DNA Polymerase Family B Reveals Novel Viral Diversity and Reflects Infection Strategy

• Zaina Punter, Applied Molecular Biology & Biotechnology, University of Delaware

• Shawn Polson, , University of Delaware
• Barbra Ferrell, , University of Delaware

The world’s oceans contain tens of millions of bacteriophages (phages)—viruses that infect bacteria—making them the most abundant biological entity on Earth. Phage maintain a singular central function of genome replication through lytic or temperate infection of their bacterial host, and the outcomes of phage infection significantly impact bacterial communities and nutrient cycling. The Viral Ecology and Informatics Laboratory uses genes that encode proteins involved in replication, such as DNA polymerases, as markers of bacteriophage lifestyle. DNA Polymerase B (PolB) exhibits potential as a viral marker gene given that it is evolutionarily ancient, important to viral biology, and is well represented in publicly available databases, diverse phage lineages, and across ecologically important groups such as cyanophage, which infect photosynthetic cyanobacteria. This research project characterizes conserved domains and active sites in DNA polymerase B and uses this knowledge to validate DNA polymerase B in environmental samples. Putative DNA polymerases are retrieved from a collection of environmental viral genomes based on similarity to reference sequences and annotated domains relating to PolB. Conserved domains and motifs are identified through literature review and multi-sequence alignments. Phylogenetic analysis reveals sequence motifs that may be predictive of particular protein clusters and uncovers viral diversity not observed in PolB-carrying bacterial hosts and populations.  Future research will explore the diversity and abundance of PolB-carrying viral populations and their impacts on host communities and ecosystems.