Diversity and distribution of bacterial DNA polymerases

DNA polymerases are key players in DNA replication, repair, and maintenance. However, the overall abundance, diversity, and distribution of bacterial DNA polymerases have not been systematically explored. To close this knowledge gap, we computationally identified and characterized DNA polymerases and their homologs from A, B, C, X, and Y families in over 3000 representative bacterial species with complete genomes. We found that Y-family is the most abundant, followed by C and A families, whereas B and X families are rare. All species have replicative C-family polymerases, 96% have A-family polymerases, and 88% have Y-family members. In each family, we identified and annotated distinct groups, proofreading nucleases, and interaction motifs. Based on conserved associations for DnaE2 and Y-family groups, we identified 11 types of putative multimeric error-prone DNA polymerases supported by AlphaFold modeling. Approximately 90% of the complexes belong to four major types, exemplified by Meiothermus silvanus PolY-RecA complex, Mycobacterium tuberculosis ImuA-ImuB-DnaE2, Escherichia coli Pol V (UmuC-UmuD'2-RecA), and Bacillus subtilis YqjW-YqjX-RecA. We found that distribution patterns of distinct polymerase groups and multimeric complexes are shaped by bacterial lineages, replication-system types, and environmental factors. Our results thus provide a comprehensive picture of DNA polymerase diversity and distribution across the bacterial domain.