Stop codons in bacteria are not selectively equivalent

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  • dc.contributor.author Povolotskaya, Inna, 1986-ca
  • dc.contributor.author Kondrashov, Fyodor A., 1979-ca
  • dc.contributor.author Ledda, Aliceca
  • dc.contributor.author Vlasov, Peter K.ca
  • dc.date.accessioned 2016-05-27T12:55:57Z
  • dc.date.available 2016-05-27T12:55:57Z
  • dc.date.issued 2012
  • dc.description.abstract Background: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes. Results: We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG. Conclusions: Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.ca
  • dc.description.sponsorship The work has been supported by a Plan Nacional grant from the Spanish Ministry of Science and Innovation, EMBO Young Investigator and Howard Hughes Medical Institute International Early Career Scientist awards.
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Povolotskaya IS, Kondrashov FA, Ledda A, Vlasov PK. Stop codons in bacteria are not selectively equivalent. Biology direct. 2012; 7: 30. DOI 10.1186/1745-6150-7-30ca
  • dc.identifier.doi http://dx.doi.org/10.1186/1745-6150-7-30
  • dc.identifier.issn 1745-6150
  • dc.identifier.uri http://hdl.handle.net/10230/26769
  • dc.language.iso engca
  • dc.publisher BioMed Centralca
  • dc.relation.ispartof Biology direct. 2010; 7: 30
  • dc.rights © 2012 Povolotskaya 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,/ndistribution, and reproduction in any medium, provided the original work is properly citedca
  • dc.rights.accessRights info:eu-repo/semantics/openAccessca
  • dc.rights.uri http://creativecommons.org/licenses/by/2.0ca
  • dc.subject.other Genomes bacteriansca
  • dc.title Stop codons in bacteria are not selectively equivalentca
  • dc.type info:eu-repo/semantics/articleca
  • dc.type.version info:eu-repo/semantics/publishedVersionca

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