Computer analysis of control signals in bacterial genomes. Attenuators of operons of aromatic amino acids metabolism

Here we predict attenuators in operons of aromatic amino acids metabolism in the gamma-subclass of proteobacteria Salmonella typhi, Yersinia pestis, Vibrio cholerae, Haemophilus influenzae, Actinobacillus actino-mycetemcomitans, Xanthomonas campestris and chlamydia Chlamydia trachomatis. Alternative secondary structures of mRNA governing transcription pathway selection as well as the related control leader peptide were constructed. Comparison with homologous Escherichia coli operons was used for the prediction. This control mechanism takes place in operons ap (tryptophan), phe (phenylalanine), and pheST coding for the large and small subunits of phenylalanine tRNA synthase in the considered gamma-proteobacteria. Secondary structures of mRNA in the leader region of tnaAB operon possibly involved in rho-dependent attenuation were predicted in certain enterobacteria.