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

Short-sequence DNA repeats in prokaryotic genomes

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

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.

Integrity signals

Registry

Crossref · 10.1128/mmbr.62.2.275-293.1998

Cites

223 of 223 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Previous explanations for possible mechanisms underlying chromosomal inversion included illegitimate recombination, intra-chromosomally homologous recombination, and integrase-mediated site-specific recombination.

    “Based on these molecular evidences, previous explanations for the possible mechanisms underlying chromosomal inversion included illegitimate recombination,51–53 intra-chromosomally homologous recombination,54 as well as integrase-mediated site-specific recombination.55 , 56”

Cites

Flagged first, then by citations

1 of the 224 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

Authors
van Belkum, A., Scherer, S., van Alphen, L., & Verbrugh, H.
Affiliations
  • <!--label omitted: 1-->Department of Medical Microbiology &amp; Infectious Diseases, Erasmus Medical Center Rotterdam, 3015 GD Rotterdam,1 and
  • <!--label omitted: 2-->Department of Medical Microbiology, Academic Medical Center, 1105 AZ Amsterdam,2 The Netherlands
  • Erasmus MC (NL)
Venue
Microbiology and Molecular Biology Reviews
Published
1998-06
Volume
62
Issue
2
Pages
275-293
ISSN
  • 1092-2172 (ISSN-L)
  • 1098-5557
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
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 › Agricultural and Biological Sciences › Plant Science › 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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review