[Modeling evolution of regulatory signals for gene expression in bacteria].

A model of evolution of a regulatory signal along the phylogenetic tree of species taking into account the secondary RNA structure is suggested. Based on this model, an algorithm is presented. It inputs the extant primary structure of a signal for the leaves of the phylogenetic tree and computes the primary and secondary structures of all the nodes.

[Search for alternative secondary structures of RNA, regulating expression of bacterial genes].

Expression of many bacterial genes is regulated by formation of alternative secondary RNA structure within the leader mRNA sequence. Our algorithm designed to search for these structures (basing on analysis of one nucleotide sequence) was applied to analyze operons of amino acid biosynthesis in alpha- and gamma-proteobacteria. The attenuators of these operons are predicted for genomes of some poorly known gamma-proteobacteria including Shewanella putrefaciens, attenuators of the tryptophan operon in some alpha-proteobacteria are also predicted.