The strength of translational selection for codon usage varies in the three replicons of Sinorhizobium meliloti

The genome of the nitrogen-fixing bacterium Sinorhizobium meliloti is composed of three replicons of 3.65 (chromosome), 1.35 (pSymA) and 1.68 Mb (pSymB), respectively. While the chromosome encodes for most of the housekeeping functions, the three elements may contribute to symbiosis, though pSymA is absolutely necessary for nodulation and nitrogen fixation, since it harbours all the characterized nodulation and symbiotic fixation genes. On the other hand, the majority of the sequences located in this megaplasmid are probably not expressed during the free-living stage of the organism. Since most of the sequences located in pSymA are transcribed only at the stage of bacteroids when most probably the fate of the bacterium is to die, the mutations occurring at this stage will not be fixed in the population. Therefore, if natural selection contributes to the codon usage pattern in this species, its effect will be much weaker for the genes placed in pSymA. A codon usage analysis of the genes comprising the three replicons is consistent with the conclusion that selection for translational speed shapes the codon usage of the two replicons which are important for competitive cell growth while the codon usage of the third replicon reflects primarily the mutational bias. (C) 2003 Elsevier B.V. All rights reserved.