Evolution of Protein Superfamilies and Bacterial Genome Size

Ranea, Juan A. G.; Buchan, Daniel W. A.; Thornton, Janet M.; Orengo, Christine A.

doi:10.1016/j.jmb.2003.12.044

Cited by 95 publications

(81 citation statements)

References 52 publications

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“…This probably reflects a requirement for more complex regulation of genome expression, as metabolic and cellular complexity increases proportional to genome size. Certain other functional categories in bacterial genomes have previously been described to correlate either positively or negatively with genome size (Konstantinidis & Tiedje, 2004;Ranea et al, 2004). Our analysis of the six genomes identified such categories that display the same pattern for the two largest genomes, namely transport and metabolism of carbohydrates, amino acids and secondary metabolites.…”

Section: Lactobacillus Orthologues and Taxon-specific Proteinsmentioning

confidence: 52%

Diversity of the genus Lactobacillus revealed by comparative genomics of five species

et al. 2006

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The genus Lactobacillus contains over 80 recognized species, and is characterized by a high level of diversity, reflected in its complex phylogeny. The authors' recent determination of the genome sequence of Lactobacillus salivarius means that five complete genomes of Lactobacillus species are available for comparative genomics: L. salivarius, L. plantarum, L. acidophilus, L. johnsonii and L. sakei. This paper now shows that there is no extensive synteny of the genome sequences of these five lactobacilli. Phylogeny based on whole-genome alignments suggested that L. salivarius was closer to L. plantarum than to L. sakei, which was closest to Enterococcus faecalis, in contrast to 16S rRNA gene relatedness. A total of 593 orthologues common to all five species were identified. Species relatedness based on this protein set was largely concordant with genome synteny-based relatedness. A Lactobacillus supertree, combining individual phylogenetic trees from each of 354 core proteins, had four main branches, comprising L. salivarius-L. plantarum; L. sakei; E. faecalis; and L. acidophilus-L. johnsonii. The extreme divergence of the Lactobacillus genomes analysed supports the recognition of new subgeneric divisions.

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Section: Lactobacillus Orthologues and Taxon-specific Proteinsmentioning

confidence: 52%

Diversity of the genus Lactobacillus revealed by comparative genomics of five species

et al. 2006

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“…However, apart from a phylogenetic signal, functional similarities can also arise due to similarities in genome size (van Nimwegen 2003;Konstantinidis and Tiedje 2004;Ranea et al 2004). When correcting for the dependency between genome size have been collected at distinct sites, covering a distance of more than 600 miles; collection was at different water depths and sampling dates.…”

Section: à13mentioning

confidence: 99%

A global network of coexisting microbes from environmental and whole-genome sequence data

Chaffron¹,

Rehrauer²,

Pernthaler³

et al. 2010

Genome Res.

440

322

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Microbes are the most abundant and diverse organisms on Earth. In contrast to macroscopic organisms, their environmental preferences and ecological interdependencies remain difficult to assess, requiring laborious molecular surveys at diverse sampling sites. Here, we present a global meta-analysis of previously sampled microbial lineages in the environment. We grouped publicly available 16S ribosomal RNA sequences into operational taxonomic units at various levels of resolution and systematically searched these for co-occurrence across environments. Naturally occurring microbes, indeed, exhibited numerous, significant interlineage associations. These ranged from relatively specific groupings encompassing only a few lineages, to larger assemblages of microbes with shared habitat preferences. Many of the coexisting lineages were phylogenetically closely related, but a significant number of distant associations were observed as well. The increased availability of completely sequenced genomes allowed us, for the first time, to search for genomic correlates of such ecological associations. Genomes from coexisting microbes tended to be more similar than expected by chance, both with respect to pathway content and genome size, and outliers from these trends are discussed. We hypothesize that groupings of lineages are often ancient, and that they may have significantly impacted on genome evolution.

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“…It may be reasonable due to unique genomic and evolutionary features and ancient metabolic adaptation. Nevertheless, these protein families can be evolved into present bacterial lineages at a slow evolution rate (Ranea et al 2004;Dupont et al 2010). It suggests that methanogens have typical metal transporter as compared to present bacterial system.…”

Section: Discussionmentioning

confidence: 99%

In silico description of cobalt and nickel assimilation systems in the genomes of methanogens

Chellapandi

2011

Syst Synth Biol

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Methanogens are a diverse group of organisms that can live in a wide range of environments. Herein, cobalt and tungsten assimilation pathways have proposed to be established in the genomes of Methanococcus maripaludies C5 and Methanosarcina mazei Go1, respectively. All of the proteins involved in the proposed pathways were identified from public domain databases and then complied manually to reconstruct the pathways. The function of proteins with unknown function was assigned by a combined prediction approach. Totally, 17 proteins were identified to cobalt transport and assimilation processes whereas 7 proteins reported to tungsten assimilation system. Phylogenetic analysis of this study revealed that heavy metal transporter of methanogens could be evolved from closely related members in the different genera of methanogens. Nevertheless, genes encoding for metal resistance proteins could be originated from thermophilic and sulfur reducing bacteria. Many metalloenzymes in methanogens were very unique to the species of methanogens. It implied that these metal ions were utilized to produce the precursors for energy driven processes of methanogens. This study suggested that in combination of systems models and evolutionary inference can only correlate metabolic fluxes and physiological changes in methanogens. In silico models of this study will provide insights to design experiments for heavy metal assimilation processes of methanogens growing under heavy metal-rich environments and or in a laboratory condition.

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Evolution of Protein Superfamilies and Bacterial Genome Size

Cited by 95 publications

References 52 publications

Diversity of the genus Lactobacillus revealed by comparative genomics of five species

Diversity of the genus Lactobacillus revealed by comparative genomics of five species

A global network of coexisting microbes from environmental and whole-genome sequence data

In silico description of cobalt and nickel assimilation systems in the genomes of methanogens

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