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Article: An analysis of determinants of amino acids substitution rates in bacterial proteins

TitleAn analysis of determinants of amino acids substitution rates in bacterial proteins
Authors
Issue Date2004
PublisherOxford University Press. The Journal's web site is located at http://mbe.oxfordjournals.org/
Citation
Molecular Biology and Evolution, 2004, v. 21 n. 1, p. 108-116 How to Cite?
AbstractThe variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category, essentiality, or metabolic costs of its amino acid residues may play an important role. However, the relative importance of each variable has not yet been evaluated in comparative analyses. To this aim, we made regression analyses combining data available on these variables and on evolutionary rates, in two well-documented model bacteria, Escherichia coli and Bacillus subtilis. In both bacteria, the level of expression of the protein in the cell was by far the most important driving force constraining the amino acids substitution rate. Subsequent inclusion in the analysis of the other variables added little further information. Furthermore, when the rates of synonymous substitutions were included in the analysis of the E. coli data, only the variable expression levels remained statistically significant. The rate of nonsynonymous substitution was shown to correlate with expression levels independently of the rate of synonymous substitution. These results suggest an important direct influence of expression levels, or at least codon usage bias for translation optimization, on the rates of nonsynonymous substitutions in bacteria. They also indicate that when a control for this variable is included, essentiality plays no significant role in the rate of protein evolution in bacteria, as is the case in eukaryotes.
Persistent Identifierhttp://hdl.handle.net/10722/224219
ISSN
2015 Impact Factor: 13.649
2015 SCImago Journal Rankings: 8.168

 

DC FieldValueLanguage
dc.contributor.authorRocha, EPC-
dc.contributor.authorDanchin, A-
dc.date.accessioned2016-03-30T03:41:33Z-
dc.date.available2016-03-30T03:41:33Z-
dc.date.issued2004-
dc.identifier.citationMolecular Biology and Evolution, 2004, v. 21 n. 1, p. 108-116-
dc.identifier.issn0737-4038-
dc.identifier.urihttp://hdl.handle.net/10722/224219-
dc.description.abstractThe variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category, essentiality, or metabolic costs of its amino acid residues may play an important role. However, the relative importance of each variable has not yet been evaluated in comparative analyses. To this aim, we made regression analyses combining data available on these variables and on evolutionary rates, in two well-documented model bacteria, Escherichia coli and Bacillus subtilis. In both bacteria, the level of expression of the protein in the cell was by far the most important driving force constraining the amino acids substitution rate. Subsequent inclusion in the analysis of the other variables added little further information. Furthermore, when the rates of synonymous substitutions were included in the analysis of the E. coli data, only the variable expression levels remained statistically significant. The rate of nonsynonymous substitution was shown to correlate with expression levels independently of the rate of synonymous substitution. These results suggest an important direct influence of expression levels, or at least codon usage bias for translation optimization, on the rates of nonsynonymous substitutions in bacteria. They also indicate that when a control for this variable is included, essentiality plays no significant role in the rate of protein evolution in bacteria, as is the case in eukaryotes.-
dc.languageeng-
dc.publisherOxford University Press. The Journal's web site is located at http://mbe.oxfordjournals.org/-
dc.relation.ispartofMolecular Biology and Evolution-
dc.subject.meshAmino Acids - genetics - metabolism-
dc.subject.meshBacillus subtilis - genetics-
dc.subject.meshBacterial Proteins - genetics-
dc.subject.meshEscherichia coli - genetics-
dc.subject.meshMutation - genetics-
dc.titleAn analysis of determinants of amino acids substitution rates in bacterial proteins-
dc.typeArticle-
dc.identifier.emailDanchin, A: adanchin@hkucc.hku.hk-
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1093/molbev/msh004-
dc.identifier.pmid14595100-
dc.identifier.scopuseid_2-s2.0-1242284655-
dc.identifier.hkuros95406-
dc.identifier.volume21-
dc.identifier.issue1-
dc.identifier.spage108-
dc.identifier.epage116-
dc.publisher.placeUnited States-

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