A Ubiquitylation Site in Cockayne Syndrome B Required for Repair of Oxidative DNA Damage, but Not for Transcription-coupled Nucleotide Excision Repair

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2016 Apr 10

PMID 27060134

Citations 18

Authors

Michael Ranes

Stefan Boeing

Yuming Wang

Franziska Wienholz

Herve Menoni

Jane Walker

Vesela Encheva

Probir Chakravarty

Pierre-Olivier Mari

Aengus Stewart

Giuseppina Giglia-Mari

Ambrosius P Snijders

Wim Vermeulen

Jesper Q Svejstrup

Affiliations

Soon will be listed here.

Abstract

Cockayne syndrome B (CSB), best known for its role in transcription-coupled nucleotide excision repair (TC-NER), contains a ubiquitin-binding domain (UBD), but the functional connection between protein ubiquitylation and this UBD remains unclear. Here, we show that CSB is regulated via site-specific ubiquitylation. Mass spectrometry analysis of CSB identified lysine (K) 991 as a ubiquitylation site. Intriguingly, mutation of this residue (K991R) does not affect CSB's catalytic activity or protein stability, but greatly affects genome stability, even in the absence of induced DNA damage. Moreover, cells expressing CSB K991R are sensitive to oxidative DNA damage, but proficient for TC-NER. K991 becomes ubiquitylated upon oxidative DNA damage, and while CSB K991R is recruited normally to such damage, it fails to dissociate in a timely manner, suggesting a requirement for K991 ubiquitylation in CSB activation. Interestingly, deletion of CSB's UBD gives rise to oxidative damage sensitivity as well, while CSB ΔUBD and CSB K991R affects expression of overlapping groups of genes, further indicating a functional connection. Together, these results shed new light on the regulation of CSB, with K991R representing an important separation-of-function-mutation in this multi-functional protein.

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References

Groisman R, Kuraoka I, Chevallier O, Gaye N, Magnaldo T, Tanaka K . CSA-dependent degradation of CSB by the ubiquitin-proteasome pathway establishes a link between complementation factors of the Cockayne syndrome. Genes Dev. 2006; 20(11):1429-34. PMC: 1475755. DOI: 10.1101/gad.378206. View

Fousteri M, Vermeulen W, van Zeeland A, Mullenders L . RETRACTED: Cockayne syndrome A and B proteins differentially regulate recruitment of chromatin remodeling and repair factors to stalled RNA polymerase II in vivo. Mol Cell. 2006; 23(4):471-82. DOI: 10.1016/j.molcel.2006.06.029. View

van Cuijk L, van Belle G, Turkyilmaz Y, Poulsen S, Janssens R, Theil A . SUMO and ubiquitin-dependent XPC exchange drives nucleotide excision repair. Nat Commun. 2015; 6:7499. PMC: 4501428. DOI: 10.1038/ncomms8499. View

Anindya R, Mari P, Kristensen U, Kool H, Giglia-Mari G, Mullenders L . A ubiquitin-binding domain in Cockayne syndrome B required for transcription-coupled nucleotide excision repair. Mol Cell. 2010; 38(5):637-48. PMC: 2885502. DOI: 10.1016/j.molcel.2010.04.017. View

Scheibye-Knudsen M, Mitchell S, Fang E, Iyama T, Ward T, Wang J . A high-fat diet and NAD(+) activate Sirt1 to rescue premature aging in cockayne syndrome. Cell Metab. 2014; 20(5):840-855. PMC: 4261735. DOI: 10.1016/j.cmet.2014.10.005. View

Hartmann A, Agurell E, Beevers C, Brendler-Schwaab S, Burlinson B, CLAY P . Recommendations for conducting the in vivo alkaline Comet assay. 4th International Comet Assay Workshop. Mutagenesis. 2002; 18(1):45-51. DOI: 10.1093/mutage/18.1.45. View

Kuraoka I, Endou M, Yamaguchi Y, Wada T, Handa H, Tanaka K . Effects of endogenous DNA base lesions on transcription elongation by mammalian RNA polymerase II. Implications for transcription-coupled DNA repair and transcriptional mutagenesis. J Biol Chem. 2002; 278(9):7294-9. DOI: 10.1074/jbc.M208102200. View

Povlsen L, Beli P, Wagner S, Poulsen S, Sylvestersen K, Poulsen J . Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. Nat Cell Biol. 2012; 14(10):1089-98. DOI: 10.1038/ncb2579. View

Menoni H, Hoeijmakers J, Vermeulen W . Nucleotide excision repair-initiating proteins bind to oxidative DNA lesions in vivo. J Cell Biol. 2012; 199(7):1037-46. PMC: 3529521. DOI: 10.1083/jcb.201205149. View

10.

Wilson M, Saponaro M, Leidl M, Svejstrup J . MultiDsk: a ubiquitin-specific affinity resin. PLoS One. 2012; 7(10):e46398. PMC: 3463603. DOI: 10.1371/journal.pone.0046398. View

11.

Laine J, Egly J . Initiation of DNA repair mediated by a stalled RNA polymerase IIO. EMBO J. 2006; 25(2):387-97. PMC: 1383516. DOI: 10.1038/sj.emboj.7600933. View

12.

Charlet-Berguerand N, Feuerhahn S, Kong S, Ziserman H, Conaway J, Conaway R . RNA polymerase II bypass of oxidative DNA damage is regulated by transcription elongation factors. EMBO J. 2006; 25(23):5481-91. PMC: 1679758. DOI: 10.1038/sj.emboj.7601403. View

13.

Jaarsma D, van der Pluijm I, van der Horst G, Hoeijmakers J . Cockayne syndrome pathogenesis: lessons from mouse models. Mech Ageing Dev. 2013; 134(5-6):180-95. DOI: 10.1016/j.mad.2013.04.003. View

14.

Hoogstraten D, Nigg A, Heath H, Mullenders L, van Driel R, Hoeijmakers J . Rapid switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo. Mol Cell. 2002; 10(5):1163-74. DOI: 10.1016/s1097-2765(02)00709-8. View

15.

Tornaletti S, Maeda L, Lloyd D, Reines D, HANAWALT P . Effect of thymine glycol on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II. J Biol Chem. 2001; 276(48):45367-71. PMC: 3373304. DOI: 10.1074/jbc.M105282200. View

16.

Schmickel R, Chu E, Trosko J, Chang C . Cockayne syndrome: a cellular sensitivity to ultraviolet light. Pediatrics. 1977; 60(2):135-9. View

17.

Mehdi S, Qamar A . Paraquat-induced ultrastructural changes and DNA damage in the nervous system is mediated via oxidative-stress-induced cytotoxicity in Drosophila melanogaster. Toxicol Sci. 2013; 134(2):355-65. DOI: 10.1093/toxsci/kft116. View

18.

Troelstra C, Van Gool A, de Wit J, Vermeulen W, BOOTSMA D, Hoeijmakers J . ERCC6, a member of a subfamily of putative helicases, is involved in Cockayne's syndrome and preferential repair of active genes. Cell. 1992; 71(6):939-53. DOI: 10.1016/0092-8674(92)90390-x. View

19.

Franken N, Rodermond H, Stap J, Haveman J, van Bree C . Clonogenic assay of cells in vitro. Nat Protoc. 2007; 1(5):2315-9. DOI: 10.1038/nprot.2006.339. View

20.

Mayne L, Lehmann A . Failure of RNA synthesis to recover after UV irradiation: an early defect in cells from individuals with Cockayne's syndrome and xeroderma pigmentosum. Cancer Res. 1982; 42(4):1473-8. View