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Liu J, Nie B, Yu B, Xu F, Zhang Q, Wang Y, Xu W. Rice ubiquitin-conjugating enzyme OsUbc13 negatively regulates immunity against pathogens by enhancing the activity of OsSnRK1a. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37102249 PMCID: PMC10363768 DOI: 10.1111/pbi.14059] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 02/28/2023] [Accepted: 04/05/2023] [Indexed: 06/19/2023]
Abstract
Ubc13 is required for Lys63-linked polyubiquitination and innate immune responses in mammals, but its functions in plant immunity still remain largely unknown. Here, we used molecular biological, pathological, biochemical, and genetic approaches to evaluate the roles of rice OsUbc13 in response to pathogens. The OsUbc13-RNA interference (RNAi) lines with lesion mimic phenotypes displayed a significant increase in the accumulation of flg22- and chitin-induced reactive oxygen species, and in defence-related genes expression or hormones as well as resistance to Magnaporthe oryzae and Xanthomonas oryzae pv oryzae. Strikingly, OsUbc13 directly interacts with OsSnRK1a, which is the α catalytic subunit of SnRK1 (sucrose non-fermenting-1-related protein kinase-1) and acts as a positive regulator of broad-spectrum disease resistance in rice. In the OsUbc13-RNAi plants, although the protein level of OsSnRK1a did not change, its activity and ABA sensitivity were obviously enhanced, and the K63-linked polyubiquitination was weaker than that of wild-type Dongjin (DJ). Overexpression of the deubiquitinase-encoding gene OsOTUB1.1 produced similar effects with inhibition of OsUbc13 in affecting immunity responses, M. oryzae resistance, OsSnRK1a ubiquitination, and OsSnRK1a activity. Furthermore, re-interfering with OsSnRK1a in one OsUbc13-RNAi line (Ri-3) partially restored its M. oryzae resistance to a level between those of Ri-3 and DJ. Our data demonstrate OsUbc13 negatively regulates immunity against pathogens by enhancing the activity of OsSnRK1a.
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Affiliation(s)
- Jianping Liu
- Center for Plant Water-use and Nutrition Regulation and College of Resources and Environment, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bo Nie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Boling Yu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feiyun Xu
- Center for Plant Water-use and Nutrition Regulation and College of Resources and Environment, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian Zhang
- Center for Plant Water-use and Nutrition Regulation and College of Resources and Environment, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ya Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Resources and Environment, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
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Liu W, Tang X, Fu X, Zhang H, Zhu C, Zhang N, Si H. Functional Characterization of Potato UBC13- UEV1s Genes Required for Ubiquitin Lys63 Chain to Polyubiquitination. Int J Mol Sci 2023; 24:ijms24032412. [PMID: 36768743 PMCID: PMC9917286 DOI: 10.3390/ijms24032412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/28/2023] Open
Abstract
Ubiquitin-conjugating enzymes (E2s/UBC) are components of the ubiquitin proteasome system (UPS), and the ubiquitin-conjugating enzyme variant (UEV) is one of E2s (ubiquitin-conjugating enzymes, UBC) subfamily. The UEVs and UBC13 play an auxiliary role in mediating Lys63-linked polyUb chain assembly, which is correlated with target protein non-proteolytic functions, such as DNA repair or response to stress. However, the collaborative mechanism of StUBC13 (homologue of AtUBC13) and StUEVs (the UEVs in potato) involved in potato are not fully understood understood. Here, we identified two StUBC13 and seven StUEVs from potato genome. We analyzed protein motif and conserved domain, gene structure, phylogenetic features, cis-acting elements of StUBC13 and StUEVs. Subsequently, we screened StUBC13 partners protein and verified interaction between StUBC13 and StUEVs using yeast two-hybrid, split luciferase complementation (SLC) and bimolecular fluorescence complementation (BiFC) approach. The expression profile and qRT-PCR analysis suggested that StUBC13 and StUEVs gene exhibited a tissue-specific expression and were induced by different stress. Overall, this investigative study provides a comprehensive reference and view for further functional research on StUBC13 and StUEV1s in potato.
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Affiliation(s)
- Weigang Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xue Fu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Huanhuan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Cunlan Zhu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence:
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Kumasaruge I, Wen R, Wang L, Gao P, Peng G, Xiao W. Systematic characterization of Brassica napus UBC13 genes involved in DNA-damage response and K63-linked polyubiquitination. BMC PLANT BIOLOGY 2023; 23:24. [PMID: 36631796 PMCID: PMC9835285 DOI: 10.1186/s12870-023-04035-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ubc13 is the only known ubiquitin conjugating enzyme (Ubc/E2) dedicated to promoting Lys (K)63-linked polyubiquitination, and this process requires a Ubc/E2 variant (UEV). Unlike conventional K48-linked polyubiquitination that targets proteins for degradation, K63-linked polyubiquitination, which is involved in several cellular processes, does not target proteins for degradation but alter their activities. RESULTS In this study we report the identification and functional characterization of 12 Brassica napus UBC13 genes. All the cloned UBC13 gene products were able to physically interact with AtUev1D, an Arabidopsis UEV, to form stable complexes that are capable of catalyzing K63-linked polyubiquitination in vitro. Furthermore, BnUBC13 genes functionally complemented the yeast ubc13 null mutant defects in spontaneous mutagenesis and DNA-damage responses, suggesting that BnUBC13s can replace yeast UBC13 in mediating K63-linked polyubiquitination and error-free DNA-damage tolerance. CONCLUSION Collectively, this study provides convincing data to support notions that B. napus Ubc13s promote K63-linked polyubiquitination and are probably required for abiotic stress response. Since plant Ubc13-UEV are also implicated in other developmental and stress responses, this systematic study sets a milestone in exploring roles of K63-linked polyubiquitination in this agriculturally important crop.
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Affiliation(s)
- Ivanthi Kumasaruge
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Rui Wen
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2, Canada
| | - Lipu Wang
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Peng Gao
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2, Canada
| | - Gary Peng
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2, Canada
| | - Wei Xiao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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Yang K, Xiao W. Functions and mechanisms of the Ubc13-UEV complex and lysine 63-linked polyubiquitination in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5372-5387. [PMID: 35640002 DOI: 10.1093/jxb/erac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitination is one of the best-known post-translational modifications in eukaryotes, in which different linkage types of polyubiquitination result in different outputs of the target proteins. Distinct from the well-characterized K48-linked polyubiquitination that usually serves as a signal for degradation of the target protein, K63-linked polyubiquitination often requires a unique E2 heterodimer Ubc13-UEV and alters the target protein activity instead of marking it for degradation. This review focuses on recent advances on the roles of Ubc13-UEV-mediated K63-linked polyubiquitination in plant growth, development, and response to environmental stresses.
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Affiliation(s)
- Kun Yang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, China
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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5
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DNA-damage tolerance through PCNA ubiquitination and sumoylation. Biochem J 2021; 477:2655-2677. [PMID: 32726436 DOI: 10.1042/bcj20190579] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022]
Abstract
DNA-damage tolerance (DDT) is employed by eukaryotic cells to bypass replication-blocking lesions induced by DNA-damaging agents. In budding yeast Saccharomyces cerevisiae, DDT is mediated by RAD6 epistatic group genes and the central event for DDT is sequential ubiquitination of proliferating cell nuclear antigen (PCNA), a DNA clamp required for replication and DNA repair. DDT consists of two parallel pathways: error-prone DDT is mediated by PCNA monoubiquitination, which recruits translesion synthesis DNA polymerases to bypass lesions with decreased fidelity; and error-free DDT is mediated by K63-linked polyubiquitination of PCNA at the same residue of monoubiquitination, which facilitates homologous recombination-mediated template switch. Interestingly, the same PCNA residue is also subjected to sumoylation, which leads to inhibition of unwanted recombination at replication forks. All three types of PCNA posttranslational modifications require dedicated conjugating and ligation enzymes, and these enzymes are highly conserved in eukaryotes, from yeast to human.
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Guo H, Wang L, Hu R, He Y, Xiao W. Molecular cloning and functional characterization of Physcomitrella patens UBC13-UEV1 genes required for Lys63-linked polyubiquitination. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110518. [PMID: 32563457 DOI: 10.1016/j.plantsci.2020.110518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/07/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
Ubc13 and Ubc/E2 variant (Uev) form a stable heterodimer to mediate Lys63-linked polyubiquitination. Unicellular eukaryotic genomes often contain single UBC13 and UEV gene; however, multiple homologs were found in higher plants. As initial land plants, Physcomitrella patens occupies a key evolutionary position between green algae and higher plants. In this study, we report the identification and functional characterization of two UBC13 and three UEV1 genes from P. patens. Both PpUbc13s form heterodimers with PpUev1B or PpUev1C, which catalyze Lys63-linked polyubiquitination in vitro and functionally complement the yeast ubc13 mms2 null mutant from killing by DNA-damaging agents. In contrast, PpUev1A is unable to interact with Ubc13s and cannot complement the yeast mms2 mutant. Two single mutations, PpUev1A-D12N and ΔCT, barely have any effect; however, the corresponding double mutation makes PpUev1A functional in both heterodimer formation and complementation. This study identifies a critical Uev residue located in the Ubc13-Uev interface and reveals that mosses began to evolve multiple UBC13 and UEV orthologs in order to adapt to the terrestrial environment. The evolutionary significance of PpUEV1A is discussed.
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Affiliation(s)
- Huiping Guo
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Linxiao Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ruoyang Hu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yikun He
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Wei Xiao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China; Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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7
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Liu W, Tang X, Qi X, Fu X, Ghimire S, Ma R, Li S, Zhang N, Si H. The Ubiquitin Conjugating Enzyme: An Important Ubiquitin Transfer Platform in Ubiquitin-Proteasome System. Int J Mol Sci 2020; 21:E2894. [PMID: 32326224 PMCID: PMC7215765 DOI: 10.3390/ijms21082894] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 11/24/2022] Open
Abstract
Owing to a sessile lifestyle in nature, plants are routinely faced with diverse hostile environments such as various abiotic and biotic stresses, which lead to accumulation of free radicals in cells, cell damage, protein denaturation, etc., causing adverse effects to cells. During the evolution process, plants formed defense systems composed of numerous complex gene regulatory networks and signal transduction pathways to regulate and maintain the cell homeostasis. Among them, ubiquitin-proteasome pathway (UPP) is the most versatile cellular signal system as well as a powerful mechanism for regulating many aspects of the cell physiology because it removes most of the abnormal and short-lived peptides and proteins. In this system, the ubiquitin-conjugating enzyme (E2) plays a critical role in transporting ubiquitin from the ubiquitin-activating enzyme (E1) to the ubiquitin-ligase enzyme (E3) and substrate. Nevertheless, the comprehensive study regarding the role of E2 enzymes in plants remains unexplored. In this review, the ubiquitination process and the regulatory role that E2 enzymes play in plants are primarily discussed, with the focus particularly put on E2's regulation of biological functions of the cell.
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Affiliation(s)
- Weigang Liu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (S.G.); (R.M.); (S.L.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (X.T.); (X.Q.); (X.F.)
| | - Xun Tang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (X.T.); (X.Q.); (X.F.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Xuehong Qi
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (X.T.); (X.Q.); (X.F.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Xue Fu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (X.T.); (X.Q.); (X.F.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Shantwana Ghimire
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (S.G.); (R.M.); (S.L.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (X.T.); (X.Q.); (X.F.)
| | - Rui Ma
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (S.G.); (R.M.); (S.L.)
| | - Shigui Li
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (S.G.); (R.M.); (S.L.)
| | - Ning Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Huaijun Si
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (W.L.); (S.G.); (R.M.); (S.L.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (X.T.); (X.Q.); (X.F.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
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Wang Q, Liu M, Zang Y, Xiao W. The C-terminal extension of Arabidopsis Uev1A/B with putative prenylation site plays critical roles in protein interaction, subcellular distribution and membrane association. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110324. [PMID: 31928655 DOI: 10.1016/j.plantsci.2019.110324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Lysine (K) 63-linked polyubiquitination plays important roles in cellular processes including DNA-damage tolerance (DDT), NF-κB signaling and endocytosis. Compared to yeast and mammals, little is known about K63-linked polyubiquitination in plants. To date, a Uev-Ubc13 complex is the only known Ub-conjugating enzyme to catalyze K63-linked polyubiquitination, in which Uev serves as a regulatory subunit. The Arabidopsis thaliana genome contains four UEV1 genes that can be classified into two subfamilies (UEV1A/B and UEV1C/D), in which Uev1A/B have a C-terminal extension. Database analysis reveals that all higher plant genomes contain both subfamily UEV1s, which were evolved as early as angiosperm plants. Interestingly, all C-terminal tails in the Uev1A/B subfamily contain a putative prenylation motif, CaaX. Combined experimental results using AtUev1B demonstrated that it is most likely farnesylated and that its C-terminal tail, particularly the catalytic Cys residue in the CaaX motif, plays critical roles in protein-protein interaction, nuclear exclusion and membrane association. Using AtUev1B as bait for a yeast-two-hybrid screen, we identified 14 interaction proteins in a prenylation-dependent manner. These results collectively imply that prenylation of AtUev1A/B plays a critical role in its functional differentiation from AtUev1C/D.
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Affiliation(s)
- Qian Wang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China; Shanxi Provincial People's Hospital, Taiyuan, Shanxi, 030012, China
| | - Maoqing Liu
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuepeng Zang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China; Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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9
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Wang L, Wen R, Wang J, Xiang D, Wang Q, Zang Y, Wang Z, Huang S, Li X, Datla R, Fobert PR, Wang H, Wei Y, Xiao W. Arabidopsis UBC13 differentially regulates two programmed cell death pathways in responses to pathogen and low-temperature stress. THE NEW PHYTOLOGIST 2019; 221:919-934. [PMID: 30218535 DOI: 10.1111/nph.15435] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 08/02/2018] [Indexed: 05/17/2023]
Abstract
UBC13 is required for Lys63-linked polyubiquitination and innate immune responses in mammals, but its functions in plant immunity remain to be defined. Here we used genetic and pathological methods to evaluate roles of Arabidopsis UBC13 in response to pathogens and environmental stresses. Loss of UBC13 failed to activate the expression of numerous cold-responsive genes and resulted in hypersensitivity to low-temperature stress, indicating that UBC13 is involved in plant response to low-temperature stress. Furthermore, the ubc13 mutant displayed low-temperature-induced and salicylic acid-dependent lesion mimic phenotypes. Unlike typical lesion mimic mutants, ubc13 did not enhance disease resistance against virulent bacterial and fungal pathogens, but diminished hypersensitive response and compromised effector-triggered immunity against avirulent bacterial pathogens. UBC13 differently regulates two types of programmed cell death in response to low temperature and pathogen. The lesion mimic phenotype in the ubc13 mutant is partially dependent on SNC1. UBC13 interacts with an F-box protein CPR1 that regulates the homeostasis of SNC1. However, the SNC1 protein level was not altered in the ubc13 mutant, implying that UBC13 is not involved in CPR1-regulated SNC1 protein degradation. Taken together, our results revealed that UBC13 is a key regulator in plant response to low temperature and pathogens.
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Affiliation(s)
- Lipu Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
- National Research Council Canada, Saskatoon, SK, Canada, S7N 0W9
| | - Rui Wen
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5
| | - Jinghe Wang
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5
| | - Daoquan Xiang
- National Research Council Canada, Saskatoon, SK, Canada, S7N 0W9
| | - Qian Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuepeng Zang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Zheng Wang
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5
| | - Shuai Huang
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Xin Li
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Raju Datla
- National Research Council Canada, Saskatoon, SK, Canada, S7N 0W9
| | - Pierre R Fobert
- National Research Council Canada, Saskatoon, SK, Canada, S7N 0W9
| | - Hong Wang
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E2
| | - Wei Xiao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5
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10
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Romero-Barrios N, Vert G. Proteasome-independent functions of lysine-63 polyubiquitination in plants. THE NEW PHYTOLOGIST 2018; 217:995-1011. [PMID: 29194634 DOI: 10.1111/nph.14915] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/12/2017] [Indexed: 05/21/2023]
Abstract
Contents Summary 995 I. Introduction 995 II. The plant Ub machinery 996 III. From Ub to Ub linkage types in plants 997 IV. Increasing analytical resolution for K63 polyUb in plants 998 V. How to build K63 polyUb chains? 998 VI. Cellular roles of K63 polyUb in plants 999 VII. Physiological roles of K63 polyUb in plants 1004 VIII. Future perspectives: towards the next level of the Ub code 1006 Acknowledgements 1006 References 1007 SUMMARY: Ubiquitination is a post-translational modification essential for the regulation of eukaryotic proteins, having an impact on protein fate, function, localization or activity. What originally appeared to be a simple system to regulate protein turnover by the 26S proteasome is now known to be the most intricate regulatory process cells have evolved. Ubiquitin can be arranged in countless chain assemblies, triggering various cellular outcomes. Polyubiquitin chains using lysine-63 from ubiquitin represent the second most abundant type of ubiquitin modification. Recent studies have exposed their common function in proteasome-independent functions in non-plant model organisms. The existence of lysine-63 polyubiquitination in plants is, however, only just emerging. In this review, we discuss the recent advances on the characterization of ubiquitin chains and the molecular mechanisms driving the formation of lysine-63-linked ubiquitin modifications. We provide an overview of the roles associated with lysine-63 polyubiquitination in plant cells in the light of what is known in non-plant models. Finally, we review the crucial roles of lysine-63 polyubiquitin-dependent processes in plant growth, development and responses to environmental conditions.
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Affiliation(s)
- Natali Romero-Barrios
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Grégory Vert
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
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11
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Nikitaki Z, Holá M, Donà M, Pavlopoulou A, Michalopoulos I, Angelis KJ, Georgakilas AG, Macovei A, Balestrazzi A. Integrating plant and animal biology for the search of novel DNA damage biomarkers. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 775:21-38. [DOI: 10.1016/j.mrrev.2018.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
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12
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Zhou B, Zeng L. Conventional and unconventional ubiquitination in plant immunity. MOLECULAR PLANT PATHOLOGY 2017; 18:1313-1330. [PMID: 27925369 PMCID: PMC6638253 DOI: 10.1111/mpp.12521] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/23/2016] [Accepted: 11/27/2016] [Indexed: 05/16/2023]
Abstract
Ubiquitination is one of the most abundant types of protein post-translational modification (PTM) in plant cells. The importance of ubiquitination in the regulation of many aspects of plant immunity has been increasingly appreciated in recent years. Most of the studies linking ubiquitination to the plant immune system, however, have been focused on the E3 ubiquitin ligases and the conventional ubiquitination that leads to the degradation of the substrate proteins by the 26S proteasome. By contrast, our knowledge about the role of unconventional ubiquitination that often serves as non-degradative, regulatory signal remains a significant gap. We discuss, in this review, the recent advances in our understanding of ubiquitination in the modulation of plant immunity, with a particular focus on the E3 ubiquitin ligases. We approach the topic from a perspective of two broadly defined types of ubiquitination in an attempt to highlight the importance, yet current scarcity, in our knowledge about the regulation of plant immunity by unconventional ubiquitination.
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Affiliation(s)
- Bangjun Zhou
- Center for Plant Science Innovation and Department of Plant PathologyUniversity of NebraskaLincolnNE68583USA
| | - Lirong Zeng
- Center for Plant Science Innovation and Department of Plant PathologyUniversity of NebraskaLincolnNE68583USA
- Southern Regional Collaborative Innovation Center for Grain and Oil CropsHunan Agricultural UniversityChangsha410128China
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Wang Q, Zang Y, Zhou X, Xiao W. Characterization of four rice UEV1 genes required for Lys63-linked polyubiquitination and distinct functions. BMC PLANT BIOLOGY 2017; 17:126. [PMID: 28716105 PMCID: PMC5513143 DOI: 10.1186/s12870-017-1073-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/03/2017] [Indexed: 05/28/2023]
Abstract
BACKGROUND The error-free branch of the DNA-damage tolerance (DDT) pathway is orchestrated by Lys63-linked polyubiquitination of proliferating cell nuclear antigen (PCNA), and this polyubiquitination is mediated by a Ubc13-Uev complex in yeast. We have previously cloned OsUBC13 from rice, whose product functions as an E2 to promote Lys63-linked ubiquitin chain assembly in the presence of yeast or human Uev. RESULTS Here we identify four highly conserved UEV1 genes in rice whose products are able to form stable heterodimers with OsUbc13 and mediate Lys63-linked ubiquitin chain assembly. Expression of OsUEV1s is able to rescue the yeast mms2 mutant from death caused by DNA-damaging agents. Interestingly, OsUev1A contains a unique C-terminal tail with a conserved prenylation site not found in the other three OsUev1s, and this post-translational modification appears to be required for its unique subcellular distribution and association with the membrane. The analysis of OsUEV1 expression profiles obtained from the Genevestigator database indicates that these genes are differentially regulated. CONCLUSIONS We speculate that different OsUev1s play distinct roles by serving as a regulatory subunit of the Ubc13-Uev1 complex to respond to diverse cellular, developmental and environmental signals.
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Affiliation(s)
- Qian Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuepeng Zang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xuan Zhou
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Wei Xiao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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Guo H, Wen R, Liu Z, Datla R, Xiao W. Molecular Cloning and Functional Characterization of Two Brachypodium distachyon UBC13 Genes Whose Products Promote K63-Linked Polyubiquitination. FRONTIERS IN PLANT SCIENCE 2016; 6:1222. [PMID: 26779244 PMCID: PMC4703986 DOI: 10.3389/fpls.2015.01222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/18/2015] [Indexed: 05/24/2023]
Abstract
Living organisms are constantly subject to DNA damage from environmental sources. Due to the sessile nature of plants, UV irradiation is a major genotoxic agent and imposes a significant threat on plant survival, genome stability and crop yield. In addition, other environmental chemicals can also influence the stability of the plant genome. Eukaryotic organisms have evolved a mechanism to cope with replication-blocking lesions and stabilize the genome. This mechanism is known as error-free DNA damage tolerance, and is mediated by K63-linked PCNA polyubiquitination. Genes related to K63-linked polyubiquitination have been isolated recently from model plants like Arabidopsis and rice, but we are unaware of such reports on the crop model Brachypodium distachyon. Here, we report the identification and functional characterization of two B. distachyon UBC13 genes. Both Ubc13s form heterodimers with Uevs from other species, which are capable of catalyzing K63 polyubiquitination in vitro. Both genes can functionally rescue the yeast ubc13 null mutant from killing by DNA-damaging agents. These results suggest that Ubc13-Uev-promoted K63-linked polyubiquitination is highly conserved in eukaryotes including B. distachyon. Consistent with recent findings that K63-linked polyubiquitination is involved in several developmental and stress-responsive pathways, the expression of BdUbc13s appears to be constitutive and is regulated by abnormal temperatures.
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Affiliation(s)
- Huiping Guo
- College of Life Sciences, Capital Normal UniversityBeijing, China
| | - Rui Wen
- National Research Council CanadaSaskatoon, SK, Canada
| | - Zhi Liu
- College of Life Sciences, Capital Normal UniversityBeijing, China
| | - Raju Datla
- National Research Council CanadaSaskatoon, SK, Canada
| | - Wei Xiao
- College of Life Sciences, Capital Normal UniversityBeijing, China
- Department of Microbiology and Immunology, University of SaskatchewanSaskatoon, SK, Canada
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Guo H, Wen R, Wang Q, Datla R, Xiao W. Three Brachypodium distachyon Uev1s Promote Ubc13-Mediated Lys63-Linked Polyubiquitination and Confer Different Functions. FRONTIERS IN PLANT SCIENCE 2016; 7:1551. [PMID: 27803708 PMCID: PMC5067413 DOI: 10.3389/fpls.2016.01551] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/03/2016] [Indexed: 05/08/2023]
Abstract
In this study, we report the identification and functional characterization of three Brachypodium distachyon UEV genes. All three BdUev1s form heterodimers with BdUbc13s, which are capable of catalyzing Lys63-linked polyubiquitination in vitro. The three BdUEV1 genes are also able to functionally complement the budding yeast mms2 mutant defective in DNA-damage tolerance. BdUev1A differs from the other two BdUev1s in that it contains an 18-amino acid tail, which appears to compromise its function in yeast, as deletion of this tail restores full function. BdUev1A is excluded from the nucleus, whereas BdUev1B, BdUev1C and the C-terminally truncated BdUev1A are mainly found in the nucleus. These and the BdUEV1 gene expression analysis allow us to speculate that although all three BdUev1s function by promoting Lys63-linked polyubiquitination, BdUev1B and BdUev1C are involved in DNA-damage response and possibly other nuclear functions, while BdUev1A is required for non-nuclear function(s).
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Affiliation(s)
- Huiping Guo
- College of Life Sciences, Capital Normal UniversityBeijing, China
| | - Rui Wen
- National Research Council Canada, SaskatoonSK, Canada
| | - Qianqian Wang
- College of Life Sciences, Capital Normal UniversityBeijing, China
| | - Raju Datla
- National Research Council Canada, SaskatoonSK, Canada
| | - Wei Xiao
- College of Life Sciences, Capital Normal UniversityBeijing, China
- Department of Microbiology and Immunology, University of Saskatchewan, SaskatoonSK, Canada
- *Correspondence: Wei Xiao,
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Wang Y, Xu MY, Liu JP, Wang MG, Yin HQ, Tu JM. Molecular identification and interaction assay of the gene (OsUbc13) encoding a ubiquitin-conjugating enzyme in rice. J Zhejiang Univ Sci B 2015; 15:624-37. [PMID: 25001222 DOI: 10.1631/jzus.b1300273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ubiquitin (Ub)-conjugating enzyme, Ubc13, has been known to be involved in error-free DNA damage tolerance (or post-replication repair) via catalyzing Lys63-linked polyubiquitin chains formation together with a Ubc variant. However, its functions remain largely unknown in plant species, especially in monocotyledons. In this study, we cloned a Ub-conjugating enzyme, OsUbc13, that shares the conserved domain of Ubc with AtUBC13B in Oryza sativa L., which encodes a protein of 153 amino acids; the deduced sequence shares high similarities with other homologs. Real-time quantitative polymerase chain reaction (PCR) indicated that OsUbc13 transcripts could be detected in all tissues examined, and the expression level was higher in palea, pistil, stamen, and leaf, and lower in root, stem, and lemma; the expression of OsUbc13 was induced by low temperature, methylmethane sulfate (MMS), and H(2)O(2), but repressed by mannitol, abscisic acid (ABA), and NaCl. OsUbc13 was probably localized in the plasma and nuclear membranes. About 20 proteins, which are responsible for the positive yeast two-hybrid interaction of OsUbc13, were identified. These include the confirmed OsVDAC (correlated with apoptosis), OsMADS1 (important for development of floral organs), OsB22EL8 (related to reactive oxygen species (ROS) scavenging and DNA protection), and OsCROC-1 (required for formation of Lys63 polyubiquitylation and error-free DNA damage tolerance). The molecular characterization provides a foundation for the functional study of OsUbc13.
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Affiliation(s)
- Ya Wang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
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Wen R, Wang S, Xiang D, Venglat P, Shi X, Zang Y, Datla R, Xiao W, Wang H. UBC13, an E2 enzyme for Lys63-linked ubiquitination, functions in root development by affecting auxin signaling and Aux/IAA protein stability. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:424-36. [PMID: 25142088 DOI: 10.1111/tpj.12644] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 07/21/2014] [Accepted: 08/12/2014] [Indexed: 05/21/2023]
Abstract
Unlike conventional lysine (K) 48-linked polyubiquitination, K63-linked polyubiquitination plays signaling roles in yeast and animals. Thus far, UBC13 is the only known ubiquitin-conjugating enzyme (E2) specialized in K63-linked polyubiquitination. Previous identification of Arabidopsis genes encoding UBC13 as well as its interacting partner UEV1 indicates that the UBC13-mediated ubiquitination pathway is conserved in plants; however, little is known about functions and signaling mediated through K63-linked polyubiquitination in plants. To address the functions of UBC13-mediated ubiquitination in plants, we created Arabidopsis ubc13 null mutant lines in which the two UBC13 genes were disrupted. The double mutant displayed altered root development, including shorter primary root, fewer lateral roots and only a few short root hairs in comparison with the wild type and single mutant plants, indicating that UBC13 activity is critical for all major aspects of root development. The double mutant plants were insensitive to auxin treatments, suggesting that the strong root phenotypes do not simply result from a reduced level of auxin. Instead, the ubc13 mutant had a reduced auxin response, as indicated by the expression of an auxin-responsive DR5 promoter-GFP. Furthermore, both the enzymatic activity and protein level of an AXR3/IAA17-GUS reporter were greatly increased in the ubc13 mutant, whereas the induction of many auxin-responsive genes was suppressed. Collectively, these results suggest that Aux/IAA proteins accumulate in the ubc13 mutant, resulting in a reduced auxin response and defective root development. Hence, this study provides possible mechanistic links between UBC13-mediated protein ubiquitination, root development and auxin signaling.
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Affiliation(s)
- Rui Wen
- College of Life Sciences, Capital Normal University, Beijing, 100048, China; Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5; Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5
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