Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair

Abstract

The heterotrimeric eukaryotic Replication protein A (RPA) is a master regulator of numerous DNA metabolic processes. For a long time, it has been viewed as an inert protector of ssDNA and a platform for assembly of various genome maintenance and signaling machines. Later, the modular organization of the RPA DNA binding domains suggested a possibility for dynamic interaction with ssDNA. This modular organization has inspired several models for the RPA-ssDNA interaction that aimed to explain how RPA, the high-affinity ssDNA binding protein, is replaced by the downstream players in DNA replication, recombination, and repair that bind ssDNA with much lower affinity. Recent studies, and in particular single-molecule observations of RPA-ssDNA interactions, led to the development of a new model for the ssDNA handoff from RPA to a specific downstream factor where not only stability and structural rearrangements but also RPA conformational dynamics guide the ssDNA handoff. Here we will review the current knowledge of the RPA structure, its dynamic interaction with ssDNA, and how RPA conformational dynamics may be influenced by posttranslational modification and proteins that interact with RPA, as well as how RPA dynamics may be harnessed in cellular decision making.

Keywords:

• Conformational protein dynamics
• replication protein A (RPA)
• DNA replication
• DNA repair
• homologous recombination
• protein-DNA interctions
• single-molecule

Acknowledgments

We thank Members of the Spies’ lab for critical reading of the manuscript and for valuable discussions. We thank Dr. Luke Yates and Prof. Xiaodong Zhang (Imperial College London) for sharing coordinates of the S. cerevisiae 2xRPA-ssDNA complex model and the CryoEM 2D class average depiction, and Prof. Adrian Elcock (University of Iowa) for the model of the complete human RPA heterotrimer. We also acknowledge Prof. Marc Wold (University of Iowa) for many valuable discussions regarding RPA dynamics, regulation, and functions.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The present work was financially supported by the National Institutes of Health [NIH/NIGMS R35GM131704, NIH/NCI R01 CA232425], DOD/CDMRP [BC180227P1], and National Science Foundation [1836351 EAGER] to M.S., and by a National Institutes of Health Pharmacological Sciences Training Grant [NIH T32 GM067795] to C.C.C.