Determinants of Base-Pair Substitution Patterns Revealed by Whole-Genome Sequencing of DNA Mismatch Repair Defective...

Area of Science:

• Molecular Biology
• Genetics
• Microbiology

Background:

• DNA mismatch repair (MMR) is crucial for maintaining genomic stability and replication fidelity.
• The efficiency of MMR can be influenced by sequence context and the specific type of DNA mismatch.
• Understanding mutation patterns in MMR-defective organisms provides insights into spontaneous mutation processes.

Purpose of the Study:

• To characterize the base-pair substitution (BPS) spectrum in MMR-defective *Escherichia coli*.
• To identify sequence contexts and environmental conditions that act as hotspots for mutations.
• To compare mutational patterns in MMR-defective and MMR-proficient strains to understand MMR's role.

Main Methods:

• Mutation accumulation experiments were conducted in MMR-defective *E. coli* strains.
• Whole-genome sequencing was employed to identify approximately 30,000 base-pair substitutions.
• Comparative analysis was performed with data from MMR-proficient strains.

Main Results:

• A:T to G:C transitions dominated the BPS spectrum, particularly within 5'NAC3'/5'GTN3' triplets.
• Mononucleotide runs were mutation hotspots, with increased rates correlating with run length.
• Mutations were strand-biased in MMR-defective strains, with a preference for lagging-strand templates.
• Loss of nucleotide diphosphate kinase exacerbated specific A:T to G:C transitions, with differing strand bias depending on the strand synthesized.

Conclusions:

• Specific sequence contexts, like 5'NAC3'/5'GTN3' triplets and mononucleotide runs, are prone to replication errors.
• Environmental factors such as minimal medium and low temperature can modulate mutation rates.
• Lagging-strand synthesis appears more error-prone or less efficiently proofread than leading-strand synthesis in *E. coli*.