Nucleic Acids Research, Vol 27, Issue 17 3567-3576, Copyright © 1999 by Oxford University Press
EP Rocha, A Danchin and A Viari
We analysed the Bacillus subtilis protein coding sequences termini, and
compared it to other genomes. The analysis focused on signals, com-
positional biases of nucleotides, oligonucleotides, codons and amino acids
and mRNA secondary structure. AUG is the preferred start codon in all
genomes, independent of their G+C content, and seems to induce less stable
mRNA structures. However, it is not conserved between homologous genes
neither is it preferred in highly expressed genes. In B.subtilis the
ribosome binding site is very strong. We found that downstream boxes do not
seem to exist either in Escherichia coli or in B.subtilis. UAA stop codon
usage is correlated with the G+C content and is strongly selected in highly
expressed genes. We found less stable mRNA structures at both termini,
which we related to mRNA-ribosome and mRNA- release-factor interactions.
This pattern seems to impose a peculiar A- rich nucleotide and codon usage
bias in these regions. Finally the analysis of all proteins from B.subtilis
revealed a similar amino acid bias near both termini of proteins consisting
of over-representation of hydrophilic residues. This bias near the stop
codon is partially release-factor specific.
ARTICLES
Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis
Atelier de BioInformatique, Universite Paris VI, 12 Rue Cuvier, 75005 Paris, France. erocha@abi.snv.jussieu.fr
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