Evolutionary genomics: Thermotoga heats up lateral gene transfer

Logsdon, John M.; Faguy, David M.

doi:10.1016/s0960-9822(99)80474-6

Cited by 73 publications

(37 citation statements)

References 19 publications

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“…5, which is published as supporting information on the PNAS web site); this value is greater than that for any bacterial species except Thermotoga maritima (16) and Aquifex aeolicus (17). The presence of so many Archaeal-like proteins can be explained by multiple scenarios including the loss or rapid rate of evolution of these genes in other bacteria (18) or past lateral gene transfer between the C. tepidum and Archaeal lineages. Because C. tepidum is apparently not deeply branching within the bacterial tree (15), for the gene loss͞rapid evolution explanations to be correct, such events would have to have occurred in all of the earlier branching bacterial lineages.…”

Section: Resultsmentioning

confidence: 89%

The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium

Eisen

Nelson

Paulsen

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

353

303

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The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum Chlorobia, whose members perform anoxygenic photosynthesis by the reductive tricarboxylic acid cycle. Genome comparisons have identified genes in C. tepidum that are highly conserved among photosynthetic species. Many of these have no assigned function and may play novel roles in photosynthesis or photobiology. Phylogenomic analysis reveals likely duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism of sulfur and nitrogen as well as strong similarities between metabolic processes in C. tepidum and many Archaeal species.

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Section: Resultsmentioning

confidence: 89%

The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium

Eisen

Nelson

Paulsen

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

353

303

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“…However, Kyrpides & Olsen (1999) and Logsdon & Faguy (1999) point out correctly that vertical inheritance, plus differential losses and differential rates of change, are often overlooked by suggestions like those of Nelson et al (1999) and Aravind et al (1998) of massive lateral gene transfer based simply on overall similarity. Proper phylogenetic analysis is needed to demonstrate lateral transfer, including correctly rooted trees with the right topology.…”

Section: Lateral Gene Transfer and Hyperthermophilymentioning

confidence: 99%

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Cavalier‐Smith¹

2002

International Journal of Systematic and Evolutionary Microbiology

418

590

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Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms : Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translationarrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids ; flagellar shaft of glycoprotein, not flagellin ; DNA-binding protein 10b ; specially modified tRNA ; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles ; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of T. Cavalier-Smith quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution : the fact that, during major evolutionary transformations, some org...

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“…Another group of genes with low GC3s, composed mainly of hypothetical proteins conserved among thermophilic prokaryotes and ABC transporters, is clustered around position 1,340,000. Since the majority of the predicted genes in these two regions are most similar to proteins in thermophilic prokaryotes, it seems reasonable to suppose that they were relatively recently acquired by horizontal transfer from thermophilic genomes more biased toward A + T. This phenomenon has been postulated to be very common in Thermotoga (Nelson et al 1999;Logsdon and Faguy 1999).…”

Section: Codon Usagementioning

confidence: 99%

“…This genome is characterized by an average genomic G + C content of 46% and consists of 1860 kbp with 1846 predicted coding regions, but perhaps the most striking result that emerged from its sequencing was the finding that 24% of its genes seem to be derived from Archaea (Nelson et al 1999;Logsdon and Faguy 1999).…”

Section: Introductionmentioning

confidence: 99%

Trends in Codon and Amino Acid Usage in Thermotoga maritima

Zavala

Naya

Romero

et al. 2002

Journal of Molecular Evolution

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Abstract. The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon usage. Surprisingly the usage of UGU and UGC (synonymous triplets coding for Cys, the least frequent amino acid in this species) was detected as the second most prominent source of variation. However, this result is probably an artifact due to the very low frequency of Cys together with the nonbiased composition of this genome. The third trend was related to the preferential usage of a subset of codons among highly expressed genes, and these triplets are presumed to be translationally optimal. Concerning the amino acid usage, the hydropathy level of each protein (and therefore the frequency of charged residues) was the main trend, while the second factor was related to the frequency of usage of the smaller residues, suggesting that the cell economy strongly influences the architecture of the proteins. The third axis of the analysis discriminated the usage of Phe, Tyr, Trp (aromatic residues) plus Cys, Met, and His. These six residues have in common the property of being the preferential targets of reactive oxygen species, and therefore the anaerobic condition of T. maritima is an important factor for the amino acid frequencies. Finally, the Cys content of each protein was the fourth trend.

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Evolutionary genomics: Thermotoga heats up lateral gene transfer

Cited by 73 publications

References 19 publications

The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium

The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Trends in Codon and Amino Acid Usage in Thermotoga maritima

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