A plant-specific in vitro ubiquitination analysis system

Plant Journal

Volumn 74, Issue 3, 2013, Pages 524-533

  Hao, Qingzhen ^a,b   Tian, Miaomiao ^a   Li, Qingliang ^a   Cui, Feng ^a   Liu, Lijing ^a   Yin, Bojiao ^a   Xie, Qi ^a  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^b LIAOCHENG UNIVERSITY   (China)

Author keywords

E2 E3 specificity; in vitro assay; technical advance; ubiquitin; ubiquitin ligase; ubiquitin conjugating enzyme; ubiquitination

Indexed keywords

E2/E3 SPECIFICITY; IN-VITRO ASSAYS; TECHNICAL ADVANCES; UBIQUITIN; UBIQUITIN LIGASES; UBIQUITIN-CONJUGATING ENZYMES; UBIQUITINATION;

ASSAYS; ENZYMES; ESCHERICHIA COLI; GENES;

PROTEINS;

ARABIDOPSIS PROTEIN; UBC32 PROTEIN, ARABIDOPSIS; UBIQUITIN CONJUGATING ENZYME;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; ENZYME ACTIVATION; ENZYME SPECIFICITY; ENZYME STABILITY; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PLANT GENE; POINT MUTATION; PROTEIN TERTIARY STRUCTURE; UBIQUITINATION;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CONSERVED SEQUENCE; ENZYME ACTIVATION; ENZYME STABILITY; ESCHERICHIA COLI; GENES, PLANT; POINT MUTATION; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY; UBIQUITIN-CONJUGATING ENZYMES; UBIQUITINATION;

ARABIDOPSIS; ESCHERICHIA COLI; EUKARYOTA;

EID: 84876674517     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12127     Document Type: Article

References (36)

1. Bachmair, A., Novatchkova, M., Potuschak, T., and, Eisenhaber, F., (2001) Ubiquitylation in plants: a post-genomic look at a post-translational modification. Trends Plant Sci. 6, 463-470.
2. Bu, Q., Li, H., Zhao, Q., et al. (2009) The Arabidopsis RING finger E3 ligase RHA2a is a novel positive regulator of abscisic acid signaling during seed germination and early seedling development. Plant Physiol. 150, 463-481.
3. Callis, J., Carpenter, T., Sun, C.W., and, Vierstra, R.D., (1995) Structure and evolution of genes encoding polyubiquitin and ubiquitin-like proteins in Arabidopsis thaliana ecotype Columbia. Genetics, 139, 921-939.
4. Christensen, D.E., and, Klevit, R.E., (2009) Dynamic interactions of proteins in complex networks: identifying the complete set of interacting E2s for functional investigation of E3-dependent protein ubiquitination. FEBS J. 276, 5381-5389.
5. Criqui, M.C., de Almeida Engler, J., Camasses, A., Capron, A., Parmentier, Y., Inze, D., and, Genschik, P., (2002) Molecular characterization of plant ubiquitin-conjugating enzymes belonging to the UbcP4/E2-C/UBCx/UbcH10 gene family. Plant Physiol. 130, 1230-1240.
6. Dong, C.H., Agarwal, M., Zhang, Y., Xie, Q., and, Zhu, J.K., (2006) The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proc. Natl Acad. Sci. USA, 103, 8281-8286.
7. Garnett, M.J., Mansfeld, J., Godwin, C., Matsusaka, T., Wu, J., Russell, P., Pines, J., and, Venkitaraman, A.R., (2009) UBE2S elongates ubiquitin chains on APC/C substrates to promote mitotic exit. Nat. Cell Biol. 11, 1363-1369.
8. Hardtke, C.S., Okamoto, H., Stoop-Myer, C., and, Deng, X.W., (2002) Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8). Plant J. 30, 385-394.
9. Hatfield, P.M., Gosink, M.M., Carpenter, T.B., and, Vierstra, R.D., (1997) The ubiquitin-activating enzyme (E1) gene family in Arabidopsis thaliana. Plant J. 11, 213-226.
10. Kerscher, O., Felberbaum, R., and, Hochstrasser, M., (2006) Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu. Rev. Cell Dev. Biol. 22, 159-180.
11. Kraft, E., Stone, S.L., Ma, L., Su, N., Gao, Y., Lau, O.S., Deng, X.W., and, Callis, J., (2005) Genome analysis and functional characterization of the E2 and RING-type E3 ligase ubiquitination enzymes of Arabidopsis. Plant Physiol. 139, 1597-1611.
12. Lee, H.K., Cho, S.K., Son, O., Xu, Z., Hwang, I., and, Kim, W.T., (2009) Drought stress-induced Rma1H1, a RING membrane-anchor E3 ubiquitin ligase homolog, regulates aquaporin levels via ubiquitination in transgenic Arabidopsis plants. Plant Cell, 21, 622-641.
13. Liu, J., Zhang, Y., Qin, G., et al. (2008) Targeted degradation of the cyclin-dependent kinase inhibitor ICK4/KRP6 by RING-type E3 ligases is essential for mitotic cell cycle progression during Arabidopsis gametogenesis. Plant Cell, 20, 1538-1554.
14. Liu, L., Zhang, Y., Tang, S., Zhao, Q., Zhang, Z., Zhang, H., Dong, L., Guo, H., and, Xie, Q., (2010) An efficient system to detect protein ubiquitination by agroinfiltration in Nicotiana benthamiana. Plant J. 61, 893-903.
15. Markson, G., Kiel, C., Hyde, R., et al. (2009) Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res. 19, 1905-1911.
16. Matsuda, N., Suzuki, T., Tanaka, K., and, Nakano, A., (2001) Rma1, a novel type of RING finger protein conserved from Arabidopsis to human, is a membrane-bound ubiquitin ligase. J. Cell Sci. 114, 1949-1957.
17. Michelle, C., Vourc'h, P., Mignon, L., and, Andres, C.R., (2009) What was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor? J. Mol. Evol. 68, 616-628.
18. Moon, J., Parry, G., and, Estelle, M., (2004) The ubiquitin-proteasome pathway and plant development. Plant Cell, 16, 3181-3195.
19. Pruneda, J.N., Littlefield, P.J., Soss, S.E., Nordquist, K.A., Chazin, W.J., Brzovic, P.S., and, Klevit, R.E., (2012) Structure of an E3:E2-Ub complex reveals an allosteric mechanism shared among RING/U-box ligases. Mol. Cell, 47, 933-942.
20. Sadowski, M., Suryadinata, R., Lai, X., Heierhorst, J., and, Sarcevic, B., (2010) Molecular basis for lysine specificity in the yeast ubiquitin-conjugating enzyme Cdc34. Mol. Cell. Biol. 30, 2316-2329.
21. Seo, H.S., Watanabe, E., Tokutomi, S., Nagatani, A., and, Chua, N.H., (2004) Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling. Genes Dev. 18, 617-622.
22. Serniwka, S.A., and, Shaw, G.S., (2009) The structure of the UbcH8-ubiquitin complex shows a unique ubiquitin interaction site. Biochemistry, 48, 12169-12179.
23. Smalle, J., and, Vierstra, R.D., (2004) The ubiquitin 26S proteasome proteolytic pathway. Annu. Rev. Plant Biol. 55, 555-590.
24. Stone, S.L., Hauksdottir, H., Troy, A., Herschleb, J., Kraft, E., and, Callis, J., (2005) Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis. Plant Physiol. 137, 13-30.
25. Summers, M.K., Pan, B., Mukhyala, K., and, Jackson, P.K., (2008) The unique N terminus of the UbcH10 E2 enzyme controls the threshold for APC activation and enhances checkpoint regulation of the APC. Mol. Cell, 31, 544-556.
26. Sun, L., and, Chen, Z.J., (2004) The novel functions of ubiquitination in signaling. Curr. Opin. Cell Biol. 16, 119-126.
27. Vierstra, R.D., (2003) The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins. Trends Plant Sci. 8, 135-142.
28. Vierstra, R.D., (2009) The ubiquitin-26S proteasome system at the nexus of plant biology. Nat. Rev. Mol. Cell Biol. 10, 385-397.
29. Wen, R., Newton, L., Li, G., Wang, H., and, Xiao, W., (2006) Arabidopsis thaliana UBC13: implication of error-free DNA damage tolerance and Lys63-linked polyubiquitylation in plants. Plant Mol. Biol. 61, 241-253.
30. Wen, R., Torres-Acosta, J.A., Pastushok, L., Lai, X., Pelzer, L., Wang, H., and, Xiao, W., (2008) Arabidopsis UEV1D promotes lysine-63-linked polyubiquitination and is involved in DNA damage response. Plant Cell, 20, 213-227.
31. van Wijk, S.J., de Vries, S.J., Kemmeren, P., Huang, A., Boelens, R., Bonvin, A.M., and, Timmers, H.T., (2009) A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system. Mol. Syst. Biol. 5, 295.
32. Wu, T., Merbl, Y., Huo, Y., Gallop, J.L., Tzur, A., and, Kirschner, M.W., (2010) UBE2S drives elongation of K11-linked ubiquitin chains by the anaphase-promoting complex. Proc. Natl Acad. Sci. USA. 107, 1355-1360.
33. Xia, Z.P., Sun, L., Chen, X., Pineda, G., Jiang, X., Adhikari, A., Zeng, W., and, Chen, Z.J., (2009) Direct activation of protein kinases by unanchored polyubiquitin chains. Nature, 461, 114-119.
34. Xie, Q., Guo, H.S., Dallman, G., Fang, S., Weissman, A.M., and, Chua, N.H., (2002) SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals. Nature, 419, 167-170.
35. Ye, Y., and, Rape, M., (2009) Building ubiquitin chains: E2 enzymes at work. Nat. Rev. Mol. Cell Biol. 10, 755-764.
36. Zhang, Y., Yang, C., Li, Y., Zheng, N., Chen, H., Zhao, Q., Gao, T., Guo, H., and, Xie, Q., (2007) SDIR1 is a RING finger E3 ligase that positively regulates stress-responsive abscisic acid signaling in Arabidopsis. Plant Cell, 19, 1912-1929.