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Zhang C, Wang H, Tian X, Lin X, Han Y, Han Z, Sha H, Liu J, Liu J, Zhang J, Bu Q, Fang J. A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination. Nat Commun 2024; 15:2211. [PMID: 38480722 PMCID: PMC10937917 DOI: 10.1038/s41467-024-46420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Low-temperature germination (LTG) is an important agronomic trait for rice (Oryza sativa). Japonica rice generally has greater capacity for germination at low temperatures than the indica subpopulation. However, the genetic basis and molecular mechanisms underlying this complex trait are poorly understood. Here, we report that OsUBC12, encoding an E2 ubiquitin-conjugating enzyme, increases low-temperature germinability in japonica, owing to a transposon insertion in its promoter enhancing its expression. Natural variation analysis reveals that transposon insertion in the OsUBC12 promoter mainly occurs in the japonica lineage. The variation detected in eight representative two-line male sterile lines suggests the existence of this allele introgression by indica-japonica hybridization breeding, and varieties carrying the japonica OsUBC12 locus (transposon insertion) have higher low-temperature germinability than varieties without the locus. Further molecular analysis shows that OsUBC12 negatively regulate ABA signaling. OsUBC12-regulated seed germination and ABA signaling mainly depend on a conserved active site required for ubiquitin-conjugating enzyme activity. Furthermore, OsUBC12 directly associates with rice SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), promoting its degradation. OsSnRK1.1 inhibits LTG by enhancing ABA signaling and acts downstream of OsUBC12. These findings shed light on the underlying mechanisms of UBC12 regulating LTG and provide genetic reference points for improving LTG in indica rice.
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Affiliation(s)
- Chuanzhong Zhang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Xinyan Lin
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, 136000, China
| | - Yunfei Han
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Zhongmin Han
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Hanjing Sha
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Jia Liu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Jianfeng Liu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, 136000, China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Jun Fang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China.
- Yazhouwan National Laboratory, Sanya, 572024, China.
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Karimian P, Trusov Y, Botella JR. Conserved Role of Heterotrimeric G Proteins in Plant Defense and Cell Death Progression. Genes (Basel) 2024; 15:115. [PMID: 38255003 PMCID: PMC10815853 DOI: 10.3390/genes15010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Programmed cell death (PCD) is a critical process in plant immunity, enabling the targeted elimination of infected cells to prevent the spread of pathogens. The tight regulation of PCD within plant cells is well-documented; however, specific mechanisms remain elusive or controversial. Heterotrimeric G proteins are multifunctional signaling elements consisting of three distinct subunits, Gα, Gβ, and Gγ. In Arabidopsis, the Gβγ dimer serves as a positive regulator of plant defense. Conversely, in species such as rice, maize, cotton, and tomato, mutants deficient in Gβ exhibit constitutively active defense responses, suggesting a contrasting negative role for Gβ in defense mechanisms within these plants. Using a transient overexpression approach in addition to knockout mutants, we observed that Gβγ enhanced cell death progression and elevated the accumulation of reactive oxygen species in a similar manner across Arabidopsis, tomato, and Nicotiana benthamiana, suggesting a conserved G protein role in PCD regulation among diverse plant species. The enhancement of PCD progression was cooperatively regulated by Gβγ and one Gα, XLG2. We hypothesize that G proteins participate in two distinct mechanisms regulating the initiation and progression of PCD in plants. We speculate that G proteins may act as guardees, the absence of which triggers PCD. However, in Arabidopsis, this G protein guarding mechanism appears to have been lost in the course of evolution.
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Affiliation(s)
| | | | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (P.K.); (Y.T.)
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Ding L, Wu Z, Xiang J, Cao X, Xu S, Zhang Y, Zhang D, Teng N. A LlWRKY33-LlHSFA4-LlCAT2 module confers resistance to Botrytis cinerea in lily. HORTICULTURE RESEARCH 2024; 11:uhad254. [PMID: 38274648 PMCID: PMC10809907 DOI: 10.1093/hr/uhad254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/14/2023] [Indexed: 01/27/2024]
Abstract
Gray mold caused by Botrytis cinerea is one of the major threats in lily production. However, limited information is available about the underlying defense mechanism against B. cinerea in lily. Here, we characterized a nuclear-localized class A heat stress transcription factor (HSF)-LlHSFA4 from lily (Lilium longiflorum), which positively regulated the response to B. cinerea infection. LlHSFA4 transcript and its promoter activity were increased by B. cinerea infection in lily, indicating its involvement in the response to B. cinerea. Virus-induced gene silencing (VIGS) of LlHSFA4 impaired the resistance of lily to B. cinerea. Consistent with its role in lily, overexpression of LlHSFA4 in Arabidopsis (Arabidopsis thaliana) enhanced the resistance of transgenic Arabidopsis to B. cinerea infection. Further analysis showed that LlWRKY33 directly activated LlHSFA4 expression. We also found that both LlHSFA4 and LlWRKY33 positively regulated plant response to B. cinerea through reducing cell death and H2O2 accumulation and activating the expression of the reactive oxygen species (ROS) scavenging enzyme gene LlCAT2 (Catalase 2) by binding its prompter, which might contribute to reducing H2O2 accumulation in the infected area. Taken together, our data suggested that there may be a LlWRKY33-LlHSFA4-LlCAT2 regulatory module which confers B. cinerea resistance via reducing cell death and the ROS accumulation.
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Affiliation(s)
- Liping Ding
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd., Nanjing 210043, China
| | - Ze Wu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd., Nanjing 210043, China
| | - Jun Xiang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd., Nanjing 210043, China
| | - Xing Cao
- College of Architecture, Yantai University, Yantai, 264005, China
| | - Sujuan Xu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd., Nanjing 210043, China
| | - Yinyi Zhang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd., Nanjing 210043, China
| | - Dehua Zhang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd., Nanjing 210043, China
| | - Nianjun Teng
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd., Nanjing 210043, China
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Wang Y, Yue J, Yang N, Zheng C, Zheng Y, Wu X, Yang J, Zhang H, Liu L, Ning Y, Bhadauria V, Zhao W, Xie Q, Peng YL, Chen Q. An ERAD-related ubiquitin-conjugating enzyme boosts broad-spectrum disease resistance and yield in rice. NATURE FOOD 2023; 4:774-787. [PMID: 37591962 DOI: 10.1038/s43016-023-00820-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
Rice is a staple crop for over half of the global population. However, blast disease caused by Magnaporthe orzae can result in more than a 30% loss in rice yield in epidemic years. Although some major resistance genes bolstering blast resistance have been identified in rice, their stacking in elite cultivars usually leads to yield penalties. Here we report that OsUBC45, a ubiquitin-conjugating enzyme functioning in the endoplasmic reticulum-associated protein degradation system, promotes broad-spectrum disease resistance and yield in rice. OsUBC45 is induced upon infection by M. oryzae, and its overexpression enhances resistance to blast disease and bacterial leaf blight by elevating pathogen-associated molecular pattern-triggered immunity (PTI) while nullifying the gene-attenuated PTI. The OsUBC45 overexpression also increases grain yield by over 10%. Further, OsUBC45 enhances the degradation of glycogen synthase kinase 3 OsGSK3 and aquaporin OsPIP2;1, which negatively regulate the grain size and PTI, respectively. The OsUBC45 reported in our study has the potential for improving yield and disease resistance for sustainable rice production.
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Affiliation(s)
- Yu Wang
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Jiaolin Yue
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Nan Yang
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Chuan Zheng
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Yunna Zheng
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Xi Wu
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Jun Yang
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Huawei Zhang
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Lijing Liu
- School of Life Sciences, Shandong University, Qingdao, China
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Vijai Bhadauria
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Wensheng Zhao
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - You-Liang Peng
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China.
| | - Qian Chen
- MOA Key Lab of Pest Monitoring and Green Management and Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China.
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Nizan S, Amitzur A, Dahan-Meir T, Benichou JIC, Bar-Ziv A, Perl-Treves R. Mutagenesis of the melon Prv gene by CRISPR/Cas9 breaks papaya ringspot virus resistance and generates an autoimmune allele with constitutive defense responses. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4579-4596. [PMID: 37137337 PMCID: PMC10433930 DOI: 10.1093/jxb/erad156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023]
Abstract
The majority of plant disease resistance (R) genes encode nucleotide binding-leucine-rich repeat (NLR) proteins. In melon, two closely linked NLR genes, Fom-1 and Prv, were mapped and identified as candidate genes that control resistance to Fusarium oxysporum f.sp. melonis races 0 and 2, and to papaya ringspot virus (PRSV), respectively. In this study, we validated the function of Prv and showed that it is essential for providing resistance against PRSV infection. We generated CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] mutants using Agrobacterium-mediated transformation of a PRSV-resistant melon genotype, and the T1 progeny proved susceptible to PRSV, showing strong disease symptoms and viral spread upon infection. Three alleles having 144, 154, and ~3 kb deletions, respectively, were obtained, all of which caused loss of resistance. Interestingly, one of the Prv mutant alleles, prvΔ154, encoding a truncated product, caused an extreme dwarf phenotype, accompanied by leaf lesions, high salicylic acid levels, and defense gene expression. The autoimmune phenotype observed at 25 °C proved to be temperature dependent, being suppressed at 32 °C. This is a first report on the successful application of CRISPR/Cas9 to confirm R gene function in melon. Such validation opens up new opportunities for molecular breeding of disease resistance in this important vegetable crop.
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Affiliation(s)
- Shahar Nizan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Arie Amitzur
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Tal Dahan-Meir
- Plant and Environmental Sciences, Weizmann Institute of Science, Israel
| | | | - Amalia Bar-Ziv
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Rafael Perl-Treves
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
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6
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Abstract
Background Identifying CO2-binding proteins is vital for our knowledge of CO2-regulated molecular processes. The carbamate post-translational modification is a reversible CO2-mediated adduct that can form on neutral N-terminal α-amino or lysine ε-amino groups. Methods We have developed triethyloxonium ion (TEO) as a chemical proteomics tool to trap the carbamate post-translational modification on protein covalently. We use 13C-NMR and TEO and identify ubiquitin as a plant CO2-binding protein. Results We observe the carbamate post-translational modification on the Arabidopsis thaliana ubiquitin ε-amino groups of lysines 6, 33, and 48. We show that biologically relevant near atmospheric PCO2 levels increase ubiquitin conjugation dependent on lysine 6. We further demonstrate that CO2 increases the ubiquitin E2 ligase (AtUBC5) charging step via the transthioesterification reaction in which Ub is transferred from the E1 ligase active site to the E2 active site. Conclusions and general significance Therefore, plant ubiquitin is a CO2-binding protein, and the carbamate post-translational modification represents a potential mechanism through which plant cells can respond to fluctuating PCO2.
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Affiliation(s)
- Harry G Gannon
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Martin J Cann
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
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Zhao L, Wang HJ, Martins PD, van Dongen JT, Bolger AM, Schmidt RR, Jing HC, Mueller-Roeber B, Schippers JHM. The Arabidopsis thaliana onset of leaf death 12 mutation in the lectin receptor kinase P2K2 results in an autoimmune phenotype. BMC PLANT BIOLOGY 2023; 23:294. [PMID: 37264342 DOI: 10.1186/s12870-023-04300-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/20/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Plant immunity relies on the perception of immunogenic signals by cell-surface and intracellular receptors and subsequent activation of defense responses like programmed cell death. Under certain circumstances, the fine-tuned innate immune system of plants results in the activation of autoimmune responses that cause constitutive defense responses and spontaneous cell death in the absence of pathogens. RESULTS Here, we characterized the onset of leaf death 12 (old12) mutant that was identified in the Arabidopsis accession Landsberg erecta. The old12 mutant is characterized by a growth defect, spontaneous cell death, plant-defense gene activation, and early senescence. In addition, the old12 phenotype is temperature reversible, thereby exhibiting all characteristics of an autoimmune mutant. Mapping the mutated locus revealed that the old12 phenotype is caused by a mutation in the Lectin Receptor Kinase P2-TYPE PURINERGIC RECEPTOR 2 (P2K2) gene. Interestingly, the P2K2 allele from Landsberg erecta is conserved among Brassicaceae. P2K2 has been implicated in pathogen tolerance and sensing extracellular ATP. The constitutive activation of defense responses in old12 results in improved resistance against Pseudomonas syringae pv. tomato DC3000. CONCLUSION We demonstrate that old12 is an auto-immune mutant and that allelic variation of P2K2 contributes to diversity in Arabidopsis immune responses.
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Affiliation(s)
- Liming Zhao
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Beijng Academy, Beijing, 100028, China
| | - Hao-Jie Wang
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
- Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074, Aachen, Germany
| | - Patricia Dalcin Martins
- Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074, Aachen, Germany
| | - Joost T van Dongen
- Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074, Aachen, Germany
| | - Anthony M Bolger
- Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074, Aachen, Germany
- IBG-4: Bioinformatik,Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Romy R Schmidt
- Institute of Biology I, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074, Aachen, Germany
- Plant Biotechnology Group, Faculty of Biology, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bernd Mueller-Roeber
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Ruski 139 Blvd, Plovdiv, 4000, Bulgaria
| | - Jos H M Schippers
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
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Kahlon PS, Förner A, Muser M, Oubounyt M, Gigl M, Hammerl R, Baumbach J, Hückelhoven R, Dawid C, Stam R. Laminarin-triggered defence responses are geographically dependent in natural populations of Solanum chilense. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3240-3254. [PMID: 36880316 DOI: 10.1093/jxb/erad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/06/2023] [Indexed: 05/21/2023]
Abstract
Natural plant populations are polymorphic and show intraspecific variation in resistance properties against pathogens. The activation of the underlying defence responses can depend on variation in perception of pathogen-associated molecular patterns or elicitors. To dissect such variation, we evaluated the responses induced by laminarin (a glucan, representing an elicitor from oomycetes) in the wild tomato species Solanum chilense and correlated this to observed infection frequencies of Phytophthora infestans. We measured reactive oxygen species burst and levels of diverse phytohormones upon elicitation in 83 plants originating from nine populations. We found high diversity in basal and elicitor-induced levels of each component. Further we generated linear models to explain the observed infection frequency of P. infestans. The effect of individual components differed dependent on the geographical origin of the plants. We found that the resistance in the southern coastal region, but not in the other regions, was directly correlated to ethylene responses and confirmed this positive correlation using ethylene inhibition assays. Our findings reveal high diversity in the strength of defence responses within a species and the involvement of different components with a quantitatively different contribution of individual components to resistance in geographically separated populations of a wild plant species.
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Affiliation(s)
- Parvinderdeep S Kahlon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Andrea Förner
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Michael Muser
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Mhaned Oubounyt
- Research Group of Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607, Hamburg, Germany
| | - Michael Gigl
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Richard Hammerl
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Jan Baumbach
- Research Group of Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607, Hamburg, Germany
- Computational BioMedicine lab, Institute of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Remco Stam
- Department of Phytopathology and Crop Protection, Institute for Phytopathology, Kiel University, Hermann Rodewald Str 9, 24118 Kiel, Germany
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Saxena H, Negi H, Sharma B. Role of F-box E3-ubiquitin ligases in plant development and stress responses. PLANT CELL REPORTS 2023:10.1007/s00299-023-03023-8. [PMID: 37195503 DOI: 10.1007/s00299-023-03023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 04/27/2023] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and environmental adaptation. This review presents a background of E3 ligases with particular emphasis on the F-box proteins, their structural assembly, and their mechanism of action during substrate recognition. We discuss how the F-box proteins regulate and participate in the signaling mechanisms of plant development and environmental responses. We highlight an urgent need for research on the molecular basis of the F-box E3-ubiquitin ligases in plant physiology, systems biology, and biotechnology. Further, the developments and outlooks of the potential technologies targeting the E3-ubiquitin ligases for developing crop improvement strategies have been discussed.
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Affiliation(s)
- Harshita Saxena
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia Griffin Campus, 1109 Experiment Street, Griffin, GA, 30223, USA
| | - Harshita Negi
- Department of Biological Sciences, University of South Carolina, 715 Sumter Street, Columbia, SC, 29208, USA
| | - Bhaskar Sharma
- School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Geelong, VIC, 3216, Australia.
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA, 92521, USA.
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Song J, Sajad S, Xia D, Jiang S. Identification of F-box gene family in Brassica oleracea and expression analysis in response to low-temperature stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107717. [PMID: 37150011 DOI: 10.1016/j.plaphy.2023.107717] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/12/2023] [Accepted: 04/23/2023] [Indexed: 05/09/2023]
Abstract
Unfavorable climatic conditions, such as low temperatures, often hinder the growth and production of crops worldwide. The F-box protein-encoding gene family performs an essential role in plant stress resistance. However, a comprehensive analysis of the F-box gene family in cabbage (Brassica oleracea var capitata L.) has not been reported yet. In this study, genome-wide characterization of F-box proteins in cabbage yielded 303 BoFBX genes and 224 BoFBX genes unevenly distributed on 9 chromosomes of cabbage. Phylogenetic analysis of 303 BoFBX genes was classified into nine distinct subfamily groups (GI-GIX). Analysis of the gene structure of BoFBX genes indicated that most genes within the same clade are highly conserved. In addition, tissue-specific expression analysis revealed that six F-box genes in cabbage showed the highest expression in rosette leaves, followed by roots and stems and the lowest expression was observed in the BoFBX156 gene. In contrast, the expression of the other five genes, BoFBX100, BoFBX117, BoFBX136, BoFBX137 and BoFBX213 was observed to be upregulated in response to low-temperature stress. Moreover, we found that the expression level of the BoFBX gene in the cold-tolerant cultivar "ZG" was higher than that in cold-sensitive "YC" with the extension of stress duration, while expression levels of each gene in "ZG" were higher than "YC" at 24 h. Knowledge of the various functions provided by BoFBXs genes and their expression patterns provides a firm theoretical foundation for explaining the functions of BoFBXs, thereby contributing to the molecular breeding process of cabbage.
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Affiliation(s)
- Jianghua Song
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, 230036, Hefei, Anhui, China.
| | - Shoukat Sajad
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, 230036, Hefei, Anhui, China
| | - Dongjian Xia
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, 230036, Hefei, Anhui, China
| | - Shuhan Jiang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, 230036, Hefei, Anhui, China
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11
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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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12
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Luo R, Yang K, Xiao W. Plant deubiquitinases: from structure and activity to biological functions. PLANT CELL REPORTS 2023; 42:469-486. [PMID: 36567335 DOI: 10.1007/s00299-022-02962-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
This article attempts to provide comprehensive review of plant deubiquitinases, paying special attention to recent advances in their biochemical activities and biological functions. Proteins in eukaryotes are subjected to post-translational modifications, in which ubiquitination is regarded as a reversible process. Cellular deubiquitinases (DUBs) are a key component of the ubiquitin (Ub)-proteasome system responsible for cellular protein homeostasis. DUBs recycle Ub by hydrolyzing poly-Ub chains on target proteins, and maintain a balance of the cellular Ub pool. In addition, some DUBs prefer to cleave poly-Ub chains not linked through the conventional K48 residue, which often alter the substrate activity instead of its stability. In plants, all seven known DUB subfamilies have been identified, namely Ub-binding protease/Ub-specific protease (UBP/USP), Ub C-terminal hydrolase (UCH), Machado-Joseph domain-containing protease (MJD), ovarian-tumor domain-containing protease (OTU), zinc finger with UFM1-specific peptidase domain protease (ZUFSP), motif interacting with Ub-containing novel DUB family (MINDY), and JAB1/MPN/MOV34 protease (JAMM). This review focuses on recent advances in the structure, activity, and biological functions of plant DUBs, particularly in the model plant Arabidopsis.
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Affiliation(s)
- Runbang Luo
- 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
| | - Kun Yang
- 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
| | - 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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13
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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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15
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Sahoo DK, Hegde C, Bhattacharyya MK. Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 13:1094462. [PMID: 36714785 PMCID: PMC9878698 DOI: 10.3389/fpls.2022.1094462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. METHODS The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes. RESULTS Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier. DISCUSSION The 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Chinmay Hegde
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States
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16
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Wang L, Yang K, Wang Q, Xiao W. Genetic analysis of DNA-damage tolerance pathways in Arabidopsis. PLANT CELL REPORTS 2023; 42:153-164. [PMID: 36319861 DOI: 10.1007/s00299-022-02942-2] [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: 04/30/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Genetic analysis revealed a two-branch DNA-damage tolerance mechanism in Arabidopsis, namely translesion DNA synthesis and error-free lesion bypass, represented by Rev3 and Rad5a-Uev1C/D, respectively. DNA-damage tolerance (DDT) is a mechanism by which cells complete replication in the presence of replication-blocking lesions. In budding yeast, DDT is achieved through Rad6-Rad18-mediated monoubiquitination of proliferating cell nuclear antigen (PCNA), which promotes translesion DNA synthesis (TLS) and is followed by Ubc13-Mms2-Rad5 mediated K63-linked PCNA polyubiquitination that promotes error-free lesion bypass. Arabidopsis and other known plant genomes contain all of the above homologous genes except RAD18, and whether plants possess an intact DDT mechanism is unclear. In this study, we created Arabidopsis UEV1 (homologous to yeast MMS2) gene mutations and obtained two sets of double mutant lines Atuev1ab and Atuev1cd. It turned out that the Atuev1cd, but not the Atuev1ab mutant, was sensitive to DNA damage. Genetic analyses revealed that AtUEV1C/D and AtRAD5a function in the same pathway, while TLS represented by AtREV3 functions in a separate pathway in response to replication-blocking lesions. Furthermore, unlike budding yeast RAD5 that also functions in the TLS pathway, AtRAD5a is not required for TLS. Observations in this study collectively establish a two-branch DDT model in plants with similarity to and difference from the yeast DDT.
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Affiliation(s)
- Linxiao Wang
- 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
| | - Kun Yang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Qiuheng Wang
- 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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17
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Cao S, Guo M, Cheng J, Cheng H, Liu X, Ji H, Liu G, Cheng Y, Yang C. Aspartic proteases modulate programmed cell death and secondary cell wall synthesis during wood formation in poplar. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6876-6890. [PMID: 36040843 PMCID: PMC9629783 DOI: 10.1093/jxb/erac347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Programmed cell death (PCD) is essential for wood development in trees. However, the determination of crucial factors involved in xylem PCD of wood development is still lacking. Here, two Populus trichocarpa typical aspartic protease (AP) genes, AP17 and AP45, modulate xylem maturation, especially fibre PCD, during wood formation. AP17 and AP45 were dominantly expressed in the fibres of secondary xylem, as suggested by GUS expression in APpro::GUS transgenic plants. Cas9/gRNA-induced AP17 or AP45 mutants delayed secondary xylem fibre PCD, and ap17ap45 double mutants showed more serious defects. Conversely, AP17 overexpression caused premature PCD in secondary xylem fibres, indicating a positive modulation in wood fibre PCD. Loss of AP17 and AP45 did not alter wood fibre wall thickness, whereas the ap17ap45 mutants showed a low lignin content in wood. However, AP17 overexpression led to a significant decrease in wood fibre wall thickness and lignin content, revealing the involvement in secondary cell wall synthesis during wood formation. In addition, the ap17ap45 mutant and AP17 overexpression plants resulted in a significant increase in saccharification yield in wood. Overall, AP17 and AP45 are crucial modulators in xylem maturation during wood development, providing potential candidate genes for engineering lignocellulosic wood for biofuel utilization.
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Affiliation(s)
- Shenquan Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Mengjie Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiyao Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Hao Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiaomeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Huanhuan Ji
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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Arabidopsis Ubiquitin-Conjugating Enzymes UBC4, UBC5, and UBC6 Have Major Functions in Sugar Metabolism and Leaf Senescence. Int J Mol Sci 2022; 23:ijms231911143. [PMID: 36232444 PMCID: PMC9569852 DOI: 10.3390/ijms231911143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/23/2022] Open
Abstract
The ubiquitin-conjugating enzyme (E2) is required for protein ubiquitination. Arabidopsis has 37 E2s grouped into 14 subfamilies and the functions for many of them are unknown. We utilized genetic and biochemical methods to study the roles of Arabidopsis UBC4, UBC5, and UBC6 of the E2 subfamily IV. The Arabidopsis ubc4/5/6 triple mutant plants had higher levels of glucose, sucrose, and starch than the control plants, as well as a higher protein level of a key gluconeogenic enzyme, cytosolic fructose 1,6-bisphosphatase 1 (cyFBP). In an in vitro assay, the proteasome inhibitor MG132 inhibited the degradation of recombinant cyFBP whereas ATP promoted cyFBP degradation. In the quadruple mutant ubc4/5/6 cyfbp, the sugar levels returned to normal, suggesting that the increased sugar levels in the ubc4/5/6 mutant were due to an increased cyFBPase level. In addition, the ubc4/5/6 mutant plants showed early leaf senescence at late stages of plant development as well as accelerated leaf senescence using detached leaves. Further, the leaf senescence phenotype remained in the quadruple ubc4/5/6 cyfbp mutant. Our results suggest that UBC4/5/6 have two lines of important functions, in sugar metabolism through regulating the cyFBP protein level and in leaf senescence likely through a cyFBP-independent mechanism.
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19
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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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20
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E2 ubiquitin-conjugating enzymes (UBCs): drivers of ubiquitin signalling in plants. Essays Biochem 2022; 66:99-110. [PMID: 35766526 DOI: 10.1042/ebc20210093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/22/2022]
Abstract
Most research in the field of ubiquitination has focused on E3 ubiquitin ligases because they are the specificity determinants of the ubiquitination process. Nevertheless, E2s are responsible for the catalysis during ubiquitin transfer, and are therefore, at the heart of the ubiquitination process. Arabidopsis has 37 ubiquitin E2s with additional ones mediating the attachment of ubiquitin-like proteins (e.g. SUMO, Nedd8 and ATG8). Importantly, E2s largely determine the type of ubiquitin chain built, and therefore, the type of signal that decides over the fate of the modified protein, such as degradation by the proteasome (Lys48-linked ubiquitin chains) or relocalization (Lys63-linked ubiquitin chains). Moreover, new regulatory layers impinging on E2s activity, including post-translational modifications or cofactors, are emerging that highlight the importance of E2s.
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21
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Trenner J, Monaghan J, Saeed B, Quint M, Shabek N, Trujillo M. Evolution and Functions of Plant U-Box Proteins: From Protein Quality Control to Signaling. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:93-121. [PMID: 35226816 DOI: 10.1146/annurev-arplant-102720-012310] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Posttranslational modifications add complexity and diversity to cellular proteomes. One of the most prevalent modifications across eukaryotes is ubiquitination, which is orchestrated by E3 ubiquitin ligases. U-box-containing E3 ligases have massively expanded in the plant kingdom and have diversified into plant U-box proteins (PUBs). PUBs likely originated from two or three ancestral forms, fusing with diverse functional subdomains that resulted in neofunctionalization. Their emergence and diversification may reflect adaptations to stress during plant evolution, reflecting changes in the needs of plant proteomes to maintain cellular homeostasis. Through their close association with protein kinases, they are physically linked to cell signaling hubs and activate feedback loops by dynamically pairing with E2-ubiquitin-conjugating enzymes to generate distinct ubiquitin polymers that themselves act as signals. Here, we complement current knowledgewith comparative genomics to gain a deeper understanding of PUB function, focusing on their evolution and structural adaptations of key U-box residues, as well as their various roles in plant cells.
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Affiliation(s)
- Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany; ,
| | | | - Bushra Saeed
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany; ,
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany; ,
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA;
| | - Marco Trujillo
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany; ,
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22
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Mackinnon E, Stone SL. The Ubiquitin Proteasome System and Nutrient Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 13:867419. [PMID: 35665152 PMCID: PMC9161090 DOI: 10.3389/fpls.2022.867419] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Plants utilize different molecular mechanisms, including the Ubiquitin Proteasome System (UPS) that facilitates changes to the proteome, to mitigate the impact of abiotic stresses on growth and development. The UPS encompasses the ubiquitination of selected substrates followed by the proteasomal degradation of the modified proteins. Ubiquitin ligases, or E3s, are central to the UPS as they govern specificity and facilitate the attachment of one or more ubiquitin molecules to the substrate protein. From recent studies, the UPS has emerged as an important regulator of the uptake and translocation of essential macronutrients and micronutrients. In this review, we discuss select E3s that are involved in regulating nutrient uptake and responses to stress conditions, including limited or excess levels of nitrogen, phosphorus, iron, and copper.
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Chao WS, Li X, Horvath DP, Anderson JV. Genetic loci associated with freezing tolerance in a European rapeseed ( Brassica napus L.) diversity panel identified by genome-wide association mapping. PLANT DIRECT 2022; 6:e405. [PMID: 35647480 PMCID: PMC9132609 DOI: 10.1002/pld3.405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Winter biotypes of rapeseed (Brassica napus L.) require a vernalization treatment to enter the reproductive phase and generally produce greater yields than spring rapeseed. To find genetic loci associated with freezing tolerance in rapeseed, we first performed genotyping-by-sequencing (GBS) on a diversity panel consisting of 222 rapeseed accessions originating primarily from Europe, which identified 69,554 high-quality single-nucleotide polymorphisms (SNPs). Model-based cluster analysis suggested that there were eight subgroups. The diversity panel was then phenotyped for freezing survival (visual damage and Fv/Fo and Fv/Fm) after 2 months of cold acclimation (5°C) and a freezing treatment (-15°C for 4 h). The genotypic and phenotypic data for each accession in the rapeseed diversity panel was then used to conduct a genome-wide association study (GWAS). GWAS results showed that 14 significant markers were mapped to seven chromosomes for the phenotypes scored. Twenty-four candidate genes located within the mapped loci were identified as previously associated with lipid, photosynthesis, flowering, ubiquitination, and cytochrome P450 in rapeseed or other plant species.
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Affiliation(s)
- Wun S. Chao
- Edward T. Schafer Agricultural Research Center, Sunflower and Plant Biology Research UnitUSDA‐Agricultural Research ServiceFargoNorth DakotaUSA
| | - Xuehui Li
- Department of Plant SciencesNorth Dakota State UniversityFargoNorth DakotaUSA
| | - David P. Horvath
- Edward T. Schafer Agricultural Research Center, Sunflower and Plant Biology Research UnitUSDA‐Agricultural Research ServiceFargoNorth DakotaUSA
| | - James V. Anderson
- Edward T. Schafer Agricultural Research Center, Sunflower and Plant Biology Research UnitUSDA‐Agricultural Research ServiceFargoNorth DakotaUSA
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Wang P, Guo K, Su Q, Deng J, Zhang X, Tu L. Histone ubiquitination controls organ size in cotton (Gossypium hirsutum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1005-1020. [PMID: 35218092 DOI: 10.1111/tpj.15716] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/21/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitination plays a vital role in modifying protein activity and destiny. Ub-conjugating enzyme E2 is one of the enzymes that participates in this precise process. There are at least 169 E2 proteins in the allotetraploid cotton (Gossypium hirsutum), but their function remains unknown. Here we identify an E2 gene GhUBC2L and show its positive role in cell proliferation and expansion. Complete knock-down of GhUBC2L in cotton resulted in retarded growth and reduced organ size. Conversely, overexpression of GhUBC2L promoted cotton growth, generating enlarged organs in size. Monoubiquitination of H2A and H2B was strongly impaired in GhUBC2L-suppressed cotton but slightly enhanced in GhUBC2L-overexpressed plant. GhUbox8, a U-box type E3 ligase protein, was found to interact with GhUBC2L both in vivo and in vitro, indicating their synergistical function in protein ubiquitination. Furthermore, GhUbox8 was shown to interact with a series of histone proteins, including histone H2A and H2B, indicating its potential monoubiquitination on H2A and H2B. Expression of genes relating to cell cycle and organ development were altered when the expression of GhUBC2L was changed. Our results show that GhUBC2L modulates histone monoubiquitination synergistically with GhUbox8 to regulate the expression of genes involved in organ development and cell cycle, thus controlling organ size in cotton. This research provides new insights into the role of protein ubiquitination in organ size control. Histone monoubiquitination plays an important role in plant development. Here, we identified an E2 enzyme GhUBC2L that modulates histone monoubiquitination synergistically with an E3 ligase GhUbox8 to mediate organ size control in cotton.
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Affiliation(s)
- Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Kai Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qian Su
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jinwu Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Ubiquitination of Receptorsomes, Frontline of Plant Immunity. Int J Mol Sci 2022; 23:ijms23062937. [PMID: 35328358 PMCID: PMC8948693 DOI: 10.3390/ijms23062937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/13/2022] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
Sessile plants are constantly exposed to myriads of unfavorable invading organisms with different lifestyles. To survive, plants have evolved plasma membrane-resident pattern recognition receptors (PRRs) and intracellular nucleotide-binding domain leucine-rich repeat receptors (NLRs) to initiate sophisticated downstream immune responses. Ubiquitination serves as one of the most important and prevalent posttranslational modifications (PTMs) to fine-tune plant immune responses. Over the last decade, remarkable progress has been made in delineating the critical roles of ubiquitination in plant immunity. In this review, we highlight recent advances in the understanding of ubiquitination in the modulation of plant immunity, with a particular focus on ubiquitination in the regulation of receptorsomes, and discuss how ubiquitination and other PTMs act in concert to ensure rapid, proper, and robust immune responses.
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Genome-Wide Profiling of Alternative Splicing and Gene Fusion during Rice Black-Streaked Dwarf Virus Stress in Maize (Zea mays L.). Genes (Basel) 2022; 13:genes13030456. [PMID: 35328010 PMCID: PMC8955601 DOI: 10.3390/genes13030456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 12/26/2022] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease (MRDD), which is a viral disease that significantly affects maize yields worldwide. Plants tolerate stress through transcriptional reprogramming at the alternative splicing (AS), transcriptional, and fusion gene (FG) levels. However, it is unclear whether and how AS and FG interfere with transcriptional reprogramming in MRDD. In this study, we performed global profiling of AS and FG on maize response to RBSDV and compared it with transcriptional changes. There are approximately 1.43 to 2.25 AS events per gene in maize infected with RBSDV. GRMZM2G438622 was only detected in four AS modes (A3SS, A5SS, RI, and SE), whereas GRMZM2G059392 showed downregulated expression and four AS events. A total of 106 and 176 FGs were detected at two time points, respectively, including six differentially expressed genes and five differentially spliced genes. The gene GRMZM2G076798 was the only FG that occurred at two time points and was involved in two FG events. Among these, 104 GOs were enriched, indicating that nodulin-, disease resistance-, and chloroplastic-related genes respond to RBSDV stress in maize. These results provide new insights into the mechanisms underlying post-transcriptional and transcriptional regulation of maize response to RBSDV stress.
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Yao D, Arguez MA, He P, Bent AF, Song J. Coordinated regulation of plant immunity by poly(ADP-ribosyl)ation and K63-linked ubiquitination. MOLECULAR PLANT 2021; 14:2088-2103. [PMID: 34418551 PMCID: PMC9070964 DOI: 10.1016/j.molp.2021.08.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/24/2021] [Accepted: 08/15/2021] [Indexed: 05/02/2023]
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a posttranslational modification reversibly catalyzed by poly(ADP-ribose) polymerases (PARPs) and poly(ADP-ribose) glycohydrolases (PARGs) and plays a key role in multiple cellular processes. The molecular mechanisms by which PARylation regulates innate immunity remain largely unknown in eukaryotes. Here we show that Arabidopsis UBC13A and UBC13B, the major drivers of lysine 63 (K63)-linked polyubiquitination, directly interact with PARPs/PARGs. Activation of pathogen-associated molecular pattern (PAMP)-triggered immunity promotes these interactions and enhances PARylation of UBC13. Both parp1 parp2 and ubc13a ubc13b mutants are compromised in immune responses with increased accumulation of total pathogenesis-related (PR) proteins but decreased accumulation of secreted PR proteins. Protein disulfide-isomerases (PDIs), essential components of endoplasmic reticulum quality control (ERQC) that ensure proper folding and maturation of proteins destined for secretion, complex with PARPs/PARGs and are PARylated upon PAMP perception. Significantly, PARylation of UBC13 regulates K63-linked ubiquitination of PDIs, which may further promote their disulfide isomerase activities for correct protein folding and subsequent secretion. Taken together, these results indicate that plant immunity is coordinately regulated by PARylation and K63-linked ubiquitination.
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Affiliation(s)
- Dongsheng Yao
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252, USA
| | - Marcus A Arguez
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252, USA
| | - Ping He
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Andrew F Bent
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junqi Song
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA.
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Tang W, Wang X, Kou M, Yan H, Gao R, Li C, Song W, Zhang Y, Wang X, Liu Y, Li Z, Li Q. The sweetpotato GIGANTEA gene promoter is co-regulated by phytohormones and abiotic stresses in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:143-154. [PMID: 34628175 DOI: 10.1016/j.plaphy.2021.08.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/19/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
GIGANTEA (GI) is known to play significant roles in various molecular pathways. Nevertheless, the underlying mechanism of the transcriptional regulation of GI remains obscure in sweetpotato. In the present study, a 1518-bp promoter sequence was obtained from the Ipomoea batatas GIGANTEA (IbGI) gene, and several potential cis-elements responsive to light, phytohormones and abiotic stresses were identified by in silico analysis. In order to functionally validate the IbGI promoter, the 5' deletion analysis of the promoter was performed by cloning the full-length promoter (D0) and its four deletion fragments, D1 (1235 bp), D2 (896 bp), D3 (549 bp) and D4 (286 bp), upstream of the β-glucuronidase (GUS) reporter gene. Then, these were stably transformed in Arabidopsis plants. All transgenic seedlings exhibited stable GUS activity in the condition of control, but with decreased activity in the condition of most treatments. Interestingly, merely D1 seedlings that contained an abscisic acid responsive cis-element (ABRE-element) had an extremely powerful GUS activity under the treatment of ABA, which implies that fragment spanning nucleotides of -1235 to -896 bp might be a crucial component for the responses of ABA. Eight different types of potential transcriptional regulators of IbGI were isolated by Y1H, including TGA2.2, SPLT1 and GADPH, suggesting the complex interaction mode of protein-DNA on the IbGI promoter. Taken together, these present results help to better understand the transcriptional regulation mechanism of the IbGI gene, and provides an insight into the IbGI promoter, which can be considered as an alternation for breeding transgenic plants.
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Affiliation(s)
- Wei Tang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Xiaoxiao Wang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Meng Kou
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Hui Yan
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Runfei Gao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Chen Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Weihan Song
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Yungang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Yaju Liu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China.
| | - Qiang Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China.
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Kohlhase DR, McCabe CE, Singh AK, O’Rourke JA, Graham MA. Comparing Early Transcriptomic Responses of 18 Soybean ( Glycine max) Genotypes to Iron Stress. Int J Mol Sci 2021; 22:11643. [PMID: 34769077 PMCID: PMC8583884 DOI: 10.3390/ijms222111643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Iron deficiency chlorosis (IDC) is an abiotic stress that negatively affects soybean (Glycine max [L.] Merr.) production. Much of our knowledge of IDC stress responses is derived from model plant species. Gene expression, quantitative trait loci (QTL) mapping, and genome-wide association studies (GWAS) performed in soybean suggest that stress response differences exist between model and crop species. Our current understanding of the molecular response to IDC in soybeans is largely derived from gene expression studies using near-isogenic lines differing in iron efficiency. To improve iron efficiency in soybeans and other crops, we need to expand gene expression studies to include the diversity present in germplasm collections. Therefore, we collected 216 purified RNA samples (18 genotypes, two tissue types [leaves and roots], two iron treatments [sufficient and deficient], three replicates) and used RNA sequencing to examine the expression differences of 18 diverse soybean genotypes in response to iron deficiency. We found a rapid response to iron deficiency across genotypes, most responding within 60 min of stress. There was little evidence of an overlap of specific differentially expressed genes, and comparisons of gene ontology terms and transcription factor families suggest the utilization of different pathways in the stress response. These initial findings suggest an untapped genetic potential within the soybean germplasm collection that could be used for the continued improvement of iron efficiency in soybean.
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Affiliation(s)
- Daniel R. Kohlhase
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; (D.R.K.); (A.K.S.)
| | - Chantal E. McCabe
- U.S. Department of Agriculture (USDA)—Agricultural Research Service (ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA;
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; (D.R.K.); (A.K.S.)
| | - Jamie A. O’Rourke
- U.S. Department of Agriculture (USDA)—Agricultural Research Service (ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA;
| | - Michelle A. Graham
- U.S. Department of Agriculture (USDA)—Agricultural Research Service (ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA;
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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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Chang Y, Bai Y, Wei Y, Shi H. CAMTA3 negatively regulates disease resistance through modulating immune response and extensive transcriptional reprogramming in cassava. TREE PHYSIOLOGY 2020; 40:1520-1533. [PMID: 32705122 DOI: 10.1093/treephys/tpaa093] [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: 03/11/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
As one of the important crops in the world, cassava production is seriously threatened by Xanthomonas axonopodis pv. manihotis (Xam) all year round. Calmodulin-binding transcription activators (CAMTAs) play key roles in biotic stress and abiotic stress in plants, however, their roles in cassava remain elusive. In this study, six MeCAMTAs were identified, and MeCAMTA3 with the highest induction upon Xam infection was confirmed as a transcription factor that binds to the vCGCGb motif. MeCAMTA3 negatively regulates plant disease resistance against Xam. On the one hand, MeCAMTA3 negatively regulated endogenous salicylic acid and reactive oxygen species accumulation, pathogenesis-related genes MePRs' transcripts and callose deposition during cassava-Xam interaction but not under control conditions. On the other hand, RNA sequencing showed extensive transcriptional reprogramming by MeCAMTA3, especially 18 genes with a vCGCGb motif in the promoter region in hormone signaling, antioxidant signaling and other disease resistance signaling. Notably, chromatin immunoprecipitation-polymerase chain reaction showed that eight of these genes might be directly regulated by MeCAMTA3 through transcriptional repression. In summary, MeCAMTA3 negatively regulates plant disease resistance against cassava bacterial blight through modulation of multiple immune responses during cassava-Xam interaction and extensive transcriptional reprogramming.
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Affiliation(s)
- Yanli Chang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Yujing Bai
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China
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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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Wang S, Li Q, Zhao L, Fu S, Qin L, Wei Y, Fu YB, Wang H. Arabidopsis UBC22, an E2 able to catalyze lysine-11 specific ubiquitin linkage formation, has multiple functions in plant growth and immunity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110520. [PMID: 32563459 DOI: 10.1016/j.plantsci.2020.110520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 04/15/2020] [Accepted: 05/03/2020] [Indexed: 05/03/2023]
Abstract
Protein ubiquitination is critical for various biological processes in eukaryotes. A ubiquitin (Ub) chain can be linked through one of the seven lysine (K) residues or the N-terminus methionine of the Ub, and the Ub-conjugating enzymes called E2s play a critical role in determining the linkage specificity of Ub chains. Further, while K48-linked polyubiquitin chain is important for protein degradation, much less is known about the functions of other types of polyubiquitin chains in plants. We showed previously that UBC22 is unique in its ability to catalyze K11-dependent Ub dimer formation in vitro and ubc22 knockout mutants had defects in megasporogenesis. In this study, further analyses of the Arabidopsis ubc22 mutants revealed four subtypes of plants based on the phenotypic changes in vegetative growth. These four subtypes appeared consistently in the plants of three independent ubc22 mutants. Transcriptomic analysis showed that transcript levels of genes related to several pathways were altered differently in different subtypes of mutant plants. In one subtype, the mutant plants had increased expression of genes related to plant defenses and showed enhanced resistance to a necrotrophic plant pathogen. These results suggest multiple functions of UBC22 during plant development and stress response.
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Affiliation(s)
- Sheng Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Zhao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada; Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2, Canada
| | - Sanxiong Fu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada; Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Li Qin
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2, Canada
| | - Hong Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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Feng H, Wang S, Dong D, Zhou R, Wang H. Arabidopsis Ubiquitin-Conjugating Enzymes UBC7, UBC13, and UBC14 Are Required in Plant Responses to Multiple Stress Conditions. PLANTS 2020; 9:plants9060723. [PMID: 32521733 PMCID: PMC7355981 DOI: 10.3390/plants9060723] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 01/24/2023]
Abstract
Protein ubiquitination plays important roles in plants, including stress responses. The ubiquitin (Ub) E2 enzymes are required in the transfer of Ub to a substrate and are also important in determining the Ub-chain linkage specificity. However, for many of the 37 E2 genes in Arabidopsis thaliana, there is currently little or no understanding of their functions. In this study, we investigated three members of an E2 subfamily. The single, double, and triple mutants of UBC7, UBC13, and UBC14 did not show any phenotypic changes under normal conditions, but were more sensitive than the wild-type (WT) plants to multiple stress conditions, suggesting that the three genes are not critical for normal growth, but required in plant stress responses. The severity of the phenotypes increased from single to triple mutants, suggesting that the functions of the three genes are not completely redundant. The three E2s are closely related to the yeast Ubc7 and its homologs in animals and human, which are an important component of the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway. The stress sensitivity phenotypes of the mutants and shared evolutionary root with the Ubc7 homologs in yeast and metazoans suggest that UBC7, UBC13, and UBC14 may function in the plant ERAD pathway.
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Affiliation(s)
- Hui Feng
- College of Agriculture, Guangxi University, Nanning 530005, China; (H.F.); (D.D.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Sheng Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Dengfeng Dong
- College of Agriculture, Guangxi University, Nanning 530005, China; (H.F.); (D.D.)
| | - Ruiyang Zhou
- College of Agriculture, Guangxi University, Nanning 530005, China; (H.F.); (D.D.)
- Correspondence: (R.Z.); (H.W.)
| | - Hong Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
- Correspondence: (R.Z.); (H.W.)
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Gao Z, Liu Q, Zhang Y, Chen D, Zhan X, Deng C, Cheng S, Cao L. OsCUL3a-Associated Molecular Switches Have Functions in Cell Metabolism, Cell Death, and Disease Resistance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5471-5482. [PMID: 32320244 DOI: 10.1021/acs.jafc.9b07426] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This study applies parallel reaction monitoring (PRM) proteomics and CRISPR-Cas9 mutagenesis to identify relationships between cell metabolism, cell death, and disease resistance. In oscul3a (oscullin3a) mutants, OsCUL3a-associated molecular switches are responsible for disrupted cell metabolism that leads to increased total lipid content in rice grain, a late accumulation of H2O2 in leaves, enhanced Xanthomonas oryzae pv. oryzae disease resistance, and suppressed panicle and first internode growth. In oscul3a mutants, PRM-confirmed upregulated molecular switch proteins include lipoxygenases (CM-LOX1 and CM-LOX2), suggesting a novel connection between ferroptosis and rice lesion mimic formation. Rice immunity-associated proteins OsNPR1 and OsNPR3 were shown to interact with each other and have opposing regulatory effects based on the cell death phenotype of osnpr1/oscul3a and osnpr3/oscul3a double mutants. Together, these results describe a network that regulates plant growth, disease resistance, and grain quality that includes the E3 ligase OsCUL3a, cell metabolism-associated molecular switches, and immunity switches OsNPR1 and OsNPR3.
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Affiliation(s)
- Zhiqiang Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
- College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi 341000, People's Republic of China
| | - Qunen Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
| | - Yingxin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
| | - Daibo Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
| | - Xiaodeng Zhan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
| | - Chenwei Deng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
| | - Shihua Cheng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
| | - Liyong Cao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, Zhejiang 310006, People's Republic of China
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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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Venkatesh J, Kang BC. Current views on temperature-modulated R gene-mediated plant defense responses and tradeoffs between plant growth and immunity. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:9-17. [PMID: 30877945 DOI: 10.1016/j.pbi.2019.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/18/2019] [Accepted: 02/07/2019] [Indexed: 05/12/2023]
Abstract
Elevated ambient temperatures will likely be a key consequence of climate change over the next few decades. Adverse climatic changes could make crop plants more vulnerable to a number of biotic and abiotic stresses, which would have a major impact on worldwide food production in the future. Recent studies have indicated that elevated temperatures directly and/or indirectly affect plant-pathogen interactions. Elevated temperatures alter multiple signal transduction pathways related to stress responses in the host plant. High temperatures can also influence plant pathogenesis, but little is known about the molecular mechanisms associated with such effects. An improved understanding of the molecular genetic mechanisms involved in plant immune responses under elevated temperatures will be essential to mitigate the adverse effects of climate change to ensure future food security. In this review, we discuss recent advances in our understanding of the effects of temperature on resistance (R) gene and/or regulators of R genes in plant defense responses and summarize current evidence for tradeoffs between plant growth and immunity.
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Affiliation(s)
- Jelli Venkatesh
- Department of Plant Science, Plant Genomics & Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics & Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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Al Amin GM, Kong K, Sharmin RA, Kong J, Bhat JA, Zhao T. Characterization and Rapid Gene-Mapping of Leaf Lesion Mimic Phenotype of spl-1 Mutant in Soybean ( Glycine max (L.) Merr.). Int J Mol Sci 2019; 20:E2193. [PMID: 31058828 PMCID: PMC6539437 DOI: 10.3390/ijms20092193] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/19/2019] [Accepted: 04/30/2019] [Indexed: 01/08/2023] Open
Abstract
In plants, lesion mimic mutants (LMMs) reveal spontaneous disease-like lesions in the absence of pathogen that constitutes powerful genetic material to unravel genes underlying programmed cell death (PCD), particularly the hypersensitive response (HR). However, only a few LMMs are reported in soybean, and no related gene has been cloned until now. In the present study, we isolated a new LMM named spotted leaf-1 (spl-1) from NN1138-2 cultivar through ethyl methanesulfonate (EMS) treatment. The present study revealed that lesion formation might result from PCD and excessive reactive oxygen species (ROS) accumulation. The chlorophyll content was significantly reduced but antioxidant activities, viz., superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), as well as the malondialdehyde (MDA) contents, were detected higher in spl-1 than in the wild-type. According to segregation analysis of mutant phenotype in two genetic populations, viz., W82×spl-1 and PI378692×spl-1, the spotted leaf phenotype of spl-1 is controlled by a single recessive gene named lm1. The lm1 locus governing mutant phenotype of spl-1 was first identified in 3.15 Mb genomic region on chromosome 04 through MutMap analysis, which was further verified and fine mapped by simple sequence repeat (SSR) marker-based genetic mapping. Genetic linkage analysis narrowed the genomic region (lm1 locus) for mutant phenotype to a physical distance of ~76.23 kb. By searching against the Phytozome database, eight annotated candidate genes were found within the lm1 region. qRT-PCR expression analysis revealed that, among these eight genes, only Glyma.04g242300 showed highly significant expression levels in wild-type relative to the spl-1 mutant. However, sequencing data of the CDS region showed no nucleotide difference between spl-1 and its wild type within the coding regions of these genes but might be in the non-coding regions such as 5' or 3' UTR. Hence, the data of the present study are in favor of Glyma.04g242300 being the possible candidate genes regulating the mutant phenotype of spl-1. However, further validation is needed to prove this function of the gene as well as its role in PCD, which in turn would be helpful to understand the mechanism and pathways involved in HR disease resistance of soybean.
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Affiliation(s)
- G M Al Amin
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
- Department of Botany, Jagannath University, Dhaka 1100, Bangladesh.
| | - Keke Kong
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ripa Akter Sharmin
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiejie Kong
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Javaid Akhter Bhat
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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Zhang Y, Xu K, Pei D, Yu D, Zhang J, Li X, Chen G, Yang H, Zhou W, Li C. ShORR-1, a Novel Tomato Gene, Confers Enhanced Host Resistance to Oidium neolycopersici. FRONTIERS IN PLANT SCIENCE 2019; 10:1400. [PMID: 31787994 PMCID: PMC6854008 DOI: 10.3389/fpls.2019.01400] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/10/2019] [Indexed: 05/17/2023]
Abstract
A previous complementary cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis examined responses to the powdery mildew pathogen Oidium neolycopersici (On) of the resistant cultivar Solanum habrochiates G1.1560, carrying the Ol-1 resistance gene, and susceptible cultivar S. lycopersicum Moneymaker (MM). Among other findings, a differentially expressed transcript-derived fragment (DE-TDF) (M14E72-213) was upregulated in near isogenic line (NIL)-Ol-1, but absent in MM. This DE-TDF showed high homology to a gene of unknown function, which we named ShORR-1 (Solanum habrochaites Oidium Resistance Required-1). However, MM homolog of ShORR-1 (named ShORR-1-M) was still found with 95.26% nucleic acid sequence similarity to ShORR-1 from G1.1560 (named ShORR-1-G); this was because the cut sites of restriction enzymes in the previous complementary cDNA-AFLP analysis was absent in ShORR-1-M and differs at 13 amino acids from ShORR-1-G. Transient expression in onion epidermal cells showed that ShORR-1 is a membrane-localized protein. Virus-induced gene silencing (VIGS) of ShORR-1-G in G1.1560 plants increased susceptibility to On. Furthermore, overexpressing of ShORR-1-G conferred MM with resistance to On, involving extensive hydrogen peroxide accumulation and formation of abnormal haustoria. Knockdown of ShORR-1-M in MM did not affect its susceptibility to On, while overexpressing of ShORR-1-M enhanced MM's susceptibility to On. We also found that changes in transcript levels of six well-known hormone signaling and defense-related genes are involved in ShORR-1-G-mediated resistance to On. The results indicate that ShORR-1-M and ShORR-1-G have antagonistic effects in tomato responses to On, and that ShORR-1 is essential for Ol-1-mediated resistance in tomato.
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Affiliation(s)
- Yi Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou, China
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou, China
| | - Dongli Pei
- Department of Life Science, Shangqiu Normal University, Shangqiu, China
| | - Deshui Yu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou, China
| | - Ju Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou, China
| | - Xiaoli Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou, China
| | - Guo Chen
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou, China
| | - Hui Yang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou, China
| | - Wenjie Zhou
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou, China
| | - Chengwei Li
- Henan Engineering Research Center of Grain Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang, China
- *Correspondence: Chengwei Li,
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