Role of HECT ubiquitin protein ligases in Arabidopsis thaliana
Article Sidebar
Main Article Content
Abstract
Ubiquitination is a kind of posttranslational modification of proteins in eukaryotes, and it plays an important role in the growth and development of organisms. The ubiquitination of proteins is a cascade enzymatic reaction involving three enzymes. The homologous to E6-AP carboxy terminus ubiquitin-protein ligases (HECT E3s) family is an important ubiquitin-protein ligases family. The family all have a HECT domain of approximately 350 amino acids in the C-terminus. However, studies on plant HECT E3s, such as structural features, prediction of HECT domain function, and their regulatory mechanisms, are very limited. In this paper, Arabidopsis thaliana HECT family genes were analyzed, including gene structure and functional domains and its limited known functions in protein degradation, gene transcription regulation, epigenetically regulation or other functions, finally speculate their roles in plant morphologies, aging or responsive to environmental stress.
Article Details
Copyright (c) 2018 Lan W, et al.
This work is licensed under a Creative Commons Attribution 4.0 International License.
The Journal of Plant Science and Phytopathology is committed in making it easier for people to share and build upon the work of others while maintaining consistency with the rules of copyright. In order to use the Open Access paradigm to the maximum extent in true terms as free of charge online access along with usage right, we grant usage rights through the use of specific Creative Commons license.
License: Copyright © 2017 - 2025 | 
Open Access by Journal of Plant Science and Phytopathology is licensed under a Creative Commons Attribution 4.0 International License. Based on a work at Heighten Science Publications Inc.
With this license, the authors are allowed that after publishing with the journal, they can share their research by posting a free draft copy of their article to any repository or website.
Compliance 'CC BY' license helps in:
| Permission to read and download | ✓ |
| Permission to display in a repository | ✓ |
| Permission to translate | ✓ |
| Commercial uses of manuscript | ✓ |
'CC' stands for Creative Commons license. 'BY' symbolizes that users have provided attribution to the creator that the published manuscripts can be used or shared. This license allows for redistribution, commercial and non-commercial, as long as it is passed along unchanged and in whole, with credit to the author.
Please take in notification that Creative Commons user licenses are non-revocable. We recommend authors to check if their funding body requires a specific license.
Goldberg AL. Protein degradation and protection against misfolded or damaged proteins. Nature. 2003; 426: 895-899. Ref.: https://goo.gl/v2K12U
Luo H, Wong J, Wong B. Protein degradation systems in viral myocarditis leading to dilated cardiomyopathy. Cardiovasc Res. 2010; 85: 347-356. Ref.: https://goo.gl/WCVSpv
Levine B, Mizushima N, Virgin HW. Autophagy in immunity and inflammation. Nature. 2011; 469: 323-335. Ref.: https://goo.gl/4t9rKm
Pickart CM, Eddins MJ. Ubiquitin: structures, functions, mechanisms. Biochim Biophys Acta. 2004; 1695: 55-72. Ref.: https://goo.gl/iyJYyF
Luzio JP, Pryor PR, Bright NA. Lysosomes: fusion and function. Nat Rev Mol Cell Biol.2007; 8: 622-632. Ref.: https://goo.gl/4XEDgR
Husnjak K, Dikic I. Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions. Annu Rev Biochem. 2012; 81: 291-322. Ref.: https://goo.gl/qB7d7Z
Kerscher O, Felberbaum R, Hochstrasser M. Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu Rev Cell Dev Biol. 2006; 22: 159-180. Ref.: https://goo.gl/YJL8Hc
Rotin D, Kumar S. Physiological functions of the HECT family of ubiquitin ligases. Nat Rev Mol Cell Biol. 2009; 10: 398-409. Ref.: https://goo.gl/eGyxs1
Smalle J, Vierstra RD. The ubiquitin 26S proteasome proteolytic pathway. Annu Rev Plant Biol. 2004; 55: 555-590. Ref.: https://goo.gl/VNxcZu
Vierstra RD. The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins. Trends Plant Sci. 2003; 8: 135-142. Ref.: https://goo.gl/vh46mo
Glickman MH, Ciechanover A. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol Rev. 2002; 82: 373-428. Ref.: https://goo.gl/bsGuJv
Hershko A, Ciechanover A. The ubiquitin system. Annu Rev Biochem. 1998; 67: 425-479. Ref.: https://goo.gl/Fb5bzy
Scheffner M, Nuber U, Huibregtse JM. Protein ubiquitination involving an E1-E2-E3 enzyme ubiquitin thioester cascade. Nature. 1995; 373: 81-83. Ref.: https://goo.gl/7Zxck4
Wang M, Cheng D, Peng J, Pickart CM. Molecular determinants of polyubiquitin linkage selection by an HECT ubiquitin ligase. EMBO J. 2006; 25: 1710-1719. Ref.: https://goo.gl/5bpDRk
Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, et al. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol. 2003; 21: 921-926. Ref.: https://goo.gl/8reR9z
Kulathu Y, Komander D. Atypical ubiquitylation - the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages. Nat Rev Mol Cell Biol. 2012; 13: 508-523. Ref.: https://goo.gl/MGUz25
Mukhopadhyay D, Riezman H. Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science. 2007; 315: 201-205. Ref.: https://goo.gl/GuWbds
Thrower JS, Hoffman L, Rechsteiner M, Pickart CM. Recognition of the polyubiquitin proteolytic signal. EMBO J. 2000; 19: 94-102. Ref.: https://goo.gl/L1bFNc
Xu P, Duong DM, Seyfried NT, Cheng D, Xie Y, et al. Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell. 2009; 137: 133-145. Ref.: https://goo.gl/rCkV7b
Metzger MB, Hristova VA, Weissman AM. HECT and RING finger families of E3 ubiquitin ligases at a glance. J Cell Sci. 2012; 125: 531-537. Ref.: https://goo.gl/AjcYM8
Varshavsky A. The ubiquitin system, an immense realm. Annu Rev Biochem.2012; 81: 167-176. Ref.: https://goo.gl/Kj5VeD
Schwartz AL, Ciechanover A. Targeting proteins for destruction by the ubiquitin system: implications for human pathobiology. Annu Rev Pharmacol Toxicol.2009; 49: 73-96. Ref.: https://goo.gl/8U8nG2
Mazzucotelli E, Belloni S, Marone D, De Leonardis A, Guerra D, et al. The e3 ubiquitin ligase gene family in plants: regulation by degradation. Curr Genomics. 2006; 7: 509-522. Ref.: https://goo.gl/gvgc9c
Chen L, Hellmann H. Plant E3 ligases: flexible enzymes in a sessile world. Mol Plant. 2013; 6: 1388-1404. Ref.: https://goo.gl/BSNDzM
Hotton SK, Callis J. Regulation of cullin RING ligases. Annu Rev Plant Biol.2008; 59: 467-489. Ref.: https://goo.gl/1fcvky
Schwechheimer C, Calderon Villalobos LI. Cullin-containing E3 ubiquitin ligases in plant development. Curr Opin Plant Biol. 2004; 7: 677-686. Ref.: https://goo.gl/2UueSJ
Smalle J, Vierstra RD. The ubiquitin 26S proteasome proteolytic pathway. Annu Rev Plant Biol.2004; 55: 555-590. Ref.: https://goo.gl/gfTEC4
Li W, Bengtson MH, Ulbrich A, Matsuda A, Reddy VA, et al. Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling. PloS One. 2008; 3: e1487. Ref.: https://goo.gl/zTqDRL
Scheffner M, Staub O. HECT E3s and human disease. BMC Biochemistry. 2007; 8: S6. Ref.: https://goo.gl/6uucSJ
Wang D, Ma L, Wang B, Liu J, Wei W. E3 ubiquitin ligases in cancer and implications for therapies. Cancer Metastasis Rev. 2017; 36: 683-702. Ref.: https://goo.gl/yPLu6T
Lee JH, Kim WT. Regulation of abiotic stress signal transduction by E3 ubiquitin ligases in Arabidopsis. Mol Cells.2011; 31: 201-208. Ref.: https://goo.gl/Ta4tBZ
Marino D, Froidure S, Canonne J, Ben Khaled S, Khafif M, et al. Arabidopsis ubiquitin ligase MIEL1 mediates degradation of the transcription factor MYB30 weakening plant defence. Nat Commun. 2013; 4: 1476. Ref.: https://goo.gl/4SBZw5
Yee D, Goring DR. The diversity of plant U-box E3 ubiquitin ligases: from upstream activators to downstream target substrates. J Exp Bot. 2009; 60: 1109-1121. Ref.: https://goo.gl/FcRFRg
Marin I. Evolution of plant HECT ubiquitin ligases. PloS one. 2013; 8: 68536. Ref.: https://goo.gl/Zv4Sn7
Mund T, Lewis MJ, Maslen S, Pelham HR. Peptide and small molecule inhibitors of HECT-type ubiquitin ligases. Proceedings of the National Academy of Sciences of the United States of America. 2014; 111: 16736-16741. Ref.: https://goo.gl/vonLFC
Opperman KJ, Mulcahy B, Giles AC, Risley MG, Birnbaum RL, et al. The HECT Family Ubiquitin Ligase EEL-1 Regulates Neuronal Function and Development. Cell reports. 2017; 19: 822-835. Ref.: https://goo.gl/jCVGid
Kim HC, Steffen AM, Oldham ML, Chen J, Huibregtse JM. Structure and function of a HECT domain ubiquitin-binding site. EMBO reports. 2011; 12: 334-341. Ref.: https://goo.gl/zWr4Eo
Maspero E, Valentini E, Mari S, Cecatiello V, Soffientini P, et al. Structure of a ubiquitin-loaded HECT ligase reveals the molecular basis for catalytic priming. Nature structural & molecular biology. 2013; 20: 696-701. Ref.: https://goo.gl/sgae9H
Downes BP, Stupar RM, Gingerich DJ, Vierstra RD. The HECT ubiquitin-protein ligase (UPL) family in Arabidopsis: UPL3 has a specific role in trichome development. The Plant journal : for cell and molecular biology. 2003; 35: 729-742. Ref.: https://goo.gl/vS6oj8
Verdecia MA, Joazeiro CA, Wells NJ, Ferrer JL, Bowman ME, et al. Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase. Molecular cell. 2003; 11: 249-259. Ref.: https://goo.gl/5zUPkq
Huang L, Kinnucan E, Wang G, Beaudenon S, Howley PM, et al. Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade. Science. 1999; 286: 1321-1326. Ref.: https://goo.gl/ncU7C7
Grau-Bove X, Sebe-Pedros A, Ruiz-Trillo I. A genomic survey of HECT ubiquitin ligases in eukaryotes reveals independent expansions of the HECT system in several lineages. Genome biology and evolution. 2013; 5: 833-847. Ref.: https://goo.gl/z1um7e
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research. 1997; 25: 3389-3402. Ref.: https://goo.gl/Pa9As4
Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular biology and evolution. 2016; 33: 1870-1874. Ref.: https://goo.gl/gk7sRb
Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics (Oxford, England). 2015; 31: 1296-1297. Ref.: https://goo.gl/KpnLFf
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, et al. Pfam: the protein families database. Nucleic acids research. 2014; 42: 222-230.
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, et al. The InterPro protein families database: the classification resource after 15 years. Nucleic acids research. 2015; 43: 213-221. Ref.: https://goo.gl/VCqgcq
Hofmann K, Bucher P. The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway. Trends in biochemical sciences. 1996; 21: 172-173. Ref.: https://goo.gl/yk8qo9
Hofmann K, Falquet L. A ubiquitin-interacting motif conserved in components of the proteasomal and lysosomal protein degradation systems. Trends in biochemical sciences. 2001; 26: 347-350. Ref.: https://goo.gl/GDPMaQ
El Refy A, Perazza D, Zekraoui L, Valay JG, Bechtold N, et al. The Arabidopsis KAKTUS gene encodes a HECT protein and controls the number of endoreduplication cycles. Molecular genetics and genomics: MGG. 2003; 270: 403-414. Ref.: https://goo.gl/NGUBT6
Bates PW, Vierstra RD. UPL1 and 2, two 405 kDa ubiquitin-protein ligases from Arabidopsis thaliana related to the HECT-domain protein family. The Plant journal: for cell and molecular biology. 1999; 20: 183-195. Ref.: https://goo.gl/UhEDbe
Wang M, Pickart CM. Different HECT domain ubiquitin ligases employ distinct mechanisms of polyubiquitin chain synthesis. The EMBO journal. 2005; 24: 4324-4333. Ref.: https://goo.gl/6xD8Lm
Galan JM, Haguenauer-Tsapis R. Ubiquitin lys63 is involved in ubiquitination of a yeast plasma membrane protein. The EMBO journal. 1997; 16: 5847-5854. Ref.: https://goo.gl/49euRF
Chau V, Tobias JW, Bachmair A, Marriott D, Ecker DJ, Gonda DK, et al. A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein. Science. 1989; 243: 1576-1583. Ref.: https://goo.gl/XgCpRj
Mani A, Oh AS, Bowden ET, Lahusen T, Lorick KL, et al. E6AP mediates regulated proteasomal degradation of the nuclear receptor coactivator amplified in breast cancer 1 in immortalized cells. Cancer research. 2006; 66: 8680-8686. Ref.: https://goo.gl/V7JLQ4
Finley D, Sadis S, Monia BP, Boucher P, Ecker DJ, et al. Inhibition of proteolysis and cell cycle progression in a multiubiquitination-deficient yeast mutant. Molecular and cellular biology. 1994; 14: 5501-5509. Ref.: https://goo.gl/rKPdVb
Louria-Hayon I, Alsheich-Bartok O, Levav-Cohen Y, Silberman I, Berger M, et al. E6AP promotes the degradation of the PML tumor suppressor. Cell death and differentiation. 2009; 16: 1156-1166. Ref.: https://goo.gl/QXz1X3
Adhikary S, Marinoni F, Hock A, Hulleman E, Popov N, et al. The ubiquitin ligase HectH9 regulates transcriptional activation by Myc and is essential for tumor cell proliferation. Cell. 2005; 123: 409-421. Ref.: https://goo.gl/JxTvYL
Chen D, Kon N, Li M, Zhang W, Qin J, et al. ARF-BP1/Mule is a critical mediator of the ARF tumor suppressor. Cell. 2005; 121: 1071-1083. Ref.: https://goo.gl/6uRPyA
Zhong Q, Gao W, Du F, Wang X. Mule/ARF-BP1, a BH3-only E3 ubiquitin ligase, catalyzes the polyubiquitination of Mcl-1 and regulates apoptosis. Cell. 2005; 121: 1085-1095. Ref.: https://goo.gl/Jujmb4
Zhao X, Heng JI, Guardavaccaro D, Jiang R, Pagano M, et al. The HECT-domain ubiquitin ligase Huwe1 controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein. Nature cell biology. 2008; 10: 643-653. Ref.: https://goo.gl/gepC9k
Patra B, Pattanaik S, Yuan L. Ubiquitin protein ligase 3 mediates the proteasomal degradation of GLABROUS 3 and ENHANCER OF GLABROUS 3, regulators of trichome development and flavonoid biosynthesis in Arabidopsis. The Plant journal : for cell and molecular biology. 2013; 74: 435-447. Ref.: https://goo.gl/R9pcC6
Miao Y, Zentgraf U. A HECT E3 ubiquitin ligase negatively regulates Arabidopsis leaf senescence through degradation of the transcription factor WRKY53. The Plant journal: for cell and molecular biology. 2010; 63: 179-188. Ref.: https://goo.gl/h3RnAN
Deng S, Jang IC, Su L, Xu J, Chua NH. JMJ24 targets CHROMOMETHYLASE3 for proteasomal degradation in Arabidopsis. Genes & development. 2016; 30: 251-256. Ref.: https://goo.gl/y8Ti6K
Zeng S, Wang Y, Zhang T, Bai L, Wang Y, et al. E3 ligase UHRF2 stabilizes the acetyltransferase TIP60 and regulates H3K9ac and H3K14ac via RING finger domain. Protein & cell. 2017; 8: 202-218. Ref.: https://goo.gl/cXXwDZ
Luo C, Cai X T, Du J, Zhao TL, Wang PF, et al. PARAQUAT TOLERANCE3 Is an E3 Ligase That Switches off Activated Oxidative Response by Targeting Histone-Modifying PROTEIN METHYLTRANSFERASE4b. PLoS genetics. 2016; 12: 1006332. Ref.: https://goo.gl/MSw78F
Licchesi JD, Mieszczanek J, Mevissen TE, Rutherford TJ, Akutsu M, et al. An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains. Nature structural & molecular biology. 2011; 19: 62-71. Ref.: https://goo.gl/ms7xPM
Michel MA, Elliott PR, Swatek KN, Simicek M, Pruneda JN, et al. Assembly and specific recognition of k29- and k33-linked polyubiquitin. Molecular cell. 2015; 58: 95-109. Ref.: https://goo.gl/9rhBzm
Jin J, Xie X, Xiao Y, Hu H, Zou Q, et al. Epigenetic regulation of the expression of Il12 and Il23 and autoimmune inflammation by the deubiquitinase Trabid. Nature immunology. 2016; 17: 259-268. Ref.: https://goo.gl/KonC54
Huibregtse JM, Yang JC, Beaudenon SL. The large subunit of RNA polymerase II is a substrate of the Rsp5 ubiquitin-protein ligase. Proceedings of the National Academy of Sciences of the United States of America. 1997; 94: 3656-3661. Ref.: https://goo.gl/as7SRp
Somesh BP, Sigurdsson S, Saeki H, Erdjument-Bromage H, Tempst P, et al. Communication between distant sites in RNA polymerase II through ubiquitylation factors and the polymerase CTD. Cell. 2007; 129: 57-68. Ref.: https://goo.gl/epiDCi
Gao M, Labuda T, Xia Y, Gallagher E, Fang D, Liu YC, et al. Jun turnover is controlled through JNK-dependent phosphorylation of the E3 ligase Itch. Science. 2004; 306: 271-275. Ref.: https://goo.gl/i32gz8
JC C. Armadillo repeat proteins: versatile regulators of plant development and signalling. Plant Cell Monographs. 2008; 10: 299-314. Ref.: https://goo.gl/4g68Wj
Lan W, Qiu S, Ren Y, Miao Y. Expression Profile and Function of HECT E3s in Arabidopsis thaliana. Acta Botanica Boreali-Occidentalia Sinica. 2017; 37: 2112-2119.
Fu H, Sadis S, Rubin DM, Glickman M, van Nocker S, Finley D, et al. Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26 S proteasome subunit Mcb1. The Journal of biological chemistry. 1998; 273: 1970-1981. Ref.: https://goo.gl/3Wj5Ab
Sharma M, Singh A, Shankar A, Pandey A, Baranwal V, et al. Comprehensive expression analysis of rice Armadillo gene family during abiotic stress and development. DNA research: an international journal for rapid publication of reports on genes and genomes. 2014; 21: 267-283. Ref.: https://goo.gl/tGkaqh
Wang H, Lu Y, Jiang T, Berg H, Li C, et al. The Arabidopsis U-box/ARM repeat E3 ligase AtPUB4 influences growth and degeneration of tapetal cells, and its mutation leads to conditional male sterility. Plant J. 2013; 74: 511-523. Ref.: https://goo.gl/nq6h3W
Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, et al. An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PloS one. 2007; 2. Ref.: https://goo.gl/aHB14q
M H. Ubiquitin-dependent protein degradation. Annu Rev Genet. 1996; 30: 405-439.