RNase H1C Collaborates with SsDNA Binding Proteins WHY1/3 and Recombinase RecA1 to Fulfill the DNA Damage Repair in Arabidopsis Chloroplasts

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2021 Jun 16

PMID 34133716

Citations 18

Authors

Wenjie Wang

Kuan Li

Zhuo Yang

Quancan Hou

Wei W Zhao

Qianwen Sun

Affiliations

Soon will be listed here.

Abstract

Proper repair of damaged DNA is crucial for genetic integrity and organismal survival. As semi-autonomous organelles, plastids have their own genomes whose integrity must be preserved. Several factors have been shown to participate in plastid DNA damage repair; however, the underlying mechanism remains unclear. Here, we elucidate a mechanism of homologous recombination (HR) repair in chloroplasts that involves R-loops. We find that the recombinase RecA1 forms filaments in chloroplasts during HR repair, but aggregates as puncta when RNA:DNA hybrids accumulate. ssDNA-binding proteins WHY1/3 and chloroplast RNase H1 AtRNH1C are recruited to the same genomic sites to promote HR repair. Depletion of AtRNH1C or WHY1/3 significantly suppresses the binding of RNA polymerase to the damaged DNA, thus reducing HR repair and modulating microhomology-mediated double-strand break repair. Furthermore, we show that DNA polymerase IB works with AtRNH1C genetically to complete the DNA damage repair process. This study reveals the positive role of R-loops in facilitating the activities of WHY1/3 and RecA1, which in turn secures HR repair and organellar development.

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References

Kohl S, Bock R . Transposition of a bacterial insertion sequence in chloroplasts. Plant J. 2009; 58(3):423-36. DOI: 10.1111/j.1365-313X.2009.03787.x. View

Liu S, Hua Y, Wang J, Li L, Yuan J, Zhang B . RNA polymerase III is required for the repair of DNA double-strand breaks by homologous recombination. Cell. 2021; 184(5):1314-1329.e10. DOI: 10.1016/j.cell.2021.01.048. View

Ohle C, Tesorero R, Schermann G, Dobrev N, Sinning I, Fischer T . Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair. Cell. 2016; 167(4):1001-1013.e7. DOI: 10.1016/j.cell.2016.10.001. View

Chang H, Pannunzio N, Adachi N, Lieber M . Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol. 2017; 18(8):495-506. PMC: 7062608. DOI: 10.1038/nrm.2017.48. View

Li C, Wen A, Shen B, Lu J, Huang Y, Chang Y . FastCloning: a highly simplified, purification-free, sequence- and ligation-independent PCR cloning method. BMC Biotechnol. 2011; 11:92. PMC: 3207894. DOI: 10.1186/1472-6750-11-92. View

Crossley M, Bocek M, Cimprich K . R-Loops as Cellular Regulators and Genomic Threats. Mol Cell. 2019; 73(3):398-411. PMC: 6402819. DOI: 10.1016/j.molcel.2019.01.024. View

Kazama T, Okuno M, Watari Y, Yanase S, Koizuka C, Tsuruta Y . Curing cytoplasmic male sterility via TALEN-mediated mitochondrial genome editing. Nat Plants. 2019; 5(7):722-730. DOI: 10.1038/s41477-019-0459-z. View

Miller-Messmer M, Kuhn K, Bichara M, Le Ret M, Imbault P, Gualberto J . RecA-dependent DNA repair results in increased heteroplasmy of the Arabidopsis mitochondrial genome. Plant Physiol. 2012; 159(1):211-26. PMC: 3375962. DOI: 10.1104/pp.112.194720. View

Shedge V, Arrieta-Montiel M, Christensen A, Mackenzie S . Plant mitochondrial recombination surveillance requires unusual RecA and MutS homologs. Plant Cell. 2007; 19(4):1251-64. PMC: 1913765. DOI: 10.1105/tpc.106.048355. View

10.

Shapiguzov A, Vainonen J, Hunter K, Tossavainen H, Tiwari A, Jarvi S . Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors. Elife. 2019; 8. PMC: 6414205. DOI: 10.7554/eLife.43284. View

11.

Xu W, Xu H, Li K, Fan Y, Liu Y, Yang X . The R-loop is a common chromatin feature of the Arabidopsis genome. Nat Plants. 2017; 3(9):704-714. DOI: 10.1038/s41477-017-0004-x. View

12.

Sessa G, Gomez-Gonzalez B, Silva S, Perez-Calero C, Beaurepere R, Barroso S . BRCA2 promotes DNA-RNA hybrid resolution by DDX5 helicase at DNA breaks to facilitate their repair‡. EMBO J. 2021; 40(7):e106018. PMC: 8013831. DOI: 10.15252/embj.2020106018. View

13.

DAlessandro G, Whelan D, Howard S, Vitelli V, Renaudin X, Adamowicz M . BRCA2 controls DNA:RNA hybrid level at DSBs by mediating RNase H2 recruitment. Nat Commun. 2018; 9(1):5376. PMC: 6299093. DOI: 10.1038/s41467-018-07799-2. View

14.

Cappadocia L, Marechal A, Parent J, Lepage E, Sygusch J, Brisson N . Crystal structures of DNA-Whirly complexes and their role in Arabidopsis organelle genome repair. Plant Cell. 2010; 22(6):1849-67. PMC: 2910959. DOI: 10.1105/tpc.109.071399. View

15.

San Filippo J, Sung P, Klein H . Mechanism of eukaryotic homologous recombination. Annu Rev Biochem. 2008; 77:229-57. DOI: 10.1146/annurev.biochem.77.061306.125255. View

16.

Yang E, Yoo C, Liu J, Wang H, Cao J, Li F . NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches. Nat Commun. 2019; 10(1):2630. PMC: 6570768. DOI: 10.1038/s41467-019-10517-1. View

17.

Sollier J, Cimprich K . Breaking bad: R-loops and genome integrity. Trends Cell Biol. 2015; 25(9):514-22. PMC: 4554970. DOI: 10.1016/j.tcb.2015.05.003. View

18.

Furlan-Magaril M, Rincon-Arano H, Recillas-Targa F . Sequential chromatin immunoprecipitation protocol: ChIP-reChIP. Methods Mol Biol. 2009; 543:253-66. DOI: 10.1007/978-1-60327-015-1_17. View

19.

Gualberto J, Newton K . Plant Mitochondrial Genomes: Dynamics and Mechanisms of Mutation. Annu Rev Plant Biol. 2017; 68:225-252. DOI: 10.1146/annurev-arplant-043015-112232. View

20.

Bhatia V, Barroso S, Garcia-Rubio M, Tumini E, Herrera-Moyano E, Aguilera A . BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature. 2014; 511(7509):362-5. DOI: 10.1038/nature13374. View