Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues

Gupta, Radhey S.; Pereira, Mark P.; Chandrasekera, Charu; Johari, Vanessa

doi:10.1099/ijs.0.02720-0

Cited by 33 publications

(28 citation statements)

References 43 publications

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“…If any of these bacteria were present 2.7 Gyr ago, cyanobacteria must have been also. Hopanols evolved no later than the common ancestor of cyanobacteria and proteobacteria; as cyanobacteria are holophyletic (Gupta et al 2003), their common ancestor with Gracilicutes had both hopanols and two contrasting photosystems. Unless a reason other than the origin of oxygenic photosynthesis can be found for divergence of two photosystems in one cell, then this glycobacterial common ancestor already had at least primitive oxygenic photosynthesis.…”

Section: Synthesis: How Microbial Quantum Evolution Changed the Worldmentioning

confidence: 99%

Cell evolution and Earth history: stasis and revolution

Cavalier‐Smith

2006

Phil. Trans. R. Soc. B

251

278

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This synthesis has three main parts. The first discusses the overall tree of life and nature of the last common ancestor (cenancestor). I emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. Second, I map the tree onto the fossil record and discuss dates of key events and their biogeochemical impact. Finally, I present a broad synthesis, discussing evidence for a three-phase history of life. The first phase began perhaps ca 3.5 Gyr ago, when the origin of cells and anoxic photosynthesis generated the arguably most primitive prokaryote phylum, Chlorobacteria (ZChloroflexi), the first negibacteria with cells bounded by two acyl ester phospholipid membranes. After this 'chlorobacterial age' of benthic anaerobic evolution protected from UV radiation by mineral grains, two momentous quantum evolutionary episodes of cellular innovation and microbial radiation dramatically transformed the Earth's surface: the glycobacterial revolution initiated an oxygenic 'age of cyanobacteria' and, as the ozone layer grew, the rise of plankton; immensely later, probably as recently as ca 0.9 Gyr ago, the neomuran revolution ushered in the 'age of eukaryotes', Archaebacteria (arguably the youngest bacterial phylum), and morphological complexity. Diversification of glycobacteria ca 2.8 Gyr ago, predominantly inhabiting stratified benthic mats, I suggest caused serial depletion of 13 C by ribulose 1,5-bis-phosphate caboxylase/oxygenase (Rubisco) to yield ultralight late Archaean organic carbon formerly attributed to methanogenesis plus methanotrophy. The late origin of archaebacterial methanogenesis ca 720 Myr ago perhaps triggered snowball Earth episodes by slight global warming increasing weathering and reducing CO 2 levels, to yield runaway cooling; the origin of anaerobic methane oxidation ca 570 Myr ago reduced methane flux at source, stabilizing Phanerozoic climates. I argue that the major cellular innovations exhibit a pattern of quantum evolution followed by very rapid radiation and then substantial stasis, as described by Simpson. They yielded organisms that are a mosaic of extremely conservative and radically novel features, as characterized by De Beer's phrase 'mosaic evolution'. Evolution is not evenly paced and there are no real molecular clocks.

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Section: Synthesis: How Microbial Quantum Evolution Changed the Worldmentioning

confidence: 99%

Cell evolution and Earth history: stasis and revolution

Cavalier‐Smith

2006

Phil. Trans. R. Soc. B

251

278

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“…Several indels, which constitute distinctive molecular markers, have been identified for phyla such as Proteobacteria, Chlamidiae, Cyanobacteria, and "DeinococcusThermus" (157,163,166). The taxonomic resolution of some of the techniques mentioned above, in particular with respect to FIG.…”

Section: New Approaches To Investigate Taxonomic Relationships Inmentioning

confidence: 99%

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Ventura

Canchaya

Tauch

et al. 2007

Microbiol Mol Biol Rev

946

638

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SUMMARY Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.

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“…The 11 genome sequences included in this study represent freshwater, marine, and hot spring species, including four closely related marine cyanobacteria from the Prochlorococcus/marine Synechococcus group. Based on the shared traits of oxygenic photosynthesis, several single gene analyses (e.g., Giovannoni et al 1988), and analyses of shared indels (Gupta et al 2003), all cyanobacteria form a monophyletic phylogenetic group. Indeed, the "coherence" of cyanobacteria-by which we mean monophyly for all or the vast majority of genes-is often considered self-evident, and asserted without elaboration or citation (e.g., Hagen and Meeks 2001;Otero and Vincenzini 2004).…”

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confidence: 99%

Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events

Zhaxybayeva¹,

Gogarten²,

Charlebois³

et al. 2006

Genome Res.

298

258

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Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between cyanobacteria and other phyla. A novel method of detecting and enumerating potential horizontal gene transfer events within a group of organisms based on analyses of “embedded quartets” allows us to identify phylogenetic signal consistent with a plurality of gene families, as well as to delineate cases of conflict to the plurality signal, which include horizontally transferred genes. To infer horizontal gene transfer events between cyanobacteria and other phyla, we added homologs from 168 available genomes. We screened phylogenetic trees reconstructed for each of these extended gene families for highly supported monophyly of cyanobacteria (or lack of it). Cyanobacterial genomes reveal a complex evolutionary history, which cannot be represented by a single strictly bifurcating tree for all genes or even most genes, although a single completely resolved phylogeny was recovered from the quartets’ plurality signals. We find more conflicts within cyanobacteria than between cyanobacteria and other phyla. We also find that genes from all functional categories are subject to transfer. However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases.

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Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues

Cited by 33 publications

References 43 publications

Cell evolution and Earth history: stasis and revolution

Cell evolution and Earth history: stasis and revolution

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events

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