Inferring gene function from evolutionary change in signatures of translation efficiency

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  • dc.contributor.author Krisko, Anitaca
  • dc.contributor.author Copic, Teaca
  • dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
  • dc.contributor.author Lehner, Ben, 1978-ca
  • dc.contributor.author Supek, Franca
  • dc.date.accessioned 2015-03-19T08:37:41Z
  • dc.date.available 2015-03-19T08:37:41Z
  • dc.date.issued 2014ca
  • dc.description.abstract Background: The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the relative expression levels of genes, which can, uniquely, be quantified across the domains of life. Results: Here we describe a general statistical framework to exploit this phenomenon and to systematically associate genes with environments and phenotypic traits through changes in codon adaptation. By inferring evolutionary signatures of translation efficiency in 911 bacterial and archaeal genomes while controlling for confounding effects of phylogeny and inter-correlated phenotypes, we linked 187 gene families to 24 diverse phenotypic traits. A series of experiments in Escherichia coli revealed that 13 of 15, 19 of 23, and 3 of 6 gene families with changes in codon adaptation in aerotolerant, thermophilic, or halophilic microbes. Respectively, confer specific resistance to, respectively, hydrogen peroxide, heat, and high salinity. Further, we demonstrate experimentally that changes in codon optimality alone are sufficient to enhance stress resistance. Finally, we present evidence that multiple genes with altered codon optimality in aerobes confer oxidative stress resistance by controlling the levels of iron and NAD(P)H. Conclusions: Taken together, these results provide experimental evidence for a widespread connection between changes in translation efficiency and phenotypic adaptation. As the number of sequenced genomes increases, this novel genomic context method for linking genes to phenotypes based on sequence alone will become increasingly useful.en
  • dc.description.sponsorship This work was supported by grants from the Spanish Ministry of Economy and Competitiveness (BFU2009-9618, BFU2008-00365 and ‘Centro de Excelencia Severo Ochoa 2013-2017’ SEV-2012-0208), an ERC Starting Grant, ERASysBio PLUS, AGAUR, the EMBO Young Investigator Program, and the EMBL-CRG Systems Biology Program. The work of FS was supported in part by Marie Curie Actions and by grant ICT-2013-612944 (MAESTRA). The experimental part of this work was carried out at and financed by the Mediterranean Institute for Life Sciences (MedILS)en
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Krisko A, Copic T, Gabaldón T, Lehner B, Supek F. Inferring gene function from evolutionary change in signatures of translation efficiency. Genome Biology. 2014; 15: R44. DOI 10.1186/gb-2014-15-3-r44ca
  • dc.identifier.doi http://dx.doi.org/10.1186/gb-2014-15-3-r44
  • dc.identifier.issn 1465-6906ca
  • dc.identifier.uri http://hdl.handle.net/10230/23225
  • dc.language.iso engca
  • dc.publisher BioMed Centralca
  • dc.relation.ispartof Genome Biology. 2014; 15: R44
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2009-9618
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2008-00365
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV-2012-0208
  • dc.rights © 2014 Krisko et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.ca
  • dc.rights.accessRights info:eu-repo/semantics/openAccessca
  • dc.rights.uri http://creativecommons.org/licenses/by/2.0
  • dc.subject.other Seqüència d'aminoàcidsca
  • dc.subject.other Transcripció genèticaca
  • dc.title Inferring gene function from evolutionary change in signatures of translation efficiencyen
  • dc.type info:eu-repo/semantics/articleca
  • dc.type.version info:eu-repo/semantics/publishedVersionca

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