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Microbiol Mol Biol Rev, June 1998, p. 275-293, Vol. 62, No. 2
1092-2172/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Short-Sequence DNA Repeats in Prokaryotic Genomes

Alex van Belkum,1 * Stewart Scherer,dagger Loek van Alphen,2 Dagger and Henri Verbrugh1

Department of Medical Microbiology & Infectious Diseases, Erasmus Medical Center Rotterdam, 3015 GD Rotterdam,1 and Department of Medical Microbiology, Academic Medical Center, 1105 AZ Amsterdam,2 The Netherlands

Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10-4 per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows 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 to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant.

* Corresponding author. Mailing address: Erasmus Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands. Phone: 31-10-4635813. Fax: 31-10-4633875. E-mail: vanbelkum{at}bacl.azr.nl.

dagger Present address: Acacia BioSciences Inc., Richmond, CA 94806.

Dagger Present address: National Institute of Public Health and the Environment, LVM RIVM, 3720 BA Bilthoven, The Netherlands.

Microbiol Mol Biol Rev, June 1998, p. 275-293, Vol. 62, No. 2
1092-2172/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.


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