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Nucleic acids research
Feb 27, 2025;53 (5):

The mutational landscape of Bacillus subtilis conditional hypermutators shows how proofreading skews DNA polymerase error rates.

Ira Tanneur, Etienne Dervyn, Cyprien Guérin, Guillaume Kon Kam King, Matthieu Jules, Pierre Nicolas
Author Information
  1. Ira Tanneur: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
  2. Etienne Dervyn: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France. ORCID
  3. Cyprien Guérin: Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France. ORCID
  4. Guillaume Kon Kam King: Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France. ORCID
  5. Matthieu Jules: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France. ORCID
  6. Pierre Nicolas: Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France. ORCID
PMID: 40057377 DOI: 10.1093/nar/gkaf147

Abstract

Polymerase errors during DNA replication are a major source of point mutations in genomes. The spontaneous mutation rate also depends on the counteracting activity of DNA repair mechanisms, with mutator phenotypes appearing constantly and allowing for periods of rapid evolution in nature and in the laboratory. Here, we use the Gram-positive model bacterium Bacillus subtilis to disentangle the contributions of DNA polymerase initial nucleotide selectivity, DNA polymerase proofreading, and mismatch repair (MMR) to the mutation rate. To achieve this, we constructed several conditional hypermutators with a proofreading-deficient allele of polC and/or a deficient allele of mutL and performed mutation accumulation experiments. These conditional hypermutators enrich the B. subtilis synthetic biology toolbox for directed evolution. Using mathematical models, we investigated how to interpret the apparent probabilities with which errors escape MMR and proofreading, highlighting the difficulties of working with counts that aggregate potentially heterogeneous mutations and with unknowns about the pathways leading to mutations in the wild-type. Aware of these difficulties, the analysis shows that proofreading prevents partial saturation of the MMR in B. subtilis and that an inherent drawback of proofreading is to skew the net polymerase error rates by amplifying intrinsic biases in nucleotide selectivity.

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Grants

  1. ANR-18-CE43-0002/French National Research Agency
  2. /MathNum division of
  3. /INRAE

MeSH Term

Bacillus subtilis
DNA Mismatch Repair
DNA Replication
DNA-Directed DNA Polymerase
Mutation Rate
Mutation
Bacterial Proteins
MutL Proteins
DNA Polymerase III

Chemicals

DNA-Directed DNA Polymerase
Bacterial Proteins
PolC protein, bacteria
MutL Proteins
DNA Polymerase III
Journal Article
Article has an altmetric score of 2

Word Cloud

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