Metabolic efficiency and amino acid composition in the proteomes of
            <i>Escherichia coli</i>
            and
            <i>Bacillus subtilis</i>

Akashi, Hiroshi; Gojobori, Takashi

doi:10.1073/pnas.062526999

Cited by 616 publications

(661 citation statements)

References 48 publications

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“…Similar questions have been addressed by Akashi and Gojobori (2002), who report that metabolic efficiency is related to amino acid composition for the genomes of E. coli and B. subtilis.…”

Section: Introductionmentioning

confidence: 53%

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Carbone

Madden

2005

J Mol Evol

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Abstract. Codon bias is related to metabolic functions in translationally biased organisms, and two facts are argued about. First, genes with high codon bias describe in meaningful ways the metabolic characteristics of the organism; important metabolic pathways corresponding to crucial characteristics of the lifestyle of an organism, such as photosynthesis, nitrification, anaerobic versus aerobic respiration, sulfate reduction, methanogenesis, and others, happen to involve especially biased genes. Second, gene transcriptional levels of sets of experiments representing a significant variation of biological conditions strikingly confirm, in the case of Saccharomyces cerevisiae, that metabolic preferences are detectable by purely statistical analysis: the high metabolic activity of yeast during fermentation is encoded in the high bias of enzymes involved in the associated pathways, suggesting that this genome was affected by a strong evolutionary pressure that favored a predominantly fermentative metabolism of yeast in the wild. The ensemble of metabolic pathways involving enzymes with high codon bias is rather well defined and remains consistent across many species, even those that have not been considered as translationally biased, such as Helicobacter pylori, for instance, reveal some weak form of translational bias for this genome. We provide numerical evidence, supported by experimental data, of these facts and conclude that the metabolic networks of translationally biased genomes, observable today as projections of eons of evolutionary pressure, can be analyzed numerically and predictions of the role of specific pathways during evolution can be derived. The new concepts of Comparative Pathway Index, used to compare organisms with respect to their metabolic networks, and Evolutionary Pathway Index, used to detect evolutionarily meaningful bias in the genetic code from transcriptional data, are introduced.

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“…Similar questions have been addressed by Akashi and Gojobori (2002), who report that metabolic efficiency is related to amino acid composition for the genomes of E. coli and B. subtilis.…”

Section: Introductionmentioning

confidence: 53%

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Carbone

Madden

2005

J Mol Evol

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“…Similarly, the eight amino acids for which we did not identify complete pathways in the Ca. U. copiosus genome are among the most energetically expensive to make 38 (Supplementary Fig. 5).…”

Section: Resultsmentioning

confidence: 99%

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

et al. 2016

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Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name ‘Candidatus Udaeobacter copiosus’. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

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“…Indeed, the amino acid composition has been found to play an important role in determining the protein structural class (Chou and Zhang, 1994;Chou and Zhang, 1995;Chou, 1995;Chou and Maggiora, 1998), in identifying protein subcellular localization, and many other attributes (Chou and Elrod, 1999;Chou, 2002). Evidence has been presented that the amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis reflects a natural selection to enhance metabolic efficiency in these microorganisms (Akashi and Gojobori, 2002). Furthermore, the analysis on several Saccharomyces cerevisiae genes showed a correlation between gene expression level and amino acid composition (Raghava and Han, 2005).…”

Section: Introductionmentioning

confidence: 99%

Adaptation of model proteins from cold to hot environments involves continuous and small adjustments of average parameters related to amino acid composition

Vendittis

Castellano

Cotugno

et al. 2008

Journal of Theoretical Biology

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A c c e p t e d m a n u s c r i p t A c c e p t e d m a n u s c r i p t 2 AbstractThe growth temperature adaptation of six model proteins has been studied in

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Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

Cited by 616 publications

References 48 publications

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

Adaptation of model proteins from cold to hot environments involves continuous and small adjustments of average parameters related to amino acid composition

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