Occurrence and structure-function relationship of pentameric short sequence repeats in microbial genomes

It is suggested that genomes found in any form of cellular life contain pot entially size-variable repetitive DNA moieties. In eukaryotes, large propor tions of the multi-chromosomal genome consist of various classes of repetit ive DNA. Also in archaeal genomes, repetitive DNA is encountered and, as is the case for the eukaryotes as well, little or no function is at present a ttributable to most of it. For prokaryotes, elegant experiments have highli ghted so-called slipped strand nucleotide mispairing (SSM) as a basic and c ausal mechanism, giving rise to repeat unit number variation at a distinct locus. Illegitimate base pairing in regions of repetitive DNA during replic ation, in association with defective DNA repair and enhanced nuclease susce ptibility of replication intermediates, in the end gives rise to deletion o r addition of repeat units. Prokaryotic short sequence repeats (SSRs) harbo ur arrays of short repeat units, between one and approximately 20 nucleotid es in length. SSRs are involved in;various mechanisms of microbial gene exp ression regulation. Promoter strength can be affected by altering the spaci ng between important structural domains as can the integrity of open readin g frames. In the present communication the literature on microbial SSRs har bouring repeat units that are five nucleotides in length will be briefly re viewed. Examples of these SSRs with discrete functionality are encountered in bacterial species such as Haemophilus influenzae, Neisseria gonorrhoeae, and Pasteurella haemolytica. In addition, several of the currently known b acterial and archaeal whole genome sequences were scanned for the presence of novel examples of potential five-nucleotide SSRs (and others) in order t o gather additional knowledge on the propensity and putative functions of t his type of potential genetic switch. (C) 1999 Editions scientifiques et me dicales Elsevier SAS.