Protein evolutionary rates correlate with expression independently of synonymous substitutions in Helicobacter pylori.
In free-living microorganisms, such as Escherichia coli and Saccharomyces cerevisiae, both synonymous and nonsynonymous substitution frequencies correlate with expression levels. Here, we have tested the hypothesis that the correlation between amino acid substitution rates and expression is a by-product of selection for codon bias and translational efficiency in highly expressed genes. To this end, we have examined the correlation between protein evolutionary rates and expression in the human gastric pathogen Helicobacter pylori, where the absence of selection on synonymous sites enables the two types of substitutions to be uncoupled. The results revealed a statistically significant negative correlation between expression levels and nonsynonymous substitutions in both H. pylori and E. coli. We also found that neighboring genes located on the same, but not on opposite strands, evolve at significantly more similar rates than random gene pairs, as expected by co-expression of genes located in the same operon. However, the two species differ in that synonymous substitutions show a strand-specific pattern in E. coli, whereas the weak similarity in synonymous substitutions for neighbors in H. pylori is independent of gene orientation. These results suggest a direct influence of expression levels on nonsynonymous substitution frequencies independent of codon bias and selective constraints on synonymous sites.
Program of Molecular Evolution, Department of Evolution, Genomics and Systematics, Evolutionary Biology Center, Uppsala University, 752 36 Uppsala, Sweden.
Björn
B
Sällström
Ramy A
RA
Arnaout
Wagied
W
Davids
Pär
P
Bjelkmar
Siv G E
SG
Andersson
D019943:Amino Acid Substitution / Q000235:genetics*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics*; D002876:Chromosomes, Bacterial / Q000235:genetics; D003062:Codon / Q000235:genetics; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D014644:Genetic Variation; D016480:Helicobacter pylori / Q000737:chemistry / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
D001426:Bacterial Proteins; D003062:Codon; D012333:RNA, Messenger