Biochemical and Structural Study of RuvC and YqgF from Deinococcus radiodurans

Yiyang Sun; Jieyu Yang; Guangzhi Xu; Kaiying Cheng

doi:10.1128/mbio.01834-22

Biochemical and Structural Study of RuvC and YqgF from Deinococcus radiodurans

mBio. 2022 Oct 26;13(5):e0183422. doi: 10.1128/mbio.01834-22. Epub 2022 Aug 24.

Authors

Yiyang Sun^#¹, Jieyu Yang^#¹, Guangzhi Xu², Kaiying Cheng^{1

3}

Affiliations

¹ Department of Immunology and Microbiology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China.
² College of Food and Health, Zhejiang Agriculture and Forestry University, Zhejiang, Lin'an, China.
³ State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.

^# Contributed equally.

Abstract

Deinococcus radiodurans possesses robust DNA damage response and repair abilities, and this is mainly due to its efficient homologous recombination repair system, which incorporates an uncharacterized Holliday junction (HJ) resolution process. D. radiodurans encodes two putative HJ resolvase (HJR) homologs: RuvC (DrRuvC) and YqgF (DrYqgF). Here, both DrRuvC and DrYqgF were identified as essential proteins for the survival of D. radiodurans. The crystal structures and the biochemical properties of DrRuvC and DrYqgF were also studied. DrRuvC crystallized as a homodimer, while DrYqgF crystallized as a monomer. DrRuvC could preferentially cleave HJ at the consensus 5'-(G/C)TC↓(G/C)-3' sequence and could prefer using Mn²⁺ for catalysis in vitro, which would be different from the preferences of the other previously characterized RuvCs. On the other hand, DrYqgF was identified as a Mn²⁺-dependent RNA 5'-3' exo/endonuclease with a sequence preference for poly(A) and without any HJR activity. IMPORTANCE Deinococcus radiodurans is one of the most radioresistant bacteria in the world due to its robust DNA damage response and repair abilities, which are contributed by its efficient homologous recombination repair system. However, the late steps of homologous recombination, especially the Holliday junction (HJ) resolution process, have not yet been well-studied in D. radiodurans. We characterized the structural and biochemical features of the two putative HJ resolvases, DrRuvC and DrYqgF, in D. radiodurans. It was identified that DrRuvC and DrYqgF exhibit HJ resolvase (HJR) activity and RNA exo/endonuclease activity, respectively. Furthermore, both DrRuvC and DrYqgF digest substrates in a sequence-specific manner with a preferred sequence that is different from those of the other characterized RuvCs or YqgFs. Our findings provide new insights into the HJ resolution process and reveal a novel RNase involved in RNA metabolism in D. radiodurans.

Keywords: Deinococcus; Holliday junction (HJ); RNase; RuvC; homologous recombination (HR); protein structure.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Proteins / metabolism
DNA Repair
DNA, Cruciform*
Deinococcus* / genetics
Deinococcus* / metabolism
RNA
Ribonucleases / genetics

Substances

DNA, Cruciform
RNA
Ribonucleases
Bacterial Proteins