title: Codon usage patterns suggest independent evolution of two catabolic operons on toluene-degradative plasmid TOL pWW0 of Pseudomonas putida.
abstract: TOL plasmid pWW0 of Pseudomonas putida encodes a set of enzymes responsible for the degradation of toluene. The structural genes for these catobolic enzymes are clustered into two operons--namely, the xy/CMAB and xy/XYZLTEGFJQKIH operons. We examined the codon usage patterns of these catabolic genes by measuring the codon-usage distances between pairs of these catabolic genes. The codon-usage distance, d, between gene 1 and gene 2 was defined as d = [sigma(pj-qj)2]1/2, are the frequencies of the j-th codon in gene 1 and 2, respectively, j being any one of the 64 possible codons. We found that the genes in the same operon exhibit similar codon-usage patterns while genes in the different operons exhibit different codon bias. This observation suggests that genes in the same operon have coevolved, and that the ancestors of the xy/CMAB and xy/XYZLTEGFJQKIH operons evolved in different organisms.
authors.affiliation: Department of Medical Biochemistry, University of Geneva 1, Switzerland.
authors.forename: S
authors.initials: S
authors.lastname: Harayama
mesh_terms: D001673:Biodegradation, Environmental; D005075:Biological Evolution; D002876:Chromosomes, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D005815:Genetic Code; D016680:Genome, Bacterial; D008957:Models, Genetic; D009876:Operon / Q000235:genetics*; D010957:Plasmids / Q000235:genetics*; D016958:Pseudomonas putida / Q000235:genetics*; D014050:Toluene / Q000378:metabolism*
chemical_list: D014050:Toluene