RPA transforms RNase H1 to a bidirectional exoribonuclease for processive RNA–DNA hybrid cleavage

Yanan Li, Chao Liu, Xinshuo Jia, Lulu Bi, Zhiyun Ren, Yilin Zhao, Xia Zhang, Lijuan Guo, Yanling Bao, Cong Liu, Wei Li () and Bo Sun ()
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Yanan Li: ShanghaiTech University
Chao Liu: Guangzhou Medical University
Xinshuo Jia: ShanghaiTech University
Lulu Bi: ShanghaiTech University
Zhiyun Ren: ShanghaiTech University
Yilin Zhao: ShanghaiTech University
Xia Zhang: ShanghaiTech University
Lijuan Guo: ShanghaiTech University
Yanling Bao: ShanghaiTech University
Cong Liu: Chinese Academy of Sciences
Wei Li: Guangzhou Medical University
Bo Sun: ShanghaiTech University

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract RNase H1 has been acknowledged as an endoribonuclease specializing in the internal degradation of the RNA moiety within RNA–DNA hybrids, and its ribonuclease activity is indispensable in multifaceted aspects of nucleic acid metabolism. However, the molecular mechanism underlying RNase H1-mediated hybrid cleavage remains inadequately elucidated. Herein, using single-molecule approaches, we probe the dynamics of the hybrid cleavage by Saccharomyces cerevisiae RNase H1. Remarkably, a single RNase H1 enzyme displays 3′-to-5′ exoribonuclease activity. The directional RNA degradation proceeds processively and yet discretely, wherein unwinding approximately 6-bp hybrids as a prerequisite for two consecutive 3-nt RNA excisions limits the overall rate within each catalytic cycle. Moreover, Replication Protein A (RPA) reinforces RNase H1’s 3′-to-5′ nucleolytic rate and processivity and stimulates its 5′-to-3′ exoribonuclease activity. This stimulation is primarily realized through the pre-separation of the hybrids and consequently transfers RNase H1 to a bidirectional exoribonuclease, further potentiating its cleavage efficiency. These findings unveil unprecedented characteristics of an RNase and provide a dynamic view of RPA-enhanced processive hybrid cleavage by RNase H1.

Date: 2024
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DOI: 10.1038/s41467-024-51984-5

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