Poster #89 - Zaina Punter

Uncovering Divergent Viral DNA polymerase B Variants Using Protein Language Model Embeddings.

Zaina T.A. Punter, Zachary D. Schreiber, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson

There are 10^30 bacteriophages (phages)-viruses that infect bacteria-in the world's oceans, making them the most abundant biological entity on Earth. Phage maintain a singular central function of genome replication through lytic or lysogenic infection of their bacterial host, and the outcomes of phage infection significantly impact bacterial communities and nutrient cycling. The Viral Ecology and Informatics Laboratory (VEIL) uses phage replication proteins, such as DNA polymerases, as markers of bacteriophage lifestyle. VEIL has studied DNA polymerase A (PolA) and found that the amino acid identity at position 762 (E. coli numbering) correlated with PolA phylogeny, enzyme biochemistry, and infection strategy. However, only 25% of dsDNA phage carry PolA, such that a substantial portion of the phage community's replication machinery remains uncharacterized. DNA polymerase B (PolB) is encoded by many phage, including those that infect photosynthetic cyanobacteria microbial community members. This research characterizes PolB conserved domains and active sites, identified based on literature review and multi-sequence alignments, and validates PolB in genomic and metagenomic datasets. Putative PolB proteins are classified via protein family (Pfam) domain-based annotation, which improves classification compared to traditional homology top-hit transitive annotation. Next-generation bioinformatics approaches, such as those that leverage protein language model (PLM) embeddings, reflect traditional phylogenetic groupings and show distinct RNA-primed (rPolB) and protein-primed (pPolB) classes. Utilizing PLM embeddings allows for analysis of PolB and co-occurring replication proteins. This multi-protein framework reveals patterns within PolB classes and reflects the infection strategy of PolB-encoding phage. Future research will explore the diversity and abundance of PolB-carrying viral populations and their impacts on host communities and ecosystems.