Cited by 737Bacterial Genetics and BiotechnologyGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

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Short-Sequence DNA Repeats in Prokaryotic Genomes

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van Belkum, Alex, Scherer, Stewart, van Alphen, Loek, Verbrugh, Henri·1998·Microbiology and Molecular Biology Reviews

DOI 10.1128/mmbr.62.2.275-293.1998PMC PMC98915

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Abstract

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.

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Authors: van Belkum, A., Scherer, S., van Alphen, L., & Verbrugh, H.
Affiliations: 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
Erasmus MC (NL)
Venue: Microbiology and Molecular Biology Reviews
Publisher: American Society for Microbiology
Published: 1998-06
Volume: 62
Issue: 2
Pages: 275-293
ISSN: 1092-2172 (ISSN-L)
1098-5557
DOI: 10.1128/mmbr.62.2.275-293.1998
PMC: PMC98915
OpenAlex: W2123546399
Cited by: 737
References: 224
Citations by year: 2026: 8 · 2025: 9 · 2024: 25 · 2023: 13 · 2022: 17 · 2021: 15 · 2020: 22 · 2019: 17 · 2018: 17 · 2017: 13 · 2016: 23 · 2015: 26 · 2014: 44 · 2013: 24 · 2012: 38
FWCI: 3.22
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Microbiology and Molecular Biology Reviews (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, other-oa)
RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Keywords: prokaryotic genomes, slipped-strand mispairing, repeat number variation, bacterial pathogenesis, bacterial virulence factors, gene expression regulation, recombination, DNA repair deficiency
MeSH terms: Animals, Bacteria, Base Sequence, DNA Repair, DNA, Bacterial, Genotype, Repetitive Sequences, Nucleic Acid, Gene Expression Regulation, Bacterial, DNA, Protozoan, Genome, Bacterial, Genome, Protozoan, Adhesins, Bacterial

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Short-Sequence DNA Repeats in Prokaryotic Genomes

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