title: Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.
abstract: The relationship between codon usage in prokaryotes and their ability to grow at extreme temperatures has been given much attention over the past years. Previous studies have suggested that the difference in synonymous codon usage between (hyper)thermophiles and mesophiles is a consequence of a selective pressure linked to growth temperature. Here, we performed an updated analysis of the variation in synonymous codon usage with growth temperature; our study includes a large number of species from a wide taxonomic and growth temperature range. The presence of psychrophilic species in our study allowed us to test whether the same selective pressure acts on synonymous codon usage at very low growth temperature. Our results show that the synonymous codon usage for Arg (through the AGG, AGA and CGT codons) is the most discriminating factor between (hyper)thermophilic and non-thermophilic species, thus confirming previous studies. We report the unusual clustering of an Archaeal psychrophile with the thermophilic and hyperthermophilic species on the synonymous codon usage factorial map; the other psychrophiles in our study cluster with the mesophilic species. Our conclusion is that the difference in synonymous codon usage between (hyper)thermophilic and non-thermophilic species cannot be clearly attributed to a selective pressure linked to growth at high temperatures.
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), France. lobry@biomserv.univ-lyon1.fr <lobry@biomserv.univ-lyon1.fr>
authors.forename: J R
authors.initials: JR
authors.lastname: Lobry
authors.forename: A
authors.initials: A
authors.lastname: Necşulea
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000254:growth & development; D001419:Bacteria / Q000235:genetics* / Q000254:growth & development; D001482:Base Composition; D003062:Codon / Q000235:genetics*; D015870:Gene Expression; D006128:Growth; D008957:Models, Genetic; D015999:Multivariate Analysis; D019642:RNA, Archaeal / Q000737:chemistry / Q000235:genetics; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D013696:Temperature
chemical_list: D003062:Codon; D019642:RNA, Archaeal; D012329:RNA, Bacterial