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Nucleic Acids Research, 1994, Vol. 22, No. 6 929-936
© 1994

COMPUTATIONAL BIOLOGY

Divergence in codon usage of Lactobacillus species

Peter H. Pouwels* and Jack A.M. Leunissen1

TNO Nutrition and Food Research, Department of Molecular Genetics and Gene-technology PB 5815, 2280 HV Rijswijk 1University of Nijmegen, CAOS-CAM Center Toernooiveld, NL-6525 ED, Nijmegen, The Netherlands

*To whom correspondence should be addressed

Received January 17, 1994. Revised February 24, 1994. Accepted February 24, 1994.

We have analyzed codon usage patterns of 70 sequenced genes from different Lactobacillus species. Codon usage in lactobacilll is highly biased. Both inter-species and intra-species heterogeneity of codon usage bias was observed. Codon usage in L.acidophilus is similar to that in L.helveticus, but dissimilar to that in L.bulgaricus, L.casei, L.pentosus and L.plantarum. Codon usage in the latter three organisms is not significantly different, but is different from that in L.bulgarlcus. Inter-species differences in codon usage can, at least in part, be explained by differences in mutational drift. L.bulgarlcus shows GC drift, whereas all other species show AT drift. L.acldophllus and L.helvetlcus rarely use NNG in family-box (a set of synonymous) codons, in contrast to all other species. This result may be explained by assuming that L.acldophllus and L.helvetlcus, but not other species examined, use a single tRNA species for translation of family-box codons. Differences in expression level of genes are positively correlated with codon usage bias. Highly expressed genes show highly biased codon usage, whereas weakly expressed genes show much less biased codon usage. Codon usage patterns at the 5'-end of Lactobacillus genes is not significantly different from that of entire genes. The GC content of codons 2–6 is significantly reduced compared with that of the remainder of the gene. The possible implications of a reduced GC content for the control of translation efficiency are discussed.


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