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Microbiology 149 (2003), 855-863; DOI  10.1099/mic.0.26063-0
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Microbiology 149 (2003), 855-863; DOI  10.1099/mic.0.26063-0
© 2003 Society for General Microbiology

Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum

Héctor Musto1, Héctor Romero1,2 and Alejandro Zavala1

1 Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias, Iguá 4225, Montevideo 11400, Uruguay
2 Escuela Universitaria de Tecnología Médica, Facultad de Medicina, Avda. Italia (s/n) Hospital de Clínicas, Montevideo 11600, Uruguay

Correspondence
Héctor Musto
hmusto{at}fcien.edu.uy

Here, the codon usage patterns of two Clostridium species (Clostridium perfringens and Clostridium acetobutylicum) are reported. These prokaryotes are characterized by a strong mutational bias towards A+T, a striking excess of coding sequences and purine-rich leading strands of replication, strong GC-skews and a high frequency of genomic rearrangements. As expected, it was found that the mutational bias dominates codon usage but there is some variation of synonymous codon choices among genes in the two species. This variation was investigated using a multivariate statistical approach. In the two species, two major trends were detected. One was related to the location of the sequences in the leading or lagging strand of replication, and the other was associated with the preferential use of putatively translational optimal codons in heavily expressed genes. Analyses of the estimated number of synonymous and non-synonymous substitutions among orthologous genes permit us to postulate that optimal codons might be selected not only for speed but also for accuracy during translation.

Abbreviations: CAI, codon adaptation index; COA, correspondence analysis; RSCU, relative synonymous codon usage




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