Mutational spectra are associated with bacterial niche

Area of Science:

• Microbial genomics
• Evolutionary biology
• Molecular biology

Background:

• Mutational signatures, distinct patterns of DNA alterations, are observed in cancers, arising from mutagens and DNA repair defects.
• These mutational processes are hypothesized to also shape bacterial genomes, creating lineage-specific patterns.

Purpose of the Study:

• To reconstruct mutational spectra for diverse bacterial clades.
• To identify and characterize mutational signatures associated with DNA repair defects and environmental mutagens in bacteria.
• To explore the utility of mutational signatures in inferring bacterial replication niches and transmission routes.

Main Methods:

• Reconstruction of mutational spectra for 84 bacterial clades across 31 species.
• Identification of signatures linked to specific DNA repair defects using hypermutator lineages.
• Deconvolution of mutational spectra into multiple signatures operating within different clades.
• Comparison of mutational spectra from clades in diverse environmental and biological locations.

Main Results:

• Distinct mutational patterns and signatures were identified across bacterial clades.
• Signatures were associated with bacterial phylogeny and replication niche.
• Niche-associated mutational signatures were identified, allowing inference of replication niches for previously uncharacterized clades.
• Mutational spectra can reflect mutagen exposure differences at bacterial replication sites.

Conclusions:

• Mutational spectra provide insights into bacterial evolution, DNA repair, and environmental exposures.
• Mutational signatures can serve as powerful tools for inferring bacterial replication niches and transmission dynamics.
• This approach has implications for understanding and tracking bacterial pathogens.