Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains

Kun Wu, Zhou Hua Cheng, Emily Williams, Nathan T. Turner, Dapeng Ran, Haichao Li, Xia Zhou, Huilin Guo, Way Sung, Dong Feng Liu, Michael Lynch, Hongan Long

Research output: Contribution to journalArticlepeer-review

Abstract

Microbial strains with high genomic stability are particularly sought after for testing the quality of commercial microbiological products, such as biological media and antibiotics. Yet, using mutation-accumulation experiments and de novo assembled complete genomes based on Nanopore long-read sequencing, we find that the widely used quality-control strain Shewanella putrefaciens ATCC-8071, also a facultative pathogen, is a hypermutator, with a base-pair substitution mutation rate of 2.42 × 10-8 per nucleotide site per cell division, ∼146-fold greater than that of the wild-type strain CGMCC-1.6515. Using complementation experiments, we confirm that mutL dysfunction, which was a recent evolutionary event, is the cause for the high mutation rate of ATCC-8071. Further analyses also give insight into possible relationships between mutation and genome evolution in this important bacterium. This discovery of a well-known strain being a hypermutator necessitates screening the mutation rate of bacterial strains before any quality control or experiments.

Original languageEnglish (US)
Article numberevab148
JournalGenome biology and evolution
Volume13
Issue number8
DOIs
StatePublished - Aug 1 2021

Keywords

  • DNA mismatch repair
  • Shewanella
  • comparative genomics
  • genome evolution
  • mutation spectrum

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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