Single-molecule tracking of RNA-DNA hybrid removal enzymes important for lagging-strand replication

Abstract

The formation of RNA-DNA hybrid (RDH) primers by primase is an essential step in the recruitment of DNA polymerase during replication initiation and for the synthesis of each Okazaki fragment on the lagging strand. In addition to primers, RDHs form through misincorporation of ribonucleotides by DNA polymerase during elongation and by formation of R-loops during transcription. R-loops are three-stranded structures that form when the nascent mRNA anneals to the template DNA strand, displacing the complementary DNA strand. The persistence of RDHs is deleterious to genome stability in all cells because they increase susceptibility to mutations, impaired replication fork progression, DNA double-stranded breaks, and genomic rearrangements. In many bacteria, it is well established that components of the replicative DNA polymerase form a macromolecular complex that can be imaged using single-molecule or ensemble fluorescence approaches. The spatiotemporal regulation of proteins involved in RDH removal during lagging-strand maturation is less clear. Here, we study three proteins that are involved in the removal of RDHs from the lagging strand during DNA replication in the Gram-positive bacterium Bacillus subtilis: DNA polymerase I (Pol I), FenA, and RNase HIII. We characterized the behavior of each PAmCherry-tagged lagging-strand enzyme in living cells using single-particle tracking photactivated localization microscopy. In this work, we find that all three proteins are highly mobile, suggesting residence times at their target substrates are below our temporal resolution. We also find evidence that Pol I activity is modulated through interaction with the replisome, whereas FenA and RNase HIII are regulated through access to the nucleoid. Our results provide new insight into how enzymes are recruited to resolve RDHs during lagging-strand replication in vivo. SignificanceRNA-DNA hybrids (RDHs) are essential, transient intermediates in DNA replication, yet their presence significantly increases the susceptibility of the genome to damage. We characterized the single-molecule behavior of three proteins important for processing RDHs in Okazaki fragments in living bacteria. We find that enzyme activity is modulated by access to the replisome and nucleoid. Specifically, we find that DNA polymerase I is preferentially localized to the replisome, while FenA and RNase HIII dwell times at the replisome are very short and below our detection limit. Our work shows that Pol I, FenA, and RNase HIII turn over rapidly in cells, providing new insight into how lagging-strand replication is coordinated in vivo.