21 in one study) to Plantae that primarily have plastid functions and were postulated to have played a fundamental role in organelle evolution. Using our comprehensive approach, we identify at least 55 Chlamydiae-derived genes in algae and plants, of which 67% (37/55) are putatively plastid targeted and at least 3 have mitochondrial functions. The remainder of the proteins does not contain a bioinformatically predicted organelle import signal although one has an N-terminal extension in comparison to the Chlamydiae homolog. Our data suggest that environmental Chlamydiae were significant contributors to early Plantae genomes that extend beyond plastid metabolism. The chlamydial gene distribution and protein tree topologies provide evidence for both endosymbiotic gene transfer and a horizontal gene transfer ratchet driven by recurrent endoparasitism as explanations for gene origin. Conclusions/Significance Our findings paint a more complex picture of gene origin than can easily be explained by endosymbiotic gene transfer from an organelle-like point source. These data significantly extend the genomic impact of Chlamydiae on Plantae and show that about one-half (30/55) of the transferred genes are most closely related to sequences emanating from the genome of the only environmental isolate that is currently available. This strain, Candidatus Protochlamydia amoebophila UWE25 is an endosymbiont of Acanthamoeba and likely represents the type of endoparasite that contributed the genes to Plantae.
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Affiliation(s)
- Ahmed Moustafa
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
| | - Adrian Reyes-Prieto
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
| | - Debashish Bhattacharya
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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243
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Huang J, Gogarten JP. Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol 2008; 8:R99. [PMID: 17547748 PMCID: PMC2394758 DOI: 10.1186/gb-2007-8-6-r99] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 03/06/2007] [Accepted: 06/04/2007] [Indexed: 11/10/2022] Open
Abstract
Phylogenomic analyses of the red alga Cyanidioschyzon merolae shows that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, suggesting an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote. Background Ancient endosymbioses are responsible for the origins of mitochondria and plastids, and they contribute to the divergence of several major eukaryotic groups. Although chlamydiae, a group of obligate intracellular bacteria, are not found in plants, an unexpected number of chlamydial genes are most similar to plant homologs, which, interestingly, often contain a plastid-targeting signal. This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria. Results We conducted phylogenomic analyses of the red alga Cyanidioschyzon merolae to identify genes specifically related to chlamydial homologs. We show that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, with the donor most similar to the environmental Protochlamydia. Such an unusually high number of transferred genes suggests an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote. We hypothesize that three organisms were involved in establishing the primary photosynthetic lineage: the eukaryotic host cell, the cyanobacterial endosymbiont that provided photosynthetic capability, and a chlamydial endosymbiont or parasite that facilitated the establishment of the cyanobacterial endosymbiont. Conclusion Our findings provide a glimpse into the complex interactions that were necessary to establish the primary endosymbiotic relationship between plastid and host cytoplasms, and thereby explain the rarity with which long-term successful endosymbiotic relationships between heterotrophs and photoautotrophs were established. Our data also provide strong and independent support for a common origin of all primary photosynthetic eukaryotes and of the plastids they harbor.
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Affiliation(s)
- Jinling Huang
- Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA
- NASA Astrobiology Institute at Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125, USA
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244
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Abstract
Organisms have acquired plastids by convoluted paths that have provided multiple opportunities for gene transfer into a host nucleus from intracellular organisms, including the cyanobacterial ancestor of plastids, the proteobacterial ancestor of mitochondria, and both green and red algae whose engulfment has led to secondary acquisition of plastids. These gene movements are most accurately demonstrated by building phylogenetic trees that identify the evolutionary origin of each gene, and one effective tool for this is "PhIGs" (Phylogenetically Inferred Groups; http://PhIGs.org), a set of databases and computer tools with a Web interface for whole-genome evolutionary analysis. PhIGs takes as input gene sets of completely sequenced genomes, builds clusters of genes using a novel, graph-based approach, and reconstructs the evolutionary relationships among all gene families. The user can view and download the sequence alignments, compare intron-exon structures, and follow links to functional genomic databases. Currently, PhIGs contains 652,756 genes from 45 genomes grouped into 61,059 gene families. Graphical displays show the relative positions of these genes among genomes. PhIGs has been used to detect the evolutionary transfer of hundreds of genes from cyanobacteria and red algae into oömycete nuclear genomes, revealing that even though they have no plastids, their ancestors did, having secondarily acquired them from an intracellular red alga. A great number of genomes are soon to become available that are relevant to our broader understanding of the movement of genes among intracellular compartments after engulfing other organisms, and PhIGs will be an effective tool to interpret these gene movements.
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Affiliation(s)
- Jeffrey L Boore
- Genome Project Solutions, Hercules, California 94547, USA DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA University of California Berkeley, California 94720, USA
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245
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The multiplicity of dehydrogenases in the electron transport chain of plant mitochondria. Mitochondrion 2008; 8:47-60. [DOI: 10.1016/j.mito.2007.10.004] [Citation(s) in RCA: 247] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 08/20/2007] [Accepted: 10/02/2007] [Indexed: 12/22/2022]
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246
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The Chloroplast Protein Import Apparatus, Its Components, and Their Roles. PLANT CELL MONOGRAPHS 2008. [DOI: 10.1007/7089_2008_40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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247
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Suppanz I, Sarnighausen E, Reski R. An integrated physiological and genetic approach to the dynamics of FtsZ targeting and organisation in a moss, Physcomitrella patens. PROTOPLASMA 2007; 232:1-9. [PMID: 18094924 DOI: 10.1007/s00709-007-0284-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 07/15/2007] [Indexed: 05/25/2023]
Abstract
Plant FtsZ (filamentous temperature-sensitive Z) proteins are regarded as descendants of prokaryotic cell division proteins. We could show previously that four FtsZ isoforms of the moss Physcomitrella patens assemble into, and interact in, distinct structures inside the chloroplasts and in the cytosol. Their organisation and localisation patterns indicate an involvement in chloroplast and cell division and in the maintenance of chloroplast shape and integrity. The cellular processes of chloroplast division and maintenance of chloroplast shape were disturbed either by application of the beta-lactam antibiotic ampicillin or by a mutation that presumably affects signal transduction of the plant hormone cytokinin. When cells of these plants were analysed microscopically, there was no indication that cytosolic functions of FtsZ proteins were affected. Furthermore, FtsZ proteins continued to build three-dimensional plastoskeleton networks, even in considerably enlarged or malformed chloroplasts. On the other hand, macrochloroplast formation promoted the localisation of FtsZ proteins in filaments that emanate from the plastids and, therefore, most likely represent stromules. Annular FtsZ structures that are regarded as essential components of the division apparatus were absent from macrochloroplasts of ampicillin-treated cells. Thus, the distribution of FtsZ proteins after inhibition of chloroplast division further strengthens our hypothesis on the functions of distinct isoforms. In addition, the results provide further insight into the regulation of protein targeting and dynamics of plastoskeletal elements.
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Affiliation(s)
- I Suppanz
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Federal Republic of Germany
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248
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Sato M, Nishikawa T, Kajitani H, Kawano S. Conserved relationship between FtsZ and peptidoglycan in the cyanelles of Cyanophora paradoxa similar to that in bacterial cell division. PLANTA 2007; 227:177-87. [PMID: 17704941 DOI: 10.1007/s00425-007-0605-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 07/27/2007] [Indexed: 05/11/2023]
Abstract
Cyanelles of the biflagellate protist Cyanophora paradoxa have retained the peptidoglycan layer, which is critical for division, as indicated by the inhibitory effects of beta-lactam antibiotics. An FtsZ ring is formed at the division site during cyanelle division. We used immunofluorescence microscopy to observe the process of FtsZ ring formation, which is expected to lead cyanelle division, and demonstrated that an FtsZ arc and a split FtsZ ring emerge during the early and late stages of cyanelle division, respectively. We used an anti-FtsZ antibody to observe cyanelle FtsZ rings. We observed bright, ring-shaped fluorescence of FtsZ in cyanelles. Cyanelles were kidney-shaped shortly after division. Fluorescence indicated that FtsZ did not surround the division plane at an early stage of division, but rather formed an FtsZ arc localized at the constriction site. The constriction spread around the cyanelle, which gradually became dumbbell shaped. After the envelope's invagination, the ring split parallel to the cyanelle division plane without disappearing. Treatment of C. paradoxa cells with ampicillin, a beta-lactam antibiotic, resulted in spherical cyanelles with an FtsZ arc or ring on the division plane. Transmission electron microscopy of the ampicillin-treated cyanelle envelope membrane revealed that the surface was not smooth. Thus, the inhibition of peptidoglycan synthesis by ampicillin causes the inhibition of septum formation and a marked delay in constriction development. The formation of the FtsZ arc and FtsZ ring is the earliest sign of cyanelle division, followed by constriction and septum formation.
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Affiliation(s)
- Mayuko Sato
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg FSB-601, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan.
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249
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Patron NJ, Waller RF. Transit peptide diversity and divergence: A global analysis of plastid targeting signals. Bioessays 2007; 29:1048-58. [PMID: 17876808 DOI: 10.1002/bies.20638] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Proteins are targeted to plastids by N-terminal transit peptides, which are recognized by protein import complexes in the organelle membranes. Historically, transit peptide properties have been defined from vascular plant sequences, but recent large-scale genome sequencing from the many plastid-containing lineages across the tree of life has provided a much broader representation of targeted proteins. This includes the three lineages containing primary plastids (plants and green algae, rhodophytes and glaucophytes) and also the seven major lineages that contain secondary plastids, "secondhand" plastids derived through eukaryotic endosymbiosis. Despite this extensive spread of plastids throughout Eukaryota, an N-terminal transit peptide has been maintained as an essential plastid-targeting motif. This article provides the first global comparison of transit peptide composition and summarizes conservation of some features, the loss of an ancestral motif from the green lineages including plants, and modifications to transit peptides that have occurred in secondary and even tertiary plastids.
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Affiliation(s)
- Nicola J Patron
- School of Botany, University of Melbourne, Victoria 3010, Australia.
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250
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Kabeya Y, Kobayashi Y, Suzuki H, Itoh J, Sugita M. Transcription of plastid genes is modulated by two nuclear-encoded alpha subunits of plastid RNA polymerase in the moss Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:730-41. [PMID: 17894784 DOI: 10.1111/j.1365-313x.2007.03270.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In general, in higher plants, the core subunits of a bacterial-type plastid-encoded RNA polymerase (PEP) are encoded by the plastid rpoA, rpoB, rpoC1 and rpoC2 genes. However, an rpoA gene is absent from the moss Physcomitrella patens plastid genome, although the PpRpoA gene (renamed PpRpoA1) nuclear counterpart is present in the nuclear genome. In this study, we identified and characterized a second gene encoding the plastid-targeting alpha subunit (PpRpoA2). PpRpoA2 comprised 525 amino acids and showed 59% amino acid identity with PpRpoA1. Two PpRpoA proteins were present in the PEP active fractions separated from the moss chloroplast lysate, confirming that both proteins are alpha subunits of PEP. Northern blot analysis showed that PpRpoA2 was highly expressed in the light, but not in the dark, whereas PpRpoA1 was constitutively expressed. Disruption of the PpRpoA1 gene resulted in an increase in the PpRpoA2 transcript level, but most plastid gene transcript levels were not significantly altered. This indicates that transcription of most plastid genes depends on PpRpoA2-PEP rather than on PpRpoA1-PEP. In contrast, the transcript levels of petN, psbZ and ycf3 were altered in the PpRpoA1 gene disruptant, suggesting that these are PpRpoA1-PEP-dependent genes. These observations suggest that plastid genes are differentially transcribed by distinct PEP enzymes with either PpRpoA1 or PpRpoA2.
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Affiliation(s)
- Yukihiro Kabeya
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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