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Analysis of enteric bacteria SOS operator sequences and description of potential DNA damage-inducible genes^*

Ana T. Vasconcelos^I; Rosane S. Machado^II; Darcy F. de Almeida^II

^ILaboratório Nacional de Computação Científica, CNPq 22290-160 Rio de Janeiro, RJ, Brasil
^IILaboratório de Fisiologia Celular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, CCS, Bloco G, Cidade Universitária, 21941-590 Rio de Janeiro, RJ, Brasil. Tel.: (021) 260-6963. Fax: (021) 280-8193 ou 274-5655. Send correspondence to D.F.A.

ABSTRACT

An analysis of enteric bacteria nucleotide sequences was carried out using a computer-assisted similarity search for potential SOS boxes in Escherichia coli and Salmonella typhimurium. The strategy consisted of searching the GenBank, initially for extragenic sequences containing the consensus CTG (TA)₅CAG with up to six mismatches in the central (TA)₅ decamer. Selected sequences were individually examined for their heterology index (lE) score, which indicates their relative affinity to the repressor protein, and for the presence of associated regulatory features (-10 and -35 promoter boxes, ribosome-binding sites, and a downstream open-reading frame (ORF)) suitably placed in the neighboring regions. A total of 10 newly identified sequences were selected, seven from the E. coli and three from the S. typhimurium genome; five had lE < 7.0 and five had 15.5 > lE > 10.0. Three selected sequences (two in E. coli, one in S. typhimurium) were associated with recognizable ORFs. Others are positioned upstream of regions coding for antibiotic resistance and enterohemolysin production, while still others are ambiguously positioned relative to known coding regions, particularly between divergently transcribed genes. The results show that a search for prokaryote regulatory sequences may be useful for the identification of genes belonging to specific regulons.

Keywords: enteric bacteria; DNA; damage-inducible; genes.

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* This paper is dedicated to Prof. Carlos Chagas Filho, founder of the Institute of Biophysics, on the occasion of its 50th anniversary.