SHORT-SEQUENCE DNA REPEATS IN PROKARYOTIC GENOMES

Short-sequence DNA repeat (SSR) loci can be identified in all eukaryot ic and many prokaryotic genomes. These loci harbor short or long stret ches of repented nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous, SSRs are encounter ed in many different branches of the prokaryote kingdom. They are foun d in genes encoding products as diverse as microbial surface component s recognizing adhesive matrix molecules and specific bacterial virulen ce factors such as lipopolysaccharide-modifying enzymes or adhesins. S SRs enable genetic and consequently phenotypic flexibility. SSRs funct ion at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the indi vidual repeat sequences may result from recombination processes or pol ymerase inadequacy such as slipped-strand mispairing (SSM), either alo ne or in combination with DNA repair deficiencies. These rather comple x phenomena can occur with relative ease, with SSM approaching a frequ ency of 10(-4) per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their g enetic repertoire in response to selective environmental pressure. SSR -mediated variation has important implications for bacterial pathogene sis and evolutionary fitness. Molecular analysis of changes in SSRs al lows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness t o environmental factors, bacterial pathogenicity, epidemiology, and th e availability of full-genome sequences for increasing numbers of micr o-organisms, especially those that are medically relevant.