All cells need to duplicate their DNA during a process called DNA replication to allow for cell growth and survival. It has been known since the 1970’s that as both strands of DNA are duplicated one strand is synthesized continuously while the other strand known as the lagging strand is synthesized discontinuously in pieces referred to as Okazaki fragments.
Because the lagging strand is replicated in pieces, each Okazaki fragment begins with an RNA primer. The RNA primer of each fragment must be removed and replaced with DNA before thousands of Okazaki fragments are stitched together to make a continuous strand of DNA to complete the replication process. It was thought that removal of the RNA primer in bacteria was accomplished by a multifunctional DNA polymerase with nuclease activity known as DNA polymerase I.
Graduate student Caroline Lowder in the Simmons Lab found that a different nuclease is responsible for RNA primer removal. Caroline’s work identified FEN as the primary nuclease responsible for RNA primer removal from lagging strand fragments. She compared the enzymatic activity of FEN with that of DNA polymerase I and found that FEN was far more active on RNA-DNA hybrids that are associated with lagging strand fragments. Using a genetic approach Caroline provided evidence that FEN is the dominant nuclease for lagging strand replication in cells while DNA polymerase I fulfills the role of DNA synthesis to replace the RNA with DNA before lagging strand replication is complete. Since many bacteria contain a FEN protein, Caroline’s work suggests that lagging strand synthesis in bacteria is reliant on this newly defined FEN protein changing our view of how lagging strand replication occurs in bacteria.
