Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

Horiike, Tokumasa; Miyata, Daisuke; Hamada, Kazuo; Saruhashi, Satoshi; Shinozawa, Takao; Kumar, Sudhir; Chakraborty, Ranajit; Komiyama, Tomoyoshi; Tateno, Yoshio

doi:10.1016/j.gene.2008.10.006

Cited by 26 publications

(24 citation statements)

References 45 publications

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“…It is widely believed that genome trees based on concatenated alignments of multiple protein sequences are less susceptible to stochastic errors than those based on a single protein or gene, such as the 16S rRNA gene. Genome trees reported recently showed the power of this approach, confirming accepted phylogenies and/or presenting unexpected novel relationships at the level of phyla as well as individual species (Ciccarelli et al 2006;Wu and Eisen 2008;Ward et al 2009;Horiike et al 2009). While separation of the bacterial major phyla was largely improved in these genome trees, the inter-phyla branching order remained poorly resolved.…”

supporting

confidence: 59%

Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison

Kunisawa

2010

Antonie van Leeuwenhoek

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The phylogenetic placement of the phylum Deferribacteres was investigated on the basis of gene order comparisons of completely sequenced bacterial genomes. Two completely sequenced Deferribacteres species share five sets of gene arrangements with a group of phyla, Proteobacteria, Aquificae, Planctomycetes, Spirochaetes, Bacteroidetes, Chlorobi, Acidobacteria, Verrucomicrobia, Elusimicrobia and Nitrospirae, while the other group of phyla, Synergistetes, Firmicutes, Actinobacteria, Thermotogae, Chloroflexi and Deinococcus-Thermus, Fusobacteria, shares alternative sets of gene arrangements, suggesting that the Deferribacteres is classified in the former group of phyla. Gene transfers that are thought to have occurred in a common ancestor of the Deferribacteres, Deltaproteobacteria and Nitrospirae exclusive of virtually all other phyla were identified, which suggests that the Deferribacteres is phylogenetically proximal to the Proteobacteria and Nitrospirae.

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supporting

confidence: 59%

Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison

Kunisawa

2010

Antonie van Leeuwenhoek

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“…4) was consistent with that of the tree based on the 102 orthologous proteins with mesophilic archaea as the out-group [46] and that on the comparison of feature frequency profiles of whole proteomes [47]. In contrast, the present tree was not congruent with trees based on the cytochrome bc- complexes [48], proteins involved in chlorophyll biosynthesis [49] and 16S rDNA [26].…”

Section: Resultssupporting

confidence: 83%

Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences

2013

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Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.

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“…coli and Homo sapiens . Furthermore, A. aeolicus is in the phylum Aquificae, which some argue contains some of the earliest eubacterial species (31), and only one ATP-dependent DNA helicase homologue was identified in A.aeolicus . Therefore, the MMR pathway in A. aeolicus may have occurred very early in evolution.…”

Section: Discussionmentioning

confidence: 99%

A Human PMS2 Homologue from Aquifex aeolicus Stimulates an ATP-dependent DNA Helicase

Mauris

Evans

2010

Journal of Biological Chemistry

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Mismatch repair in Escherichia coli involves a number of proteins including MutL and UvrD. Eukaryotes also possess MutL homologues; however, no UvrD helicase homologues have been identified. The hyperthermophilic bacterium Aquifex aeolicus has a MutL protein (Aae MutL) that possesses a latent endonuclease activity similar to eukaryotic, but different from E. coli, MutL proteins. By sequence homology Aq793 is a member of the PcrA/UvrD/Rep helicase subfamily. We expressed Aae MutL and the putative A. aeolicus DNA helicase (Aq793) proteins in E. coli. Using synthetic oligonucleotide substrates, we observed that lower concentrations of Aq793 were required to unwind double-stranded DNA that had a 3′-poly(dT) overhang as compared with double-stranded DNA with a 5′-poly(dT) or lacking a poly(dT) tail. This unwinding activity was stimulated by adding Aae MutL with maximal stimulation observed at an ∼1.5:1 (MutL:Aq793) stoichiometric ratio. The enhancement of Aq793 helicase activity did not require the Aae MutL protein to retain endonuclease activity. Furthermore, the C-terminal 123 amino acid residues of Aae MutL were sufficient to stimulate Aq793 helicase activity, albeit at a significantly reduced efficacy. To the best of our knowledge this is the first time a human PMS2 homologue has been demonstrated to stimulate a PcrA/UvrD/Rep subfamily helicase, and this finding may further our understanding of the evolution of the mismatch repair pathway.

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Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

Cited by 26 publications

References 45 publications

Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison

Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison

Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences

A Human PMS2 Homologue from Aquifex aeolicus Stimulates an ATP-dependent DNA Helicase

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