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ARTICLE

Short-Sequence DNA Repeats in Prokaryotic Genomes

Alex van Belkum, Stewart Scherer, Loek van Alphen, Henri Verbrugh
Alex van Belkum
Department of Medical Microbiology & Infectious Diseases, Erasmus Medical Center Rotterdam, 3015 GD Rotterdam, and
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Stewart Scherer
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Loek van Alphen
Department of Medical Microbiology, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
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Henri Verbrugh
Department of Medical Microbiology & Infectious Diseases, Erasmus Medical Center Rotterdam, 3015 GD Rotterdam, and
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DOI: 10.1128/MMBR.62.2.275-293.1998
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SUMMARY

SUMMARY 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.

  • Copyright © 1998 American Society for Microbiology
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Short-Sequence DNA Repeats in Prokaryotic Genomes
Alex van Belkum, Stewart Scherer, Loek van Alphen, Henri Verbrugh
Microbiology and Molecular Biology Reviews Jun 1998, 62 (2) 275-293; DOI: 10.1128/MMBR.62.2.275-293.1998

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Short-Sequence DNA Repeats in Prokaryotic Genomes
Alex van Belkum, Stewart Scherer, Loek van Alphen, Henri Verbrugh
Microbiology and Molecular Biology Reviews Jun 1998, 62 (2) 275-293; DOI: 10.1128/MMBR.62.2.275-293.1998
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  • Article
    • SUMMARY
    • MOLECULAR ANALYSIS OF SSRS
    • WHOLE GENOME SEQUENCES AS A SOURCE OF SSRS
    • STRUCTURAL FEATURES OF SSRS
    • DISPERSED REPEATS IN PROKARYOTIC DNA
    • CONTIGUOUS REPEATS IN PROKARYOTIC DNA
    • SPECIFIC SSRS IN DNA FROM VARIOUS BACTERIAL SPECIES
    • SSRS IN PATHOGENIC PROTOZOA AND LOWER EUKARYOTES
    • SSRS AND MICROBIAL EVOLUTION
    • SSRS AND MICROBIAL PATHOGENESIS
    • SSRS IN MOLECULAR EPIDEMIOLOGY
    • CONCLUDING REMARKS AND PROSPECTS
    • ACKNOWLEDGMENTS
    • REFERENCES
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  • Info & Metrics
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KEYWORDS

DNA, Bacterial
Repetitive Sequences, Nucleic Acid

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