Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis

Amy J. Vogler, Christine E. Keys, Christopher Allender, Ira Bailey, Jessica Girard, Talima R Pearson, Kimothy L. Smith, David M Wagner, Paul S Keim

Research output: Contribution to journalArticle

55 Citations (Scopus)

Abstract

VNTRs are able to discriminate among closely related isolates of recently emerged clonal pathogens, including Yersinia pestis the etiologic agent of plague, because of their great diversity. Diversity is driven largely by mutation but little is known about VNTR mutation rates, factors affecting mutation rates, or the mutational mechanisms. The molecular epidemiological utility of VNTRs will be greatly enhanced when this foundational knowledge is available. Here, we measure mutation rates for 43 VNTR loci in Y. pestis using an in vitro generated population encompassing ∼96,000 generations. We estimate the combined 43-locus rate and individual rates for 14 loci. A comparison of Y. pestis and Escherichia coli O157:H7 VNTR mutation rates and products revealed a similar relationship between diversity and mutation rate in these two species. Likewise, the relationship between repeat copy number and mutation rate is nearly identical between these species, suggesting a generalized relationship that may be applicable to other species. The single- versus multiple-repeat mutation ratios and the insertion versus deletion mutation ratios were also similar, providing support for a general model for the mutations associated with VNTRs. Finally, we use two small sets of Y. pestis isolates to show how this general model and our estimated mutation rates can be used to compare alternate phylogenies, and to evaluate the significance of genotype matches, near-matches, and mismatches found in empirical comparisons with a reference database.

Original languageEnglish (US)
Pages (from-to)145-158
Number of pages14
JournalMutation Research - Fundamental and Molecular Mechanisms of Mutagenesis
Volume616
Issue number1-2
DOIs
StatePublished - Mar 1 2007

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Yersinia pestis
Minisatellite Repeats
Mutation Rate
Mutation
INDEL Mutation
Escherichia coli O157
Plague
Phylogeny
Genotype
Databases

Keywords

  • Maximum likelihood analysis
  • Microbial forensics
  • Mutation rate
  • Plague
  • VNTR
  • Yersinia pestis

ASJC Scopus subject areas

  • Health, Toxicology and Mutagenesis
  • Molecular Biology

Cite this

Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis. / Vogler, Amy J.; Keys, Christine E.; Allender, Christopher; Bailey, Ira; Girard, Jessica; Pearson, Talima R; Smith, Kimothy L.; Wagner, David M; Keim, Paul S.

In: Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 616, No. 1-2, 01.03.2007, p. 145-158.

Research output: Contribution to journalArticle

Vogler, Amy J. ; Keys, Christine E. ; Allender, Christopher ; Bailey, Ira ; Girard, Jessica ; Pearson, Talima R ; Smith, Kimothy L. ; Wagner, David M ; Keim, Paul S. / Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis. In: Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 2007 ; Vol. 616, No. 1-2. pp. 145-158.
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