Gieng UBC13 của lúa, một ứng cử viên gene housekeeping, cần thiết cho polyubiquitination liên kết K63 và khả năng chịu đựng tổn thương DNA

Andersen PL, Zhou H, Pastushok L, Moraes T, McKenna S, Ziola B, Ellison MJ, Dixit VM, Xiao W: Distinct regulation of Ubc13 functions by the two ubiquitin-conjugating enzyme variants Mms2 and Uev1A. J Cell Biol 2005, 170: 745–755. 10.1083/jcb.200502113 Anderson HJ, Vonarx EJ, Pastushok L, Nakagawa M, Katafuchi A, Gruz P, Di Rubbo A, Grice DM, Osmond MJ, Sakamoto AN, Nohmi T, Xiao W, Kunz BA: Arabidopsis thaliana Y-family DNA polymerase η catalyses translesion synthesis and interacts functionally with PCNA2. Plant J 2008, 55: 895–908. 10.1111/j.1365-313X.2008.03562.x Ardley HC, Robinson PA: E3 ubiquitin ligases. Essays Biochem 2005, 41: 15–30. 10.1042/EB0410015 Barbour L, Ball LG, Zhang K, Xiao W: DNA damage checkpoints are involved in postreplication repair. Genetics 2006, 174: 1789–1800. 10.1534/genetics.106.056283 Bartel PL, Fields S: Analyzing protein-protein interactions using two-hybrid system. Methods Enzymol 1995, 254: 241–263. Bothos J, Summers MK, Venere M, Scolnick DM, Halazonetis TD: The Chfr mitotic checkpoint protein functions with Ubc13-Mms2 to form Lys63-linked polyubiquitin chains. Oncogene 2003, 22: 7101–7107. 10.1038/sj.onc.1206831 Broomfield S, Chow BL, Xiao W: MMS2 , encoding a ubiquitin-conjugating-enzyme-like protein, is a member of the yeast error-free postreplication repair pathway. Proc Natl Acad Sci USA 1998, 95: 5678–5683. 10.1073/pnas.95.10.5678 Broomfield S, Hryciw T, Xiao W: DNA postreplication repair and mutagenesis in Saccharomyces cerevisiae . Mutat Res 2001, 486: 167–184. 10.1016/S0921-8777(01)00091-X Brusky J, Zhu Y, Xiao W: UBC13 , a DNA-damage-inducible gene, is a member of the error-free postreplication repair pathway in Saccharomyces cerevisiae . Curr Genet 2000, 37: 168–174. 10.1007/s002940050515 Burroughs AM, Jaffee M, Iyer LM, Aravind L: Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. J Struct Biol 2008, 162: 205–218. 10.1016/j.jsb.2007.12.006 Chen IP, Mannuss A, Orel N, Heitzeberg F, Puchta H: A homolog of ScRAD5 is involved in DNA repair and homologous recombination in Arabidopsis. Plant Physiol 2008, 146: 1786–1796. 10.1104/pp.108.116806 Curtis MJ, Hays JB: Tolerance of dividing cells to replication stress in UVB-irradiated Arabidopsis roots: requirements for DNA translesion polymerases η and ζ. DNA Repair. 2007, 6: 1341–1358. 10.1016/j.dnarep.2007.03.004 Deng L, Wang C, Spencer E, Yang L, Braun A, You J, Slaughter C, Pickart C, Chen ZJ: Activation of the IκB kinase complex by TRAF6 requires a dimeric ubiquitin-conjugating enzyme complex and a unique polyubiquitin chain. Cell 2000, 103: 351–361. 10.1016/S0092-8674(00)00126-4 Deshaies RJ, Joazeiro CA: RING domain E3 ubiquitin ligases. Annu Rev Biochem 2009, 78: 399–434. 10.1146/annurev.biochem.78.101807.093809 Doil C, Mailand N, Bekker-Jensen S, Menard P, Larsen DH, Pepperkok R, Ellenberg J, Panier S, Durocher D, Bartek J, Lukas J, Lukas C: RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins. Cell 2009, 136: 435–446. 10.1016/j.cell.2008.12.041 Doss-Pepe EW, Chen L, Madura K: α-Synuclein and Parkin contribute to the assembly of ubiquitin lysine 63-linked multiubiquitin chains. J Biol Chem 2005, 280: 16619–16624. 10.1074/jbc.M413591200 Fields S, Song O: A novel genetic system to detect protein-protein interactions. Nature 1989, 340: 245–246. 10.1038/340245a0 Fritsche J, Rehli M, Krause SW, Andreesen R, Kreutz M: Molecular cloning of a 1α,25-dihydroxyvitamin D3-inducible transcript (DDVit 1) in human blood monocytes. Biochem Biophys Res Commun 1997, 235: 407–412. 10.1006/bbrc.1997.6798 Garcia-Ortiz MV, Ariza RR, Hoffman PD, Hays JB, Roldan-Arjona T: Arabidopsis thaliana AtPOLK encodes a DinB-like DNA polymerase that extends mispaired primer termini and is highly expressed in a variety of tissues. Plant J. 2004, 39: 84–97. 10.1111/j.1365-313X.2004.02112.x Hershko A, Ciechanover A: The ubiquitin system. Annu Rev Biochem 1998, 67: 425–479. 10.1146/annurev.biochem.67.1.425 Hochstrasser M: Ubiquitin-dependent protein degradation. Annu Rev Genet. 1996, 30: 405–439. Hoege C, Pfander B, Moldovan GL, Pyrowolakis G, Jentsch S: RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 2002, 419: 135–141. 10.1038/nature00991 Hofmann RM, Pickart CM: Noncanonical MMS2 -encoded ubiquitin-conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repair. Cell 1999, 96: 645–653. 10.1016/S0092-8674(00)80575-9 Hofmann RM, Pickart CM: In vitro assembly and recognition of Lys-63 polyubiquitin chains. J Biol Chem 2001, 276: 27936–27943. 10.1074/jbc.M103378200 Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P: Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Advances in bioinformatics. 2008, 2008: 420747. Huen MS, Grant R, Manke I, Minn K, Yu X, Yaffe MB, Chen J: RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly. Cell 2007, 131: 901–914. 10.1016/j.cell.2007.09.041 Huen MS, Huang J, Yuan J, Yamamoto M, Akira S, Ashley C, Xiao W, Chen J: Noncanonical E2 variant-independent function of UBC13 in promoting checkpoint protein assembly. Mol Cell Biol 2008, 28: 6104–6112. 10.1128/MCB.00987-08 Ito H, Fukuda Y, Murata K, Kimura A: Transformation of intact yeast cells treated with alkali cations. J Bacteriol 1983, 153: 163–168. James P, Halladay J, Craig EA: Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 1996, 144: 1425–1436. Kraft E, Stone SL, Ma L, Su N, Gao Y, Lau OS, Deng XW, Callis J: Genome analysis and functional characterization of the E2 and RING-type E3 ligase ubiquitination enzymes of Arabidopsis. Plant Physiol 2005, 139: 1597–1611. 10.1104/pp.105.067983 Laine A, Topisirovic I, Zhai D, Reed JC, Borden KL, Ronai Z: Regulation of p53 localization and activity by Ubc13. Mol Cell Biol 2006, 26: 8901–8913. 10.1128/MCB.01156-06 Li W, Schmidt W: A lysine-63-linked ubiquitin chain-forming conjugase, UBC13, promotes the developmental responses to iron deficiency in Arabidopsis roots. Plant J. 2010, 62: 330–343. 10.1111/j.1365-313X.2010.04150.x Lim KL, Chew KC, Tan JM, Wang C, Chung KK, Zhang Y, Tanaka Y, Smith W, Engelender S, Ross CA, Dawson VL, Dawson TM: Parkin mediates nonclassical, proteasomal-independent ubiquitination of synphilin-1: implications for Lewy body formation. J Neurosci 2005, 25: 2002–2009. 10.1523/JNEUROSCI.4474-04.2005 Ma L, Broomfield S, Lavery C, Lin SL, Xiao W, Bacchetti S: Up-regulation of CIR1/CROC1 expression upon cell immortalization and in tumor-derived human cell lines. Oncogene 1998, 17: 1321–1326. 10.1038/sj.onc.1202058 Mailand N, Bekker-Jensen S, Faustrup H, Melander F, Bartek J, Lukas C, Lukas J: RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins. Cell 2007, 131: 887–900. 10.1016/j.cell.2007.09.040 McKenna S, Spyracopoulos L, Moraes T, Pastushok L, Ptak C, Xiao W, Ellison MJ: Noncovalent interaction between ubiquitin and the human DNA repair protein Mms2 is required for Ubc13-mediated polyubiquitination. J Biol Chem 2001, 276: 40120–40126. 10.1074/jbc.M102858200 Muralidhar MG, Thomas JB: The Drosophila bendless gene encodes a neural protein related to ubiquitin-conjugating enzymes. Neuron 1993, 11: 253–266. 10.1016/0896-6273(93)90182-Q Oh CE, McMahon R, Benzer S, Tanouye MA: bendless , a Drosophila gene affecting neuronal connectivity, encodes a ubiquitin-conjugating enzyme homolog. J Neurosci 1994, 14: 3166–3179. Papouli E, Chen S, Davies AA, Huttner D, Krejci L, Sung P, Ulrich HD: Crosstalk between SUMO and ubiquitin on PCNA is mediated by recruitment of the helicase Srs2p. Mol Cell. 2005, 19: 123–133. 10.1016/j.molcel.2005.06.001 Pastushok L, Moraes TF, Ellison MJ, Xiao W: A single Mms2 "key" residue insertion into a Ubc13 pocket determines the interface specificity of a human Lys63 ubiquitin conjugation complex. J Biol Chem 2005, 280: 17891–17900. Pastushok L, Xiao W: DNA postreplication repair modulated by ubiquitination and sumoylation. Adv Protein Chem. 2004, 69: 279–306. Pfander B, Moldovan GL, Sacher M, Hoege C, Jentsch S: SUMO-modified PCNA recruits Srs2 to prevent recombination during S phase. Nature 2005, 436: 428–433. Pickart CM: Ubiquitin in chains. Trends Biochem Sci. 2000, 25: 544–548. 10.1016/S0968-0004(00)01681-9 Pickart CM, Fushman D: Polyubiquitin chains: polymeric protein signals. Curr Opin Chem Biol 2004, 8: 610–616. 10.1016/j.cbpa.2004.09.009 Rotin D, Kumar S: Physiological functions of the HECT family of ubiquitin ligases. Nat Rev Mol Cell Biol 2009, 10: 398–409. 10.1038/nrm2690 Sakamoto A, Lan VT, Hase Y, Shikazono N, Matsunaga T, Tanaka A: Disruption of the AtREV3 gene causes hypersensitivity to ultraviolet B light and gamma-rays in Arabidopsis : implication of the presence of a translesion synthesis mechanism in plants. Plant Cell. 2003, 15: 2042–2057. 10.1105/tpc.012369 Sanada T, Kim M, Mimuro H, Suzuki M, Ogawa M, Oyama A, Ashida H, Kobayashi T, Koyama T, Nagai S, Shibata Y, Gohda J, Inoue J, Mizushima T, Sasakawa C: The Shigella flexneri effector OspI deamidates UBC13 to dampen the inflammatory response. Nature 2012, 483: 623–626. 10.1038/nature10894 Sancho E, Vila MR, Sanchez-Pulido L, Lozano JJ, Paciucci R, Nadal M, Fox M, Harvey C, Bercovich B, Loukili N, Ciechanover A, Lin SL, Sanz F, Estivill X, Valencia A, Thomson TM: Role of UEV-1, an inactive variant of the E2 ubiquitin-conjugating enzymes, in in vitro differentiation and cell cycle behavior of HT-29-M6 intestinal mucosecretory cells. Mol Cell Biol 1998, 18: 576–589. Sherman F, Fink GR, Hicks J: Methods in Yeast Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; 1983. Stelter P, Ulrich HD: Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature 2003, 425: 188–191. 10.1038/nature01965 Stewart GS, Panier S, Townsend K, Al-Hakim AK, Kolas NK, Miller ES, Nakada S, Ylanko J, Olivarius S, Mendez M, Oldreive C, Wildenhain J, Tagliaferro A, Pelletier L, Taubenheim N, Durandy A, Byrd PJ, Stankovic T, Taylor AM, Durocher D: The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell 2009, 136: 420–434. 10.1016/j.cell.2008.12.042 Takahashi S, Sakamoto A, Sato S, Kato T, Tabata S, Tanaka A: Roles of Arabidopsis AtREV1 and AtREV7 in translesion synthesis. Plant Physiol 2005, 138: 870–881. 10.1104/pp.105.060236 Ulrich HD, Jentsch S: Two RING finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repair. EMBO J 2000, 19: 3388–3397. 10.1093/emboj/19.13.3388 van Wijk SJL, Timmers HTM: The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins. FASEB J 2009, 24: 981–993. VanDemark AP, Hofmann RM, Tsui C, Pickart CM, Wolberger C: Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer. Cell 2001, 105: 711–720. 10.1016/S0092-8674(01)00387-7 Vierstra RD: The ubiquitin–26 S proteasome system at the nexus of plant biology. Nat Rev Mol Cell Biol 2009, 10: 385–397. 10.1038/nrm2688 Wang C, Deng L, Hong M, Akkaraju GR, Inoue J, Chen ZJ: TAK1 is a ubiquitin-dependent kinase of MKK and IKK. Nature 2001, 412: 346–351. 10.1038/35085597 Wang S, Wen R, Shi X, Lambrecht A, Wang H, Xiao W: RAD5a and REV3 function in two alternative pathways of DNA-damage tolerance in Arabidopsis . DNA Repair. 2011, 10: 620–628. 10.1016/j.dnarep.2011.04.009 Wen R, Li J, Xu X, Cui Z, Xiao W: Zebrafish Mms2 promotes K63-linked polyubiquitination and is involved in p53-mediated DNA-damage response. DNA repair. 2012, 11: 157–166. 10.1016/j.dnarep.2011.10.015 Wen R, Newton L, Li G, Wang H, Xiao W: Arabidopsis thaliana UBC13: implication of error-free DNA damage tolerance and Lys63-linked polyubiquitylation in plants. Plant Mol Biol 2006, 61: 241–253. 10.1007/s11103-006-0007-x Wen R, Torres-Acosta JA, Pastushok L, Lai XQ, Pelzer L, Wang H, Xiao W: Arabidopsis UEV1D promotes lysine-63-linked polyubiquitination and is involved in DNA damage response. Plant Cell. 2008, 20: 213–227. 10.1105/tpc.107.051862 Wooff J, Pastushok L, Hanna M, Fu Y, Xiao W: The TRAF6 RING finger domain mediates physical interaction with Ubc13. FEBS Lett 2004, 566: 229–233. 10.1016/j.febslet.2004.04.038 Xiao W, Chow BL, Broomfield S, Hanna M: The Saccharomyces cerevisiae RAD6 group is composed of an error-prone and two error-free postreplication repair pathways. Genetics 2000, 155: 1633–1641. Xiao W, Lin SL, Broomfield S, Chow BL, Wei YF: The products of the yeast MMS2 and two human homologs ( hMMS2 and CROC-1 ) define a structurally and functionally conserved Ubc-like protein family. Nucleic Acids Res 1998, 26: 3908–3914. 10.1093/nar/26.17.3908 Xiao W, Samson L: In vivo evidence for endogenous DNA alkylation damage as a source of spontaneous mutation in eukaryotic cells. Proc Natl Acad Sci USA 1993, 90: 2117–2121. 10.1073/pnas.90.6.2117 Yin XJ, Volk S, Ljung K, Mehlmer N, Dolezal K, Ditengou F, Hanano S, Davis SJ, Schmelzer E, Sandberg G, Teige M, Palme K, Pickart C, Bachmair A: Ubiquitin lysine 63 chain forming ligases regulate apical dominance in Arabidopsis. Plant Cell. 2007, 19: 1898–1911. 10.1105/tpc.107.052035 Zhou H, Wertz I, O'Rourke K, Ultsch M, Seshagiri S, Eby M, Xiao W, Dixit VM: Bcl10 activates the NF-κB pathway through ubiquitination of NEMO. Nature 2004, 427: 167–171. 10.1038/nature02273