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Environmental Shaping of Codon Usage and Functional Adaptation Across Microbial Communities

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Encyclopedia of Metagenomics

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Definition

Whole microbial communities exhibit patterns similar to those of single microbial species in terms of synonymous codon usage, regardless of their phyletic composition. Therefore, methods applicable on single microbial genomes to predict for functionally important and lifestyle-relevant genes based on translational optimization of synonymous codons can be applied to the study of the entire metagenomes. Using these predictions opens up a possibility to discover new and functionally unannotated genes relevant for the community metabolism and overall adaptation to a particular environment. This approach presents an integrated approach to the study of microbial community genomic information and provides an in silico functional metagenomic platform to complement metaproteomic studies.

Introduction

Environmental diversity studies have bypassed the common problem where less than 1% of microbes are amenable to cultivation in laboratory conditions (Staley and Konopka 1985) by instead...

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References

  • Bruggemann H, Henne A, Hoster F, Liesegang H, Wiezer A, Strittmatter A, et al. The complete genome sequence of Propionibacterium acnes, a commensal of human skin. Science. 2004;305:671–3.

    Article  PubMed  Google Scholar 

  • Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH. Codon usage between genomes is constrained by genome-wide mutational processes. Proceedings of the National Academy of Sciences of the United States of America. 2004;101:3480–5.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Foerstner KU, von Mering C, Hooper SD, Bork P. Environments shape the nucleotide composition of genomes. EMBO reports. 2005;6:1208–13.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355–9.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hunyadkurti J, Feltoti Z, Horvath B, Nagymihaly M, Voros A, McDowell A, et al. Complete Genome Sequence of Propionibacterium acnes Type IB Strain 6609. J Bacteriol. 2011;193:4561–2.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Research. 2007;17:377–86.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ikemura T. Codon Usage and Transfer-RNA Content in Unicellular and Multicellular Organisms. Molecular Biology and Evolution. 1985;2:13–34.

    CAS  PubMed  Google Scholar 

  • Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T. Codon usage and tRNA genes in eukaryotes: Correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. Journal of Molecular Evolution. 2001;53:290–8.

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, et al. From genomics to chemical genomics: new developments in KEGG. Nucl Acids Res. 2006;34:D354–7.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Karlin S, Mrazek J. Predicted highly expressed genes of diverse prokaryotic genomes. Journal of Bacteriology. 2000;182:5238–50.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, et al. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nature Biotechnology. 2004;22:55–61.

    Article  CAS  PubMed  Google Scholar 

  • Martin HG, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, et al. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology. 2006;24:1263–9.

    Article  CAS  Google Scholar 

  • Oda Y, Larimer FW, Chain PSG, Malfatti S, Shin MV, Vergez LM, et al. Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments. Proceedings of the National Academy of Sciences of the United States of America. 2008;105:18543–8.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet. 2011;12:32–42.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rocha EPC. Codon usage bias from tRNA’s point of view: Redundancy, specialization, and efficient decoding for translation optimization. Genome Research. 2004;14:2279–86.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sharp P, Li W. The codon Adaptation Index–a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987;15(3):1281–95.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Research. 2005;33:1141–53.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF, et al. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J. 2008;3:93–105.

    Article  PubMed  Google Scholar 

  • Staley JT, Konopka A. MEASUREMENT OF IN SITU ACTIVITIES OF NONPHOTOSYNTHETIC MICROORGANISMS IN AQUATIC AND TERRESTRIAL HABITATS. Annual Review of Microbiology. 1985;39:321–46.

    Article  CAS  PubMed  Google Scholar 

  • Supek F, Škunca N, Repar J, Vlahoviček K, Šmuc T. Translational Selection Is Ubiquitous in Prokaryotes. PLoS Genet. 2010;6:e1001004.

    Article  PubMed Central  PubMed  Google Scholar 

  • Supek F, Vlahovicek K. Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. Bmc Bioinformatics. 2005;6:15.

    Article  Google Scholar 

  • Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, et al. The COG database: an updated version includes eukaryotes. Bmc Bioinformatics. 2003;4:14.

    Article  Google Scholar 

  • Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, et al. Comparative metagenomics of microbial communities. Science. 2005a;308:554–7.

    Article  CAS  PubMed  Google Scholar 

  • Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, et al. Comparative Metagenomics of Microbial Communities. Science (New York, N Y ). 2005b;308:554–7.

    Article  CAS  Google Scholar 

  • Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, Zaborske J, et al. An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation. Cell. 2010;141:344–54.

    Article  CAS  PubMed  Google Scholar 

  • Tuller T, Girshovich Y, Sella Y, Kreimer A, Freilich S, Kupiec M, et al. Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Research. 2011;39:4743–55.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–31.

    Article  PubMed  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428:37–43.

    Article  CAS  PubMed  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304:66–74.

    Article  CAS  PubMed  Google Scholar 

  • Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, et al. Shotgun metaproteomics of the human distal gut microbiota. Isme Journal. 2009;3:179–89.

    Article  CAS  PubMed  Google Scholar 

  • Vieira-Silva S, Rocha EPC. The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics. PLoS Genet. 2010;6:e1000808.

    Article  PubMed Central  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Molecular Biology Department, Division of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia

    Vedran Lucić

  2. Bioinformatics Group, Molecular Biology Department, Division of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia

    Masa Roller & Kristian Vlahoviček

  3. Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári körút 62, H-6726, Szeged, Hungary

    Istvan Nagy

Authors
  1. Vedran Lucić
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  2. Masa Roller
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  3. Istvan Nagy
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  4. Kristian Vlahoviček
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Corresponding author

Correspondence to Kristian Vlahoviček .

Editor information

Editors and Affiliations

  1. J. Craig Venter Institute, Rockville, MD, USA

    Karen E. Nelson

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Lucić, V., Roller, M., Nagy, I., Vlahoviček, K. (2015). Environmental Shaping of Codon Usage and Functional Adaptation Across Microbial Communities. In: Nelson, K.E. (eds) Encyclopedia of Metagenomics. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-7478-5_562

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