Human primosome requires replication protein A when copying DNA with inverted repeats

Abstract

The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Pol), initiates DNA synthesis on both chromosome strands by generating chimeric RNA-DNA primers for loading DNA polymerases delta and epsilon (Pol{varepsilon}). Replication protein A (RPA) tightly binds to single-stranded DNA strands, protecting them from nucleolytic digestion and unauthorized transactions. We report here that RPA plays a critical role for the human primosome during DNA synthesis across inverted repeats prone to hairpin formation. On other alternatively structured DNA, forming a G-quadruplex, RPA does not assist primosome. A stimulatory effect of RPA on DNA synthesis across hairpins was also observed for the catalytic domain of Pol but not of Pol{varepsilon}. The winged helix-turn-helix domain of RPA is essential for an efficient hairpin bypass and increases RPA-Pol cooperativity on the primed DNA template. Cryo-EM studies revealed that this domain is mainly responsible for the interaction between RPA and Pol. The flexible mode of RPA-Pol interaction during DNA synthesis implies the mechanism of template handover between them when the hairpin formation should be avoided. This work provides insight into a cooperative action of RPA and primosome on DNA, which is critical for DNA synthesis across inverted repeats. SIGNIFICANCEThis work revealed the critical role of RPA during DNA synthesis across inverted repeats by the human primosome. It was shown that a small winged helix-turn-helix domain of RPA is essential for the cooperative action of RPA and primosome, especially when copying DNA sequences prone to hairpin structure formation. Structural studies uncovered the mode of RPA and Pol integration, which assures an efficient DNA handover between them. This work provides a notable insight into the early steps of Okazaki fragments synthesis.