AnÃlise dos padrÃes de utilizaÃÃo de cÃdons sinÃnimos no genoma da bactÃria Chromobacterium violaceum

AUTOR(ES)
DATA DE PUBLICAÇÃO

2006

RESUMO

Biased codon usage may result from various factors. Among prokaryotes, it appears that the influences of natural selection and mutational biases are different if the genome is skewed towards AT or GC. A particular codon subset can often be observed in those genome regions where a maximized translational efficiency is required. Codon usage of a β-proteobacterium, Chromobacterium violaceum, is for the first time reported. The present study was aimed at the identification of the main cause of codon usage variation in C. violaceum ATCC 12472 genome. Correspondence analysis (CoA) on relative synonymous codon usage (RSCU) was used to examine the synonymous codon usage variation among the genes. The results have shown that one of the major determinants of codon bias trends in C. violaceum is, as expected, the G+C content. It shows a direct correlation with the first principal CoA axis. A strong inverse correlation between the effective number of codons (ENc) and GC3s content was also observed, showing that the codon usage was affected by gene nucleotide composition. Hydrophobicity was the second major source of variation and was significantly correlated to the second principal CoA axis. Axis 1 and 2 separated the genome in two gene groups. The minor group seems to be formed mostly by transport proteins, reflecting a putative codon usage bias of these genes. This unusual grouping may reflect the particular environment in which this bacterium dwells (river water) and is possibly related to the special features of α-proteobacterial cell walls and to a proper adaptation to environment variations. Moreover, the strong negative correlation between CAI and ENc reflected the regular use of optimal codons among these genes. Amino acid composition does not have any influence in selecting the codon usage in this organism and does not affect either Fop or CBI. In contrast to what has been observed in α-proteobacteria, strand asymmetry does not seem to influence on amino acid composition or in the number of genes, in the other hand codon usage may have some influence. The similar distribution of genes between leading and lagging strands is possibly due to an optimized translation and a very slow replication, reducing the expected conflict between transcription and replication. The generality of these observations among β-proteobacteria will depend on new studies on this group of microorganisms

ASSUNTO(S)

- proteobactÃria hidrofobicidade correspondence analysis transport proteins anÃlise de correspondÃncia assimetria das fitas genetica hydrophobicity adaptation to environment, β transporte de proteÃnas adaptaÃÃo ao ambiente, β strand asymmetry - proteobacterium

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