Plant Molecular Biology

, Volume 61, Issue 1–2, pp 241–253 | Cite as

Arabidopsis thaliana UBC13: Implication of Error-free DNA Damage Tolerance and Lys63-linked Polyubiquitylation in Plants

  • Rui Wen
  • Lindsay Newton
  • Genyi Li
  • Hong Wang
  • Wei Xiao
Article

Abstract

Ubiquitylation is an important biochemical reaction found in all eukaryotic organisms and is involved in a wide range of cellular processes. Conventional ubiquitylation requires the formation of polyubiquitin chains linked through Lys48 of the ubiquitin, which targets specific proteins for degradation. Recently polyubiquitylation through a noncanonical Lys63 chain has been reported, and is required for error-free DNA damage tolerance (or postreplication repair) in yeast. To date, Ubc13 is the only known ubiquitin-conjugating enzyme (Ubc) capable of catalyzing the Lys63-linked polyubiquitylation reaction and this function requires interaction with the Ubc variant Mms2. No information is available on either Lys63-linked ubiquitylation or error-free damage tolerance in plants. We thus cloned and functionally characterized two Arabidopsis thaliana UBC13 genes, AtUBC13A and AtUBC13B. The two genes are highly conserved with respect to chromosomal structure and protein sequence, suggesting that they are derived from a recent gene duplication event. Both AtUbc13 proteins are able to physically interact with yeast or human Mms2, implying that plants also employ the Lys63-linked polyubiquitylation reaction. Furthermore, AtUBC13 genes are able to functionally complement the yeast ubc13 null mutant for spontaneous mutagenesis and sensitivity to DNA damaging agents, suggesting the existence of an error-free DNA damage tolerance pathway in plants. The AtUBC13 genes appear to express ubiquitously and are not induced by various conditions tested.

Keywords

A rabidopsis thaliana DNA damage tolerance Lys63-linked polyubiquitylation protein–protein interaction ubiquitin-conjugating enzyme 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Andersen, P.L., Zhou, H., Pastushok, L., Moraes, T., McKenna, S., Ziola, B., Ellison, M.J., Dixit, V.M., Xiao, W. 2005Distinct regulation of Ubc13 functions by the two ubiquitin-conjugating enzyme variants Mms2 and Uev1AJ. Cell Biol.170745755PubMedCrossRefGoogle Scholar
  2. Bachmair, A., Novatchkova, M., Potuschak, T., Eisenhaber, F. 2001Ubiquitylation in plants: a post-genomic look at a post-translational modificationTrends Plant Sci.6463470PubMedCrossRefGoogle Scholar
  3. Bartel, P.L., Fields, S. 1995Analyzing protein–protein interactions using two-hybrid systemMethods Enzymol.254241263PubMedCrossRefGoogle Scholar
  4. Bemark, M., Khamlichi, A.A., Davies, S.L., Neuberger, M.S. 2000Disruption of mouse polymerase ζ (Rev3) leads to embryonic lethality and impairs blastocyst development in vitroCurr. Biol.1012131216PubMedCrossRefGoogle Scholar
  5. Britt, A.B. 1999Molecular genetics of DNA repair in higher plantsTrends Plant Sci.42025PubMedCrossRefGoogle Scholar
  6. Broomfield, S., Chow, B.L., Xiao, W. 1998 MMS2, encoding a ubiquitin-conjugating-enzyme-like protein, is a member of the yeast error-free postreplication repair pathwayProc. Natl. Acad. Sci. USA9556785683PubMedCrossRefGoogle Scholar
  7. Broomfield, S., Hryciw, T., Xiao, W. 2001DNA postreplication repair and mutagenesis in Saccharomyces cerevisiae Mutat. Res.486167184PubMedGoogle Scholar
  8. Brusky, J., Zhu, Y., Xiao, W. 2000 UBC13, a DNA-damage-inducible gene, is a member of the error-free postreplication repair pathway in Saccharomyces cerevisiae Curr. Genet.37168174PubMedCrossRefGoogle Scholar
  9. Chau, V., Tobias, J.W., Bachmair, A., Marriott, D., Ecker, D.J., Gonda, D.K., Varshavsky, A. 1989A multiubiquitin chain is confined to specific lysine in a targeted short-lived proteinScience24315761583PubMedGoogle Scholar
  10. Deng, L., Wang, C., Spencer, E., Yang, L., Braun, A., You, J., Slaughter, C., Pickart, C., Chen, Z.J. 2000Activation of the IκB kinase complex by TRAF6 requires a dimeric ubiquitin-conjugating enzyme complex and a unique polyubiquitin chainCell103351361PubMedCrossRefGoogle Scholar
  11. Esposito, G., Godindagger, I., Klein, U., Yaspo, M.L., Cumano, A., Rajewsky, K. 2000Disruption of the Rev3l-encoded catalytic subunit of polymerase ζ in mice results in early embryonic lethalityCurr. Biol.1012211224PubMedCrossRefGoogle Scholar
  12. Fields, S., Song, O. 1989A novel genetic system to detect protein–protein interactionsNature340245246PubMedCrossRefGoogle Scholar
  13. Finley, D., Bartel, B., Varshavsky, A. 1989The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesisNature338394401PubMedCrossRefGoogle Scholar
  14. Fisk, H.A., Yaffe, M.P. 1999A role for ubiquitination in mitochondrial inheritance in Saccharomyces cerevisiae J. Cell Biol.14511991208PubMedCrossRefGoogle Scholar
  15. Friedberg, E., Walker, G., Wolfram, S. 1995DNA Repair and MutagenesisASM PressWashington, D.CGoogle Scholar
  16. Garcia-Ortiz, M.V., Ariza, R.R., Hoffman, P.D., Hays, J.B., Roldan-Arjona, T. 2004 Arabidopsis thaliana AtPOLK encodes a DinB-like DNA polymerase that extends mispaired primer termini and is highly expressed in a variety of tissuesPlant J.398497PubMedCrossRefGoogle Scholar
  17. Hall, T.A. 1999BioEdit: a user-friendly biological sequence slignment editor and analysis program for Windows 95/98/NTNucl. Acids Symp. Ser.419598Google Scholar
  18. Hays, J.B. 2002 Arabidopsis thaliana, a versatile model system for study of eukaryotic genome-maintenance functionsDNA Repair1579600PubMedCrossRefGoogle Scholar
  19. Hochstrasser, M. 1996Ubiquitin-dependent protein degradationAnnu. Rev. Genet.30405439PubMedCrossRefGoogle Scholar
  20. Hoege, C., Pfander, B., Moldovan, G.L., Pyrowolakis, G., Jentsch, S. 2002 RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMONature419135141PubMedCrossRefGoogle Scholar
  21. Hoffman, P.D., Leonard, J.M., Lindberg, G.E., Bollmann, S.R., Hays, J.B. 2004Rapid accumulation of mutations during seed-to-seed propagation of mismatch-repair-defective Arabidopsis Genes Dev.1826762685PubMedCrossRefGoogle Scholar
  22. Hofmann, R.M., Pickart, C.M. 1999Noncanonical MMS2-encoded ubiquitin-conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repairCell96645653PubMedCrossRefGoogle Scholar
  23. Hofmann, R.M., Pickart, C.M. 2001 In vitro assembly and recognition of Lys−63 polyubiquitin chainsJ. Biol. Chem.2762793627943PubMedCrossRefGoogle Scholar
  24. Ito, H., Fukuda, Y., Murata, K., Kimura, A. 1983Transformation of intact yeast cells treated with alkali cationsJ. Bacteriol.153163168PubMedGoogle Scholar
  25. James, P., Halladay, J., Craig, E.A. 1996Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeastGenetics14414251436PubMedGoogle Scholar
  26. Jentsch, S. 1992The ubiquitin-conjugation systemAnnu. Rev. Genet.26179207PubMedCrossRefGoogle Scholar
  27. Jentsch, S., McGrath, J.P., Varshavsky, A. 1987The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzymeNature329131134PubMedCrossRefGoogle Scholar
  28. Kao, C.F., Hillyer, C., Tsukuda, T., Henry, K., Berger, S., Osley, M.A. 2004Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2BGenes Dev.18184195PubMedCrossRefGoogle Scholar
  29. Kimura, S., Tahira, Y., Ishibashi, T., Mori, Y., Mori, T., Hashimoto, J., Sakaguchi, K. 2004DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cellsNucleic Acids Res.3227602767PubMedCrossRefGoogle Scholar
  30. Koegl, M., Hoppe, T., Schlenker, S., Ulrich, H.D., Mayer, T.U., Jentsch, S. 1999A novel ubiquitination factor, E4, is involved in multiubiquitin chain assemblyCell96635644PubMedCrossRefGoogle Scholar
  31. McKenna, S., Spyracopoulos, L., Moraes, T., Pastushok, L., Ptak, C., Xiao, W., Ellison, M.J. 2001Noncovalent interaction between ubiquitin and the human DNA repair protein Mms2 is required for Ubc13-mediated polyubiquitinationJ. Biol. Chem.2764012040126PubMedCrossRefGoogle Scholar
  32. Pastushok, L., Moraes, T.F., Ellison, M.J., Xiao, W. 2005A single Mms2 “key” residue insertion into a Ubc13 pocket determines the interface specificity of a human Lys63 ubiquitin conjugation complexJ. Biol. Chem.2801789117900PubMedCrossRefGoogle Scholar
  33. Pastushok, L., Xiao, W. 2004DNA postreplication repair modulated by ubiquitination and sumoylationAdv. Protein Chem.69279306PubMedCrossRefGoogle Scholar
  34. Pickart, C.M. 2001aMechanisms underlying ubiquitinationAnnu. Rev. Biochem.70503533CrossRefGoogle Scholar
  35. Pickart, C.M. 2001bUbiquitin enters the new millenniumMol. Cell.8499504CrossRefGoogle Scholar
  36. Ries, G., Heller, W., Puchta, H., Sandermann, H., Seidlitz, H.K., Hohn, B. 2000Elevated UV-B radiation reduces genome stability in plantsNature40698101PubMedCrossRefGoogle Scholar
  37. Sakamoto, A., Lan, V.T., Hase, Y., Shikazono, N., Matsunaga, T., Tanaka, A. 2003Disruption 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 plantsPlant Cell1520422057PubMedCrossRefGoogle Scholar
  38. Sherman, F., Fink, G.R., Hicks, J. 1983Methods in Yeast GeneticsCold Spring Harbor Laboratory PressCold Spring Harbor, NYGoogle Scholar
  39. Sullivan, M.L., Carpenter, T.B., Vierstra, R.D. 1994Homologues of wheat ubiquitin-conjugating enzymes – TaUBC1 and TaUBC4 are encoded by small multigene families in Arabidopsis thalianaPlant Mol. Biol.24651661PubMedCrossRefGoogle Scholar
  40. Takahashi, S., Sakamoto, A., Sato, S., Kato, T., Tabata, S., Tanaka, A. 2005Roles of Arabidopsis AtREV1 and AtREV7 in translesion synthesisPlant Physiol.138870881PubMedCrossRefGoogle Scholar
  41. Toufighi, K., Brady, S.M., Austin, R., Ly, E., Provart, N.J. 2005The Botany Array Resource: e-Northerns, Expression Angling, and promoter analysesPlant J.43153163PubMedCrossRefGoogle Scholar
  42. Ulrich, H.D., Jentsch, S. 2000Two RING finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repairEMBO J.1933883397PubMedCrossRefGoogle Scholar
  43. Wang, C., Deng, L., Hong, M., Akkaraju, G.R., Inoue, J., Chen, Z.J. 2001TAK1 is a ubiquitin-dependent kinase of MKK and IKKNature412346351PubMedCrossRefGoogle Scholar
  44. Wei, W., Ayad, N.G., Wan, Y., Zhang, G.J., Kirschner, M.W., Kaelin, W.G.,Jr. 2004Degradation of the SCF component Skp2 in cell-cycle phase G1 by the anaphase-promoting complexNature428194198PubMedCrossRefGoogle Scholar
  45. Williamson, M.S., Game, J.C., Fogel, S. 1985Meiotic gene conversion mutants in Saccharomyces cerevisiae. I. Isolation and characterization of pms1–1 and pms1–2 Genetics110609646PubMedGoogle Scholar
  46. Wittschieben, J., Shivji, M.K., Lalani, E., Jacobs, M.A., Marini, F., Gearhart, P.J., Rosewell, I., Stamp, G., Wood, R.D. 2000Disruption of the developmentally regulated Rev3l gene causes embryonic lethalityCurr. Biol.1012171220PubMedCrossRefGoogle Scholar
  47. Wooff, J., Pastushok, L., Hanna, M., Fu, Y., Xiao, W. 2004The TRAF6 RING finger domain mediates physical interaction with Ubc13FEBS Lett.566229233PubMedCrossRefGoogle Scholar
  48. Xiao, W., Chow, B.L., Broomfield, S., Hanna, M. 2000The Saccharomyces cerevisiae RAD6 group is composed of an error-prone and two error-free postreplication repair pathwaysGenetics15516331641PubMedGoogle Scholar
  49. Xiao, W., Chow, B.L., Fontanie, T., Ma, L., Bacchetti, S., Hryciw, T., Broomfield, S. 1999Genetic interactions between error-prone and error-free postreplication repair pathways in Saccharomyces cerevisiae Mutat. Res.435111PubMedGoogle Scholar
  50. Xiao, W., Samson, L. 1993 In vivo evidence for endogenous DNA alkylation damage as a source of spontaneous mutation in eukaryotic cellsProc. Natl. Acad. Sci. USA9021172121PubMedCrossRefGoogle Scholar
  51. Yamaguchi, T., Kim, N.S., Sekine, S., Seino, H., Osaka, F., Yamao, F., Kato, S. 1996Cloning and expression of cDNA encoding a human ubiquitin-conjugating enzyme similar to the Drosophila bendless gene productJ. Biochem. (Tokyo)120494497Google Scholar
  52. Zhang, H.G., Wang, J., Yang, X., Hsu, H.C., Mountz, J.D. 2004Regulation of apoptosis proteins in cancer cells by ubiquitinOncogene2320092015PubMedCrossRefGoogle Scholar
  53. Zhou, H., Wertz, I., O’Rourke, K., Ultsch, M., Seshagiri, S., Eby, M., Xiao, W., Dixit, V.M. 2004Bcl10 activates the NF-κB pathway through ubiquitination of NEMONature427167171PubMedCrossRefGoogle Scholar
  54. Zwirn, P., Stary, S., Luschnig, C., Bachmair, A. 1997 Arabidopsis thaliana RAD6 homolog AtUBC2 complements UV sensitivity, but not N-end rule degradation deficiency, of Saccharomyces cerevisiae rad6 mutantsCurr. Genet.32309314PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  • Rui Wen
    • 1
  • Lindsay Newton
    • 1
  • Genyi Li
    • 2
    • 3
  • Hong Wang
    • 2
  • Wei Xiao
    • 1
  1. 1.Department of Microbiology and ImmunologyUniversity of SaskatchewanSaskatoonCanada
  2. 2.Department of BiochemistryUniversity of SaskatchewanSaskatoonCanada
  3. 3.Department of Plant ScienceUniversity of ManitobaWinnipegCanada

Personalised recommendations