Using Dynamic Programming and Phylogenetic Clustering to Reveal Structure/Function Relationships in the Y-Family DNA Polymerases That Bypass DNA Damage Caused by Mutagenic Carcinogens

Cells suffer damage to their DNA from environmental agents including ionizing radiation and DNA-binding chemicals, causing mutations and ultimately cancer.  Unrepaired DNA damage typically blocks replicative DNA polymerases (DNAPs).  Living systems have evolved lesion-bypass DNAPs, which are mostly in the Y-Family. The IV/κ -class of Y-Family DNAPs, which includes E. coli DNAP IV and human DNAP κ, evolved to accurately bypass DNA with modifications that protrude into the minor groove, notably N²-dG adducts. The V/η-class of Y-Family DNAPs, including E. coli DNAP V and human DNAP η,  evolved to accurately bypass UV photodamage.  Mutations arise when the wrong Y-Family DNAP replicates a type of DNA damage; e.g., the G->T mutagenic pathway for the N²-dG adduct of benzo[a]pyrene (the potent environmental mutagen/carcinogen) involves incorrect dATP insertion by V/η-class of Y-Family DNAPs.  Our project involves understanding how structural differences between these classes dictate their functional/mechanistic differences.  Y-family DNAPs have a unique “little finger” domain (LFD), which binds DNA and is known to play a significant role in defining the differences in bypass properties of the V/η-class vs. the IV/κ-class. Conventional computational approaches fail to properly align the amino acids in LFDs in the case of Y-Family DNAPs where the three-dimensional structure is known from X-ray studies. We applied dynamic programming techniques and phylogenetic analysis  to explore how amino acid sequence dictates LFD structure and function. Our goal is to better understand structure/function relationships around the active sites in different Y-Family DNAPs.