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Wu R, Song K, Jing R, Du L. The de-ubiquitinase UBQUITIN SPECIFIC PROTEASE 15 (UBP15) interacts with the SCF E3 complex adaptor ARABIDOPSIS SKP1 HOMOLOGUE 1 (ASK1) to regulate petal size and fertility in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112112. [PMID: 38750799 DOI: 10.1016/j.plantsci.2024.112112] [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: 11/28/2023] [Revised: 04/14/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Ubiquitination is a pivotal type of post-translational modification, which plays a far-reaching role in plant growth and development, as well as in the response of plants to stress. Just like the two sides of a coin, de-ubiquitination also plays an important role in plant life, which has been gradually discovered in recent years. Here, we demonstrate that the UBQUITIN SPECIFIC PROTEASE 15 (UBP15), which is a UBP-type de-ubiquitinase, interacts with the SCF E3 complex adaptor ARABIDOPSIS SKP1 HOMOLOGUE 1 (ASK1) and influences its protein stability to regulate plant fertility and petal size. The UBP15 is associated with the ASK1 physically, as verified by yeast-two-hybrid (Y2H) and protein pull-down in vitro assays. Disruption of ASK1 by a T-DNA insertion generates some abnormal phenotypes, such as low fertility and small petals. Genetic analysis shows that the UBP15 mutation enhances the low-fertility and small-petal phenotypes of ask1 mutant plants. By proteomic analysis, many types of proteins were identified as potential candidate downstream genes associated with the phenotypes of ubp15 ask1 double mutant plants. Taken together, these findings reveal a molecular relationship between ASK1 and UBP15 and their interaction in the regulation of petal size and fertility, which would benefit in-depth research about the ubiquitin-related pathway in plant physiological processes in the future.
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Affiliation(s)
- Ruihua Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Kaixuan Song
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Ruotong Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China.
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Wang X, Liu X, Song K, Du L. An insight into the roles of ubiquitin-specific proteases in plants: development and growth, morphogenesis, and stress response. FRONTIERS IN PLANT SCIENCE 2024; 15:1396634. [PMID: 38993940 PMCID: PMC11236618 DOI: 10.3389/fpls.2024.1396634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024]
Abstract
Ubiquitination is a highly conserved and dynamic post-translational modification in which protein substrates are modified by ubiquitin to influence their activity, localization, or stability. Deubiquitination enzymes (DUBs) counter ubiquitin signaling by removing ubiquitin from the substrates. Ubiquitin-specific proteases (UBPs), the largest subfamily of DUBs, are conserved in plants, serving diverse functions across various cellular processes, although members within the same group often exhibit functional redundancy. Here, we briefly review recent advances in understanding the biological roles of UBPs, particularly the molecular mechanism by which UBPs regulate plant development and growth, morphogenesis, and stress response, which sheds light on the mechanistic roles of deubiquitination in plants.
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Affiliation(s)
- Xiuwen Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xuan Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kaixuan Song
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Arnau G, Desfontaines L, Ehounou AE, Marie-Magdeleine C, Kouakou AM, Leinster J, Nudol E, Maledon E, Chair H. Quantitative trait loci and candidate genes for physico-chemical traits related to tuber quality in greater yam (Dioscorea alata L.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4872-4879. [PMID: 37400964 DOI: 10.1002/jsfa.12822] [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: 01/18/2023] [Revised: 05/16/2023] [Accepted: 07/04/2023] [Indexed: 07/05/2023]
Abstract
BACKGROUND Starch, dry matter content (DMC), proteins, and sugars are among the major influences on yam tuber quality. Genetic improvement programs need simple, rapid, and low-cost tools to screen large populations. The objectives of this work were, using a quantitative trait loci mapping approach (QTL) on two diploid full-sib segregating populations, (i) to acquire knowledge about the genetic control of these traits; (ii) to identify markers linked to the genomic regions controlling each trait, which are useful for marker-assisted selection (MAS); (iii) to validate the QTLs on a diversity panel; and (iv) to identify candidate genes from the validated QTLs. RESULTS Heritability for all traits was moderately high to high. Significant correlations were observed between traits. A total of 25 QTLs were identified, including six for DMC, six for sugars, six for proteins, and seven for starch. The phenotypic variance explained by individual QTLs ranged from 14.3% to 28.6%. The majority of QTLs were validated on a diversity panel, showing that they are not specific to the genetic background of the progenitors. The approximate physical location of validated QTLs allowed the identification of candidate genes for all studied traits. Those detected for starch content were mainly enzymes involved in starch and sucrose metabolism, whereas those detected for sugars were mainly involved in respiration and glycolysis. CONCLUSION The validated QTLs will be useful for breeding programs using MAS to improve the quality of yam tubers. The putative genes should be useful in providing a better understanding of the physiological and molecular basis of these important tuber quality traits. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Gemma Arnau
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Lucienne Desfontaines
- INRAE, UR 1321 ASTRO Agrosystèmes tropicaux. Centre de recherche Antilles-Guyane, Petit-Bourg, France
| | | | | | - Amani Michel Kouakou
- CNRA, Station de Recherche sur les Cultures Vivrières (SRCV), Bouaké, Côte d'Ivoire
| | - Jocelyne Leinster
- INRAE, UR 1321 ASTRO Agrosystèmes tropicaux. Centre de recherche Antilles-Guyane, Petit-Bourg, France
| | - Elie Nudol
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Petit Bourg, France
| | - Erick Maledon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Petit Bourg, France
| | - Hana Chair
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Fu W, Fan D, Liu S, Bu Y. Genome-wide identification and expression analysis of Ubiquitin-specific protease gene family in maize (Zea mays L.). BMC PLANT BIOLOGY 2024; 24:404. [PMID: 38750451 PMCID: PMC11097515 DOI: 10.1186/s12870-024-04953-5] [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: 12/25/2023] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Ubiquitin-specific proteases (UBPs) are a large family of deubiquitinating enzymes (DUBs). They are widespread in plants and are critical for plant growth, development, and response to external stresses. However, there are few studies on the functional characteristics of the UBP gene family in the important staple crop, maize (Zea mays L.). RESULTS In this study, we performed a bioinformatic analysis of the entire maize genome and identified 45 UBP genes. Phylogenetic analysis indicated that 45 ZmUBP genes can be divided into 15 subfamilies. Analysis of evolutionary patterns and divergence levels indicated that ZmUBP genes were present before the isolation of dicotyledons, were highly conserved and subjected to purifying selection during evolution. Most ZmUBP genes exhibited different expression levels in different tissues and developmental stages. Based on transcriptome data and promoter element analysis, we selected eight ZmUBP genes whose promoters contained a large number of plant hormones and stress response elements and were up-regulated under different abiotic stresses for RT-qPCR analysis, results showed that these genes responded to abiotic stresses and phytohormones to varying degrees, indicating that they play important roles in plant growth and stress response. CONCLUSIONS In this study, the structure, location and evolutionary relationship of maize UBP gene family members were analyzed for the first time, and the ZmUBP genes that may be involved in stress response and plant growth were identified by combining promoter element analysis, transcriptome data and RT-qPCR analysis. This study informs research on the involvement of maize deubiquitination in stress response.
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Affiliation(s)
- Weichao Fu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Delong Fan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, Hangzhou, 311300, China
| | - Yuanyuan Bu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China.
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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Vogel K, Isono E. Deubiquitylating enzymes in Arabidopsis thaliana endocytic protein degradation. Biochem Soc Trans 2024; 52:291-299. [PMID: 38174770 DOI: 10.1042/bst20230561] [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: 11/08/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
The regulation of ubiquitylation is key for plant growth and development, in which the activities of ubiquitylating enzymes as well as deubiquitylating enzymes (DUBs) determine the stability or function of the modified proteins. In contrast with ubiquitylating enzymes, there are less numbers of DUBs. DUBs can be classified into seven protein families according to the amino acid sequence of their catalytic domains. The catalytic domains of animal and plant DUB families show high homology, whereas the regions outside of the catalytic site can vary a lot. By hydrolyzing the ubiquitin molecules from ubiquitylated proteins, DUBs control ubiquitin-dependent selective protein degradation pathways such as the proteasomal-, autophagic-, and endocytic degradation pathways. In the endocytic degradation pathway, DUBs can modulate the endocytic trafficking and thus the stability of plasma membrane proteins including receptors and transporters. To date, three DUB families were shown to control the endocytic degradation pathway namely associated molecule with the SH3 domain of STAM (AMSH) 3, ubiquitin-specific protease (UBP) 12 and UBP13, and ovarian tumor protease (OTU) 11 and OTU12. In this review we will summarize the activity, molecular functions, and target protein of these DUBs and how they contribute to the environmental response of plants.
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Affiliation(s)
- Karin Vogel
- Department of Biology, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Erika Isono
- Department of Biology, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
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Feng H, Tan J, Deng Z. Decoding plant adaptation: deubiquitinating enzymes UBP12 and UBP13 in hormone signaling, light response, and developmental processes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:721-732. [PMID: 37904584 DOI: 10.1093/jxb/erad429] [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: 06/21/2023] [Accepted: 10/26/2023] [Indexed: 11/01/2023]
Abstract
Ubiquitination, a vital post-translational modification in plants, plays a significant role in regulating protein activity, localization, and stability. This process occurs through a complex enzyme cascade that involves E1, E2, and E3 enzymes, leading to the covalent attachment of ubiquitin molecules to substrate proteins. Conversely, deubiquitinating enzymes (DUBs) work in opposition to this process by removing ubiquitin moieties. Despite extensive research on ubiquitination in plants, our understanding of the function of DUBs is still emerging. UBP12 and UBP13, two plant DUBs, have received much attention recently and are shown to play pivotal roles in hormone signaling, light perception, photoperiod responses, leaf development, senescence, and epigenetic transcriptional regulation. This review summarizes current knowledge of these two enzymes, highlighting the central role of deubiquitination in regulating the abundance and activity of critical regulators such as receptor kinases and transcription factors during phytohormone and developmental signaling.
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Affiliation(s)
- Hanqian Feng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Jinjuan Tan
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
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Tang X, Sun F, Zhang N, Rana BB, Kharel R, Luo P, Si H. RNA-seq provides insights into potato deubiquitinase responses to drought stress in seedling stage. FRONTIERS IN PLANT SCIENCE 2023; 14:1268448. [PMID: 37780518 PMCID: PMC10539648 DOI: 10.3389/fpls.2023.1268448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Ubiquitination is a specific protein degradation and reversible post-translational modification process that can be reversed by deubiquitinase (DUBs). DUBs can hydrolyze and release ubiquitin in the substrate protein so that the substrate can avoid degradation or change its activity, and it has an impact on plant growth and development, cell cycle, abiotic stress response, and other biological processes. Transcript sequences of potato varieties "DM1-3", "Atlantic" and "Cooperation-88" downloaded from Potato Genome Resources were used for genome-wide identification of the DUB gene family using Hidden Markov Models and verified in the NCBI CD-Search tool. The characteristics of DUB genes from different potato varieties were analyzed including subcellular localization, gene structural motifs, phylogenetic tree, and sequence homology. Polyethylene glycol 6000 (PEG6000) induced drought stress transcriptome analysis was performed on the "Atlantic", and differentially expressed genes were screened, with emphasis on the characterization of deubiquitinase. DUB genes have a complex gene structure, often with a large number of exons and alternative splicing. Their promoters contain abundant abiotic stress-responsive elements, such as 425 MYC, 325 ABRE, and 320 MYB. There are also a large number of orthologous genes in the DUBs of the three potato varieties, and these genes are often clustered in similar regions on the genome. We performed transcriptome sequencing of the potato under PEG-induced drought stress and analyzed it for the first time using the Atlantic as a reference genome. We identified a total of 6067 down-regulated differentially expressed genes (DEGs) and 4950 up-regulated DEGs under PEG-induced drought stress. We screened the expression of DUBs and observed that 120 DUBs were up-regulated where most of them functioned in the nucleus, and the interacting proteins of DUBs were also localized in the nucleus. We have comprehensively identified and analyzed potato DUBs, and the accurately aligned transcriptome data which will further deepen the understanding of DUBs involved in the regulation of osmotic stress.
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Affiliation(s)
- Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fujun Sun
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Birendra Bahadur Rana
- Nepal Agricultural Research Council, National Potato Research Program, Lalitpur, Nepal
| | - Raju Kharel
- Department of Genetics and Plant Breeding, Agricultural and Forestry University, Chitwan, Nepal
| | - Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Li S, Yao X, Zhang B, Tang H, Lu L. Genome-wide characterization of the U-box gene in Camellia sinensis and functional analysis in transgenic tobacco under abiotic stresses. Gene 2023; 865:147301. [PMID: 36813060 DOI: 10.1016/j.gene.2023.147301] [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: 05/11/2022] [Revised: 12/16/2022] [Accepted: 02/16/2023] [Indexed: 02/22/2023]
Abstract
Plants U-box genes are crucial for plant survival, and they extensively regulate plant growth, reproduction and development as well as coping with stress and other processes. In this study, we identified 92 CsU-box genes through genome-wide analysis in the tea plant (Camellia sinensis), all of them contained the conserved U-box domain and were divided into 5 groups, which supported by the further genes structure analysis. The expression profiles in eight tea plant tissues and under abiotic and hormone stresses were analyzed using the TPIA database. 7 CsU-box genes (CsU-box27/28/39/46/63/70/91) were selected to verify and analyze expression patterns under PEG-induced drought and heat stress in tea plant respectively, the qRT-PCR results showed consistent with transcriptome datasets; and the CsU-box39 were further heterologous expressed in tobacco to perform gene function analysis. Phenotypic analyses of overexpression transgenic tobacco seedlings and physiological experiments revealed that CsU-box39 positively regulated the plant response to drought stress. These results lay a solid foundation for studying the biological function of CsU-box, and will provide breeding strategy basis for tea plant breeders.
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Affiliation(s)
- Shiyu Li
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Xinzhuan Yao
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Baohui Zhang
- Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China
| | - Hu Tang
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China.
| | - Litang Lu
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China.
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Zou T, Li G, Liu M, Liu R, Yang S, Wang K, Lu L, Ye Q, Liu J, Liang J, Deng Q, Wang S, Zhu J, Liang Y, Liu H, Yu X, Sun C, Li P, Li S. A ubiquitin-specific protease functions in regulating cell death and immune responses in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1312-1326. [PMID: 36624579 DOI: 10.1111/pce.14540] [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: 10/17/2022] [Revised: 12/29/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Ubiquitin-specific proteases (UBPs) process deubiquitination in eukaryotic organisms and are widely involved in plant development and responses to environmental stress. However, their role in cell death and plant immunity remains largely unknown. Here, we identified a rice lesion mimic mutant (LMM) and cloned its causative gene, LMM22. Both dysfunction and overexpression of LMM22 gave rise to the hypersensitive response-like cell death, reactive oxygen species bursts, and activated defence responses. LMM22 encodes an active UBP that is localised to the endoplasmic reticulum (ER) and displays a constitutive expression pattern in rice. LMM22 interacts with SPOTTED LEAF 35 (SPL35), a coupling of ubiquitin conjugation to ER degradation domain-containing protein that is known to participate in ubiquitination and the regulation of cell death and disease response in rice. Additional analyses suggest that LMM22 can positively regulate and stabilise the abundance of SPL35 protein likely through its deubiquitination activity. These data therefore improve our understanding of the function of UBP in rice innate immune responses by demonstrating that LMM22 functions as a critical regulator of SPL35 in cell death and disease resistance.
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Affiliation(s)
- Ting Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Gongwen Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Miaomiao Liu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Rui Liu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shangyu Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Kang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Liuhui Lu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiuyu Ye
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiaxu Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yueyang Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huainian Liu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Changhui Sun
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
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10
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Cui Y, Liu D, Zhao Z, Zhang J, Li S, Liu Z. Transcriptome analysis and identification of genes associated with leaf crude protein content in foxtail millet [ Setaria italica (L.) P. Beauv.]. Front Genet 2023; 14:1122212. [PMID: 36741329 PMCID: PMC9895776 DOI: 10.3389/fgene.2023.1122212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/06/2023] [Indexed: 01/22/2023] Open
Abstract
Introduction: Spruce spider mite is a primary insect pest of Chinese chestnut in China and seriously influences its yield and quality. However, the current management against this mite is costly and poorly effective. In previous research, we bred several foxtail millet materials for interplanting with chestnut tree, and found that they had high levels of crude protein (CP) in leaves and attracted spruce spider mite to feed on the leaves, thereby reducing chestnut damage. Methods: In this study, four foxtail millet varieties with significant differences in leaf crude protein content were used for high-throughput sequencing and identification of genes associated with leaf crude protein content. Gene enrichment analyses were carried out to comprehend the functions of these genes and the biological processes in which they are involved. In addition, transcription factors (TFs) were evaluated. Results: 435 differentially expressed genes (DEGs) were identified, suggesting their potential role in crude protein accumulation. Some differentially expressed genes were found to be associated with nitrogen metabolism and ubiquitin-mediated proteolysis pathways. Moreover, we identified 40 TF genes categorized into 11 transcription factor families. Discussion: Our findings represent an important resource that clarifies the mechanisms of accumulation and control of leaf crude protein in foxtail millet, and provide an opportunity for suppression of spruce spider mite attack on Chinese chestnut by interplanting with foxtail millet varieties with high concentrations of leaf crude protein.
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Affiliation(s)
- Yanjiao Cui
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Dan Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crop Sciences, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Zilong Zhao
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Jing Zhang
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Suying Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, China,*Correspondence: Suying Li, ; Zhengli Liu,
| | - Zhengli Liu
- Department of Life Sciences, Tangshan Normal University, Tangshan, China,*Correspondence: Suying Li, ; Zhengli Liu,
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11
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Vogel K, Bläske T, Nagel MK, Globisch C, Maguire S, Mattes L, Gude C, Kovermann M, Hauser K, Peter C, Isono E. Lipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking. Nat Commun 2022; 13:6897. [PMID: 36371501 PMCID: PMC9653390 DOI: 10.1038/s41467-022-34637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
The abundance of plasma membrane-resident receptors and transporters has to be tightly regulated by ubiquitin-mediated endosomal degradation for the proper coordination of environmental stimuli and intracellular signaling. Arabidopsis OVARIAN TUMOR PROTEASE (OTU) 11 and OTU12 are plasma membrane-localized deubiquitylating enzymes (DUBs) that bind to phospholipids through a polybasic motif in the OTU domain. Here we show that the DUB activity of OTU11 and OTU12 towards K63-linked ubiquitin is stimulated by binding to lipid membranes containing anionic lipids. In addition, we show that the DUB activity of OTU11 against K6- and K11-linkages is also stimulated by anionic lipids, and that OTU11 and OTU12 can modulate the endosomal degradation of a model cargo and the auxin efflux transporter PIN2-GFP in vivo. Our results suggest that the catalytic activity of OTU11 and OTU12 is tightly connected to their ability to bind membranes and that OTU11 and OTU12 are involved in the fine-tuning of plasma membrane proteins in Arabidopsis.
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Affiliation(s)
- Karin Vogel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Tobias Bläske
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Marie-Kristin Nagel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Christoph Globisch
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Shane Maguire
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Lorenz Mattes
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christian Gude
- grid.6936.a0000000123222966School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Kovermann
- grid.9811.10000 0001 0658 7699NMR, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Karin Hauser
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christine Peter
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Erika Isono
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
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12
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Jiang R, Zhou S, Da X, Chen T, Xu J, Yan P, Mo X. Ubiquitin-Specific Protease 2 (OsUBP2) Negatively Regulates Cell Death and Disease Resistance in Rice. PLANTS 2022; 11:plants11192568. [PMID: 36235432 PMCID: PMC9571816 DOI: 10.3390/plants11192568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022]
Abstract
Lesion mimic mutants (LMMs) are great materials for studying programmed cell death and immune mechanisms in plants. Various mechanisms are involved in the phenotypes of different LMMs, but few studies have explored the mechanisms linking deubiquitination and LMMs in rice (Oryza sativa). Here, we identified a rice LMM, rust spots rice (rsr1), resulting from the mutation of a single recessive gene. This LMM has spontaneous reddish-brown spots on its leaves, and displays enhanced resistance to both fungal leaf blast (caused by Magnaporthe oryzae) and bacterial blight (caused by Xanthomonas oryzae pv. oryzae). Map-based cloning showed that the mutated gene in rsr1 encodes a Ubiquitin-Specific Protease 2 (OsUBP2). The mutation of OsUBP2 was shown to result in reactive oxygen species (ROS) accumulation, chloroplast structural defects, and programmed cell death, while the overexpression of OsUBP2 weakened rice resistance to leaf blast. OsUBP2 is therefore a negative regulator of immune processes and ROS production. OsUBP2 has deubiquitinating enzyme activity in vitro, and the enzyme active site includes a cysteine at the 234th residue. The ubiquitinated proteomics data of rsr1 and WT provide some possible target protein candidates for OsUBP2.
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13
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Cao Y, Li Y, Wang L, Zhang L, Jiang L. Evolution and function of ubiquitin-specific proteases (UBPs): Insight into seed development roles in tung tree (Vernicia fordii). Int J Biol Macromol 2022; 221:796-805. [PMID: 36037910 DOI: 10.1016/j.ijbiomac.2022.08.163] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
The tung oil produced by the tung tree (Vernicia fordii) provides resources for the manufacture of biodiesel. Ubiquitin-specific proteases (UBPs) are the largest group of deubiquitinases and play key roles in regulating development and stress responses. Here, 21 UBPs were identified in V. fordii, roughly one-half the number found in Manihot esculenta and Hevea brasiliensis. Most UBP duplications are produced from whole-genome duplication (WGD), and significant differences in gene retention existed among Euphorbiaceae. The great majority of UBP-containing blocks in V. fordii, V. montana, Ricinus communis, and Jatropha curcas exhibited extensive conservation with the duplicated regions of M. esculenta and H. brasiliensis. These blocks formed 14 orthologous groups, indicating they shared WGD with UBPs in M. esculenta and H. brasiliensis, but most of these UBPs copies were lost. The UBP orthologs contained significant functional divergence which explained the susceptibility of V. fordii to Fusarium wilt and the resistance of V. montana to Fusarium wilt. The expression patterns and experiments suggested that Vf03G1417 could affect the seed-related traits and positively regulate the seed oil accumulation. This study provided important insights into the evolution of UBPs in Euphorbiaceae and identified important candidate VfUBPs for marker-assisted breeding in V. fordii.
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Affiliation(s)
- Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Yanli Li
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Lin Zhang
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, 430000 Wuhan, China.
| | - Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China.
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Hu H, Cai L, Zhang T, Liu T, Jiang Y, Liu H, Lu Q, Yang J, Chen J. Central Role of Ubiquitination in Wheat Response to CWMV Infection. Viruses 2022; 14:v14081789. [PMID: 36016412 PMCID: PMC9412516 DOI: 10.3390/v14081789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 11/30/2022] Open
Abstract
Ubiquitination is a major post-translational modification (PTM) involved in almost all eukaryotic biological processes and plays an essential role in plant response to pathogen infection. However, to date, large-scale profiling of the changes in the ubiquitome in response to pathogens, especially viruses, in wheat has not been reported. This study aimed to identify the ubiquitinated proteins involved in Chinese wheat mosaic virus (CWMV) infection in wheat using a combination of affinity enrichment and high-resolution liquid chromatography-tandem mass spectroscopy. The potential biological functions of these ubiquitinated proteins were further analyzed using bioinformatics. A total of 2297 lysine ubiquitination sites in 1255 proteins were identified in wheat infected with CWMV, of which 350 lysine ubiquitination sites in 192 proteins were differentially expressed. These ubiquitinated proteins were related to metabolic processes, responses to stress and hormones, plant–pathogen interactions, and ribosome pathways, as assessed via Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Furthermore, we found that the ubiquitination of Ta14-3-3 and TaHSP90, which are essential components of the innate immune system, was significantly enhanced during CWMV infection, which suggested that ubiquitination modification plays a vital role in the regulatory network of the host response to CWMV infection. In summary, our study puts forward a novel strategy for further probing the molecular mechanisms of CWMV infection. Our findings will inform future research to find better, innovative, and effective solutions to deal with CWMV infection in wheat, which is the most crucial and widely used cereal grain crop.
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Affiliation(s)
- Haichao Hu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Linna Cai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Tianye Zhang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Tingting Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yaoyao Jiang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hanhong Liu
- Junan County Bureau of Agriculture and Country, Linyi 276600, China
| | - Qisen Lu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Correspondence: (J.Y.); (J.C.)
| | - Jianping Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Correspondence: (J.Y.); (J.C.)
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15
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Ali S, Khan N, Tang Y. Epigenetic marks for mitigating abiotic stresses in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153740. [PMID: 35716656 DOI: 10.1016/j.jplph.2022.153740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 03/02/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, FL, 32611, USA
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
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16
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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. Int J Genomics 2022; 2022:1092894. [PMID: 35747076 PMCID: PMC9213152 DOI: 10.1155/2022/1092894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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17
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Ubiquitin ligases at the nexus of plant responses to biotic and abiotic stresses. Essays Biochem 2022; 66:123-133. [PMID: 35704617 DOI: 10.1042/ebc20210070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/11/2022] [Accepted: 05/30/2022] [Indexed: 01/15/2023]
Abstract
Plants must cope with an ever-changing environment, including concurrent biotic and abiotic stresses. The ubiquitin-proteasome system (UPS) is intricately involved in regulating signaling events that facilitate cellular changes required to mitigate the detrimental effects of environmental stress. A key component of the UPS are ubiquitin ligases (or E3s) that catalyze the attachment of ubiquitin molecules to select substrate proteins, which are then recognized by the 26S proteasome for degradation. With the identification of substrate proteins, a growing number of E3s are shown to differentially regulate responses to abiotic as well as bioitic stresses. The review discusses select E3s to illustrate the role of ubiquitin ligases as negative and/or positive regulators of responses to both biotic and abiotic stresses.
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18
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Qi H, Xia FN, Xiao S, Li J. TRAF proteins as key regulators of plant development and stress responses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:431-448. [PMID: 34676666 DOI: 10.1111/jipb.13182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Tumor necrosis factor receptor-associated factor (TRAF) proteins are conserved in higher eukaryotes and play key roles in transducing cellular signals across different organelles. They are characterized by their C-terminal region (TRAF-C domain) containing seven to eight anti-parallel β-sheets, also known as the meprin and TRAF-C homology (MATH) domain. Over the past few decades, significant progress has been made toward understanding the diverse roles of TRAF proteins in mammals and plants. Compared to other eukaryotic species, the Arabidopsis thaliana and rice (Oryza sativa) genomes encode many more TRAF/MATH domain-containing proteins; these plant proteins cluster into five classes: TRAF/MATH-only, MATH-BPM, MATH-UBP (ubiquitin protease), Seven in absentia (SINA), and MATH-Filament and MATH-PEARLI-4 proteins, suggesting parallel evolution of TRAF proteins in plants. Increasing evidence now indicates that plant TRAF proteins form central signaling networks essential for multiple biological processes, such as vegetative and reproductive development, autophagosome formation, plant immunity, symbiosis, phytohormone signaling, and abiotic stress responses. Here, we summarize recent advances and highlight future prospects for understanding on the molecular mechanisms by which TRAF proteins act in plant development and stress responses.
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Affiliation(s)
- Hua Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Fan-Nv Xia
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shi Xiao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
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Xie DL, Huang HM, Zhou CY, Liu CX, Kanwar MK, Qi ZY, Zhou J. HsfA1a confers pollen thermotolerance through upregulating antioxidant capacity, protein repair, and degradation in Solanum lycopersicum L. HORTICULTURE RESEARCH 2022; 9:uhac163. [PMID: 36204210 PMCID: PMC9531336 DOI: 10.1093/hr/uhac163] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/22/2022] [Accepted: 07/12/2022] [Indexed: 05/22/2023]
Abstract
The heat shock transcription factors (Hsfs) play critical roles in plant responses to abiotic stresses. However, the mechanism of Hsfs in the regulation of pollen thermotolerance and their specific biological functions and signaling remain unclear. Herein, we demonstrate that HsfA1a played a key role in tomato pollen thermotolerance. Pollen thermotolerance was reduced in hsfA1a mutants but was increased by hsfA1a overexpression, based on pollen viability and germination. Analyzing the whole transcriptome by RNA-seq data, we found that HsfA1a mainly regulated the genes involved in oxidative stress protection, protein homeostasis regulation and protein modification, as well as the response to biological stress in anthers under heat stress. The accumulation of reactive oxygen species in anthers was enhanced in hsfA1a mutants but decreased in HsfA1a-overexpressing lines. Furthermore, HsfA1a bound to the promoter region of genes involved in redox regulation (Cu/Zn-SOD, GST8, and MDAR1), protein repair (HSP17.6A, HSP70-2, HSP90-2, and HSP101) and degradation (UBP5, UBP18, RPN10a, and ATG10) and regulated the expression of these genes in tomato anthers under heat stress. Our findings suggest that HsfA1a maintains pollen thermotolerance and cellular homeostasis by enhancing antioxidant capacity and protein repair and degradation, ultimately improving pollen viability and fertility.
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Affiliation(s)
- Dong-Ling Xie
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Hua-Min Huang
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Can-Yu Zhou
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Chen-Xu Liu
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Mukesh Kumar Kanwar
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Zhen-Yu Qi
- Hainan Institute, Zhejiang University, Sanya, China
- Agricultural Experiment Station, Zhejiang University, Hangzhou 310058, China
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20
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Tang X, Ghimire S, Liu W, Fu X, Zhang H, Sun F, Zhang N, Si H. Genome-wide identification of U-box genes and protein ubiquitination under PEG-induced drought stress in potato. PHYSIOLOGIA PLANTARUM 2022; 174:e13475. [PMID: 34114235 DOI: 10.1111/ppl.13475] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/30/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
Protein ubiquitination is one of the most important posttranslational modifications in eukaryotic cells, and it is involved in a variety of biological processes, including abiotic stress response. The ubiquitination modification is highly specific, which depends on the accurate recognition of substrate proteins by ubiquitin ligase. Plant U-box (PUB) proteins are a class of ubiquitin ligases, multiple members of which have shown to participate in water-deficit stress in Arabidopsis and rice. U-box gene family and large-scale profiling of the ubiquitome in potato has not been reported to date, although it is one of the most important food crops. The identified 66 U-box genes from the potato genome database were unevenly distributed on 10 chromosomes. These StPUBs have a large number of tandem repeat sequences. Analysis of gene expression characteristics revealed that many StPUBs responded to abiotic stress. Three hundred and fourteen lys modification sites were identified under PEG-induced drought stress, which were distributed on 200 proteins, with 25 differential ubiquitination modification sites, most of which were up-regulated. The ubiquitination modification in potato protein was enhanced under PEG-induced drought stress, and U-box ubiquitin ligase was involved. This study provides an overall strategy and rich data set to clarify the effects of ubiquitination on potatoes under PEG-induced drought stress and the ubiquitination modification involved in potato U-box genes in response to PEG-induced drought stress.
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Affiliation(s)
- Xun Tang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shantwana Ghimire
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Weigang Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xue Fu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huanhuan Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Fujun Sun
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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21
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Lim J, Lim CW, Lee SC. Core Components of Abscisic Acid Signaling and Their Post-translational Modification. FRONTIERS IN PLANT SCIENCE 2022; 13:895698. [PMID: 35712559 PMCID: PMC9195418 DOI: 10.3389/fpls.2022.895698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/03/2022] [Indexed: 05/13/2023]
Abstract
Abscisic acid (ABA) is a major phytohormone that regulates plant growth, development, and abiotic/biotic stress responses. Under stress, ABA is synthesized in various plant organs, and it plays roles in diverse adaptive processes, including seed dormancy, growth inhibition, and leaf senescence, by modulating stomatal closure and gene expression. ABA receptor, clade A protein phosphatase 2C (PP2C), and SNF1-related protein kinase 2 (SnRK2) proteins have been identified as core components of ABA signaling, which is initiated via perception of ABA with receptor and subsequent activation or inactivation by phosphorylation/dephosphorylation. The findings of several recent studies have established that the post-translational modification of these components, including phosphorylation and ubiquitination/deubiquitination, play important roles in regulating their activity and stability. In this review, we discuss the functions of the core components of ABA signaling and the regulation of their activities via post-translational modification under normal and stress conditions.
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22
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Lim CW, Baek W, Lee SC. Tobacco ubiquitin-specific protease 12 (NbUBP12) positively modulates drought resistance. PLANT SIGNALING & BEHAVIOR 2021; 16:1974725. [PMID: 34658295 PMCID: PMC9208778 DOI: 10.1080/15592324.2021.1974725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 05/27/2023]
Abstract
Deubiquitination, a type of post-translational modification, cleaves ubiquitin from target proteins, thereby regulating their stability or activity. Deubiquitination enzymes, ubiquitin-specific proteases (UBP/USP), have been reported to be involved in numerous cellular processes in plants, including meristem development, circadian clock regulation, and immunity. In contrast to model plants, however, the functions of UBP in other higher plants remain poorly understood. Here, we isolated a deubiquitination enzyme, ubiquitin-specific protease 12 (NbUBP12), from Nicotiana benthamiana, which shows high sequence homology with the core enzyme regions of UBP12 from other plants. Quantitative reverse-transcription PCR analysis revealed that NbUBP12 gene expression was significantly induced after drought treatment, and its level was higher in seed than in other tissues. Using a virus-induced gene silencing technique, we generated NbUBP12-silenced tobacco plants to analyze NbUBP12 gene function in response to drought stress and found that compared with control plants, NbUBP12-silenced plants exhibited a lower survival rate after exposure to drought stress. In addition, they were characterized by lower leaf surface temperatures and larger stomatal pore size following abscisic acid (ABA) treatment. On the basis of these observations, we suggest that NbUBP12 is involved in modulating drought resistance in N. benthamiana, which is associated with ABA-mediated stomatal closure.
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Affiliation(s)
- Chae Woo Lim
- Department of Life Science (Bk21 Program), Chung-Ang University, SeoulSouth Korea
| | - Woonhee Baek
- Department of Life Science (Bk21 Program), Chung-Ang University, SeoulSouth Korea
| | - Sung Chul Lee
- Department of Life Science (Bk21 Program), Chung-Ang University, SeoulSouth Korea
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Wang T, Ye W, Wang Y, Zhang M, Aihara Y, Kinoshita T. Protease Inhibitor-Dependent Inhibition of Light-Induced Stomatal Opening. FRONTIERS IN PLANT SCIENCE 2021; 12:735328. [PMID: 34567048 PMCID: PMC8462734 DOI: 10.3389/fpls.2021.735328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Stomata in the epidermis of plants play essential roles in the regulation of photosynthesis and transpiration. Stomata open in response to blue light (BL) by phosphorylation-dependent activation of the plasma membrane (PM) H+-ATPase in guard cells. Under water stress, the plant hormone abscisic acid (ABA) promotes stomatal closure via the ABA-signaling pathway to reduce water loss. We established a chemical screening method to identify compounds that affect stomatal movements in Commelina benghalensis. We performed chemical screening using a protease inhibitor (PI) library of 130 inhibitors to identify inhibitors of stomatal movement. We discovered 17 PIs that inhibited light-induced stomatal opening by more than 50%. Further analysis of the top three inhibitors (PI1, PI2, and PI3; inhibitors of ubiquitin-specific protease 1, membrane type-1 matrix metalloproteinase, and matrix metalloproteinase-2, respectively) revealed that these inhibitors suppressed BL-induced phosphorylation of the PM H+-ATPase but had no effect on the activity of phototropins or ABA-dependent responses. The results suggest that these PIs suppress BL-induced stomatal opening at least in part by inhibiting PM H+-ATPase activity but not the ABA-signaling pathway. The targets of PI1, PI2, and PI3 were predicted by bioinformatics analyses, which provided insight into factors involved in BL-induced stomatal opening.
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Affiliation(s)
- Tenghua Wang
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Wenxiu Ye
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yin Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Institute of Ecology, Peking University, Beijing, China
| | - Maoxing Zhang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Department of Horticulture, International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Yusuke Aihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Toshinori Kinoshita
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
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He X, Zhang Q, Li B, Jin Y, Jiang L, Wu R. Network mapping of root-microbe interactions in Arabidopsis thaliana. NPJ Biofilms Microbiomes 2021; 7:72. [PMID: 34493731 PMCID: PMC8423736 DOI: 10.1038/s41522-021-00241-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are often focused on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic bases of microbial interactions that are thought to be important for microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions of Arabidopsis thaliana and find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surrounding A. thaliana root systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs, of which 91 are identified as hub QTLs. Results from gene annotation analysis suggest that most of the hub QTLs detected are in proximity to candidate genes, executing a variety of biological functions in plant growth and development, resilience against pathogens, root development, and abiotic stress resistance. This study provides a new gateway to understand how genetic variation in host plants influences microbial communities and our results could help improve crops by harnessing soil microbes.
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Affiliation(s)
- Xiaoqing He
- grid.66741.320000 0001 1456 856XBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China ,grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qi Zhang
- grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Beibei Li
- grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- grid.66741.320000 0001 1456 856XBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China ,grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- grid.66741.320000 0001 1456 856XBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China ,grid.66741.320000 0001 1456 856XCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China ,grid.29857.310000 0001 2097 4281Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA USA
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Lim CW, Baek W, Lim J, Hong E, Lee SC. Pepper ubiquitin-specific protease, CaUBP12, positively modulates dehydration resistance by enhancing CaSnRK2.6 stability. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1148-1165. [PMID: 34145668 DOI: 10.1111/tpj.15374] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/31/2021] [Accepted: 06/14/2021] [Indexed: 05/27/2023]
Abstract
Abscisic acid (ABA) is a plant hormone that activates adaptive mechanisms to environmental stress conditions. Plant adaptive mechanisms are complex and highly modulated processes induced by stress-responsive proteins; however, the precise mechanisms by which these processes function under adverse conditions remain unclear. Here, we isolated CaUBP12 (Capsicum annuum ubiquitin-specific protease 12) from pepper (C. annuum) leaves. We show that CaUBP12 expression is significantly induced after exposure to abiotic stress treatments. We conducted loss-of-function and gain-of-function genetic studies to elucidate the biological functions of CaUBP12 in response to ABA and dehydration stress. CaUBP12-silenced pepper plants and CaUBP12-overexpressing Arabidopsis plants displayed dehydration-sensitive and dehydration-tolerant phenotypes, respectively; these phenotypes were characterized by regulation of transpirational water loss and stomatal aperture. Under dehydration stress conditions, CaUBP12-silenced pepper plants and CaUBP12-overexpressing Arabidopsis plants exhibited lower and higher expression levels of stress-related genes, respectively, than the control plants. We isolated a CaUBP12 interaction protein, CaSnRK2.6, which is a homolog of Arabidopsis OST1; degradation of this protein was partially inhibited by CaUBP12. Similar to CaUBP12-silenced pepper plants and CaUBP12-overexpressing Arabidopsis plants, CaSnRK2.6-silenced pepper plants and CaSnRK2.6-overexpressing Arabidopsis displayed dehydration-sensitive and dehydration-tolerant phenotypes, respectively. Our findings suggest that CaUBP12 positively modulates the dehydration stress response by suppressing CaSnRK2.6 protein degradation.
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Affiliation(s)
- Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
| | - Woonhee Baek
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
| | - Junsub Lim
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
| | - Eunji Hong
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
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Guo Y, Ren G, Zhang K, Li Z, Miao Y, Guo H. Leaf senescence: progression, regulation, and application. MOLECULAR HORTICULTURE 2021; 1:5. [PMID: 37789484 PMCID: PMC10509828 DOI: 10.1186/s43897-021-00006-9] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 05/24/2023]
Abstract
Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.
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Affiliation(s)
- Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 Shandong China
| | - Guodong Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Kewei Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 Zhejiang China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055 Guangdong China
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Xu M, Jin P, Liu T, Gao S, Zhang T, Zhang F, Han X, He L, Chen J, Yang J. Genome-wide identification and characterization of UBP gene family in wheat ( Triticum aestivum L.). PeerJ 2021; 9:e11594. [PMID: 34178465 PMCID: PMC8212830 DOI: 10.7717/peerj.11594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/20/2021] [Indexed: 12/25/2022] Open
Abstract
Ubiquitination is essential for plant growth and development. Deubiquitination cooperates with ubiquitination to regulate the ubiquitination levels of target proteins. The ubiquitin-specific protease (UBP) family is the largest group of deubiquitinases (DUBs), which perform extensive and significant roles in eukaryotic organisms. However, the UBP genes in wheat (TaUBPs) are not identified, and the functions of TaUBPs are unknown. The present study identified 97 UBP genes in the whole genome of T. aestivum. These genes were divided into 15 groups and non-randomly distributed on chromosomes of T. aestivum. Analyses of evolutionary patterns revealed that TaUBPs mainly underwent purification selection. The studies of cis-acting regulatory elements indicated that they might be involved in response to hormones. Quantitative real-time PCR (qRT-PCR) results showed that TaUBPs were differentially expressed in different tissues. Besides, several TaUBPs were significantly up-regulated when plants were treated with salicylic acid (SA), implying that these DUBs may play a role in abiotic stress responses in plants and few TaUBPs displayed differential expression after viral infection. Furthermore, TaUBP1A.1 (TraesCS1A02G432600.1) silenced by virus-induced gene silencing (VIGS) facilitates Chinese wheat mosaic virus (CWMV) infection in wheat, indicating that TaUBP1A.1 may be involved in a defense mechanism against viruses. This study comprehensively analyzed the UBP gene family in wheat and provided a basis for further research of TaUBPs functions in wheat plant response to viral infection.
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Affiliation(s)
- Miaoze Xu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Peng Jin
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tingting Liu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shiqi Gao
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tianye Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Fan Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Xiaolei Han
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Long He
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
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Label-free quantitative proteomics of Sorghum bicolor reveals the proteins strengthening plant defense against insect pest Chilo partellus. Proteome Sci 2021; 19:6. [PMID: 33810819 PMCID: PMC8019186 DOI: 10.1186/s12953-021-00173-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spotted stem borer- Chilo partellus - a Lepidopteran insect pest of Sorghum bicolor is responsible for major economic losses. It is an oligophagous pest, which bores through the plant stem, causing 'deadheart' and hampering the development of the main cob. We applied a label-free quantitative proteomics approach on three genotypes of S. bicolor with differential resistance/ susceptibility to insect pests, intending to identify the S. bicolor's systemic protein complement contributing to C. partellus tolerance. METHODS The proteomes of S. bicolor with variable resistance to insect pests, ICSV700, IS2205 (resistant) and Swarna (susceptible) were investigated and compared using label-free quantitative proteomics to identify putative leaf proteins contributing to resistance to C. partellus. RESULTS The multivariate analysis on a total of 967 proteins led to the identification of proteins correlating with insect resistance/susceptibility of S. bicolor. Upon C. partellus infestation S. bicolor responded by suppression of protein and amino acid biosynthesis, and induction of proteins involved in maintaining photosynthesis and responding to stresses. The gene ontology analysis revealed that C. partellus-responsive proteins in resistant S. bicolor genotypes were mainly involved in stress and defense, small molecule biosynthesis, amino acid metabolism, catalytic and translation regulation activities. At steady-state, the resistant S. bicolor genotypes displayed at least two-fold higher numbers of unique proteins than the susceptible genotype Swarna, mostly involved in catalytic activities. Gene expression analysis of selected candidates was performed on S. bicolor by artificial induction to mimic C. partellus infestation. CONCLUSION The collection of identified proteins differentially expressed in resistant S. bicolor, are interesting candidates for further elucidation of their role in defense against insect pests.
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Gowda M, Makumbi D, Das B, Nyaga C, Kosgei T, Crossa J, Beyene Y, Montesinos-López OA, Olsen MS, Prasanna BM. Genetic dissection of Striga hermonthica (Del.) Benth. resistance via genome-wide association and genomic prediction in tropical maize germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:941-958. [PMID: 33388884 PMCID: PMC7925482 DOI: 10.1007/s00122-020-03744-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/02/2020] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE Genome-wide association revealed that resistance to Striga hermonthica is influenced by multiple genomic regions with moderate effects. It is possible to increase genetic gains from selection for Striga resistance using genomic prediction. Striga hermonthica (Del.) Benth., commonly known as the purple witchweed or giant witchweed, is a serious problem for maize-dependent smallholder farmers in sub-Saharan Africa. Breeding for Striga resistance in maize is complicated due to limited genetic variation, complexity of resistance and challenges with phenotyping. This study was conducted to (i) evaluate a set of diverse tropical maize lines for their responses to Striga under artificial infestation in three environments in Kenya; (ii) detect quantitative trait loci associated with Striga resistance through genome-wide association study (GWAS); and (iii) evaluate the effectiveness of genomic prediction (GP) of Striga-related traits. An association mapping panel of 380 inbred lines was evaluated in three environments under artificial Striga infestation in replicated trials and genotyped with 278,810 single-nucleotide polymorphism (SNP) markers. Genotypic and genotype x environment variations were significant for measured traits associated with Striga resistance. Heritability estimates were moderate (0.42) to high (0.92) for measured traits. GWAS revealed 57 SNPs significantly associated with Striga resistance indicator traits and grain yield (GY) under artificial Striga infestation with low to moderate effect. A set of 32 candidate genes physically near the significant SNPs with roles in plant defense against biotic stresses were identified. GP with different cross-validations revealed that prediction of performance of lines in new environments is better than prediction of performance of new lines for all traits. Predictions across environments revealed high accuracy for all the traits, while inclusion of GWAS-detected SNPs led to slight increase in the accuracy. The item-based collaborative filtering approach that incorporates related traits evaluated in different environments to predict GY and Striga-related traits outperformed GP for Striga resistance indicator traits. The results demonstrated the polygenic nature of resistance to S. hermonthica, and that implementation of GP in Striga resistance breeding could potentially aid in increasing genetic gain for this important trait.
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Affiliation(s)
- Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya.
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Christine Nyaga
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Titus Kosgei
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
- Moi University, P. O. Box 3900-30100, Eldoret, Kenya
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, D.F, Mexico
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | | | - Michael S Olsen
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
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Zhang YM, Guo P, Xia X, Guo H, Li Z. Multiple Layers of Regulation on Leaf Senescence: New Advances and Perspectives. FRONTIERS IN PLANT SCIENCE 2021; 12:788996. [PMID: 34938309 PMCID: PMC8685244 DOI: 10.3389/fpls.2021.788996] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/03/2021] [Indexed: 05/22/2023]
Abstract
Leaf senescence is the last stage of leaf development and is an orderly biological process accompanied by degradation of macromolecules and nutrient recycling, which contributes to plant fitness. Forward genetic mutant screening and reverse genetic studies of senescence-associated genes (SAGs) have revealed that leaf senescence is a genetically regulated process, and the initiation and progression of leaf senescence are influenced by an array of internal and external factors. Recently, multi-omics techniques have revealed that leaf senescence is subjected to multiple layers of regulation, including chromatin, transcriptional and post-transcriptional, as well as translational and post-translational levels. Although impressive progress has been made in plant senescence research, especially the identification and functional analysis of a large number of SAGs in crop plants, we still have not unraveled the mystery of plant senescence, and there are some urgent scientific questions in this field, such as when plant senescence is initiated and how senescence signals are transmitted. This paper reviews recent advances in the multiple layers of regulation on leaf senescence, especially in post-transcriptional regulation such as alternative splicing.
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Affiliation(s)
- Yue-Mei Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pengru Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zhonghai Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Zhonghai Li,
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Tang X, Ghimire S, Liu W, Fu X, Zhang H, Zhang N, Si H. Potato E3 ubiquitin ligase PUB27 negatively regulates drought tolerance by mediating stomatal movement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:557-563. [PMID: 32912489 DOI: 10.1016/j.plaphy.2020.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/01/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
The ubiquitin-proteasome system (UPS) is one of the main ways of eukaryotic protein degradation and post-translational modification. It has proven as an essential process for plants to respond to abiotic stresses. Plant U-box (PUB) protein acts as a ubiquitin ligase, which recognizes and ubiquitinates the target proteins. Many PUBs have been involved in water stress in Arabidopsis and rice, but similar comprehensive studies in potato remained limited. In this study, the overexpressed and interfered transgenic potato plants of StPUB27 were obtained and their performances were evaluated under osmotic stress. The result showed that overexpression of StPUB27 accelerated the dehydration of detached leaves companied with greater stomatal conductance, while the down-regulated StPUB27 expression by RNA interference (RNAi) showed a smaller stomatal conductance and a lower rate of water loss in detached leaves, thus showing higher tolerance to osmotic stress. In addition, no significant changes in the proline content were observed between StPUB27 overexpressed and RNAi potato plants. The result demonstrated that potato E3 ubiquitin ligase PUB27 may negatively regulate drought tolerance by mediating stomatal conductance.
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Affiliation(s)
- Xun Tang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Shantwana Ghimire
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China; College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Weigang Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China; College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Xue Fu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Huanhuan Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Ning Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.
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Vanhaeren H, Chen Y, Vermeersch M, De Milde L, De Vleeschhauwer V, Natran A, Persiau G, Eeckhout D, De Jaeger G, Gevaert K, Inzé D. UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2. eLife 2020; 9:52276. [PMID: 32209225 PMCID: PMC7141810 DOI: 10.7554/elife.52276] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Protein ubiquitination is a very diverse post-translational modification leading to protein degradation or delocalization, or altering protein activity. In Arabidopsis thaliana, two E3 ligases, BIG BROTHER (BB) and DA2, activate the latent peptidases DA1, DAR1 and DAR2 by mono-ubiquitination at multiple sites. Subsequently, these activated peptidases destabilize various positive growth regulators. Here, we show that two ubiquitin-specific proteases, UBP12 and UBP13, deubiquitinate DA1, DAR1 and DAR2, hence reducing their peptidase activity. Overexpression of UBP12 or UBP13 strongly decreased leaf size and cell area, and resulted in lower ploidy levels. Mutants in which UBP12 and UBP13 were downregulated produced smaller leaves that contained fewer and smaller cells. Remarkably, neither UBP12 nor UBP13 were found to be cleavage substrates of the activated DA1. Our results therefore suggest that UBP12 and UBP13 work upstream of DA1, DAR1 and DAR2 to restrict their protease activity and hence fine-tune plant growth and development.
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Affiliation(s)
- Hannes Vanhaeren
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium.,VIB Center for Medical Biotechnology, Albert Baertsoenkaai, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai, Ghent, Belgium
| | - Ying Chen
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Mattias Vermeersch
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Liesbeth De Milde
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Valerie De Vleeschhauwer
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Annelore Natran
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Geert Persiau
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Dominique Eeckhout
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Geert De Jaeger
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Albert Baertsoenkaai, Ghent, Belgium
| | - Dirk Inzé
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
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33
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Que Y, Xu Z, Wang C, Lv W, Yue X, Xu L, Tang S, Dai H, Wang Z. The putative deubiquitinating enzyme MoUbp4 is required for infection-related morphogenesis and pathogenicity in the rice blast fungus Magnaporthe oryzae. Curr Genet 2019; 66:561-576. [PMID: 31872271 DOI: 10.1007/s00294-019-01049-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 11/28/2022]
Abstract
Ubiquitination is a key regulatory mechanism that affects numerous important biological processes, including cellular differentiation and pathogenesis in eukaryotic cells. Attachment of proteins to ubiquitin is reversed by specialized proteases, deubiquitinating enzymes (DUBs), which are essential for precursor processing, maintaining ubiquitin homeostasis and promoting protein degradation by recycling ubiquitins. Here, we report the identification of a novel non-pathogenic T-DNA-tagged mutant T612 of Magnaporthe oryzae with a single insertion in the second exon of MoUBP4, which encodes a putative ubiquitin carboxyl-terminal hydrolase. Targeted gene deletion mutants of MoUBP4 are significantly reduced in mycelial growth, conidiation, and increased in tolerance to SDS and CR (Congo red) cell-wall damage. The ΔMoubp4 mutants are blocked in penetration and invasive growth, which results in the loss of pathogenicity. Many conidia produced by the ΔMoubp4 mutants are unable to form appressoria and mobilization and degradation of glycogen and lipid droplets are significantly delayed. Moreover, immunohybridization analysis revealed that total protein ubiquitination levels of the null mutants were significantly increased, indicating that MoUbp4 functions as a deubiquitination enzyme. Taken together, we conclude that MoUbp4 is required for deubiquitination, infection-related morphogenesis and pathogenicity in M. oryzae.
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Affiliation(s)
- Yawei Que
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhe Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Chunyan Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Wuyun Lv
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaofeng Yue
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Lin Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Shuai Tang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Han Dai
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhengyi Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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34
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Wu R, Zheng W, Tan J, Sammer R, Du L, Lu C. Protein partners of plant ubiquitin-specific proteases (UBPs). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:227-236. [PMID: 31630936 DOI: 10.1016/j.plaphy.2019.08.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/16/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
As one type of deubiquitinases (DUBs), ubiquitin-specific proteases (UBPs) play an extensive and significant role in plant life involving the regulation of plant development and stress responses. However, comprehensive studies are still needed to determine the functional mechanisms, which are largely unclear. Here, we summarized recent progress of plant UBPs' functional partners, particularly the molecular mechanisms by which UBPs work with their partners. We believe that functional analyses of UBPs and their partners will provide new insights into protein deubiquitination and lead to a better understanding of the physiological roles of UBPs in plants.
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Affiliation(s)
- Ruihua Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wenqing Zheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jinyi Tan
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rana Sammer
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Liang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Cunfu Lu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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35
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Hayama R, Yang P, Valverde F, Mizoguchi T, Furutani-Hayama I, Vierstra RD, Coupland G. Ubiquitin carboxyl-terminal hydrolases are required for period maintenance of the circadian clock at high temperature in Arabidopsis. Sci Rep 2019; 9:17030. [PMID: 31745110 PMCID: PMC6863813 DOI: 10.1038/s41598-019-53229-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/28/2019] [Indexed: 12/18/2022] Open
Abstract
Protein ubiquitylation participates in a number of essential cellular processes including signal transduction and transcription, often by initiating the degradation of specific substrates through the 26S proteasome. Within the ubiquitin-proteasome system, deubiquitylating enzymes (DUBs) not only help generate and maintain the supply of free ubiquitin monomers, they also directly control functions and activities of specific target proteins by modulating the pool of ubiquitylated species. Ubiquitin carboxyl-terminal hydrolases (UCHs) belong to an enzymatic subclass of DUBs, and are represented by three members in Arabidopsis, UCH1, UCH2 and UCH3. UCH1 and UCH2 influence auxin-dependent developmental pathways in Arabidopsis through their deubiquitylation activities, whereas biological and enzymatic functions of UCH3 remain unclear. Here, we demonstrate that Arabidopsis UCH3 acts to maintain the period of the circadian clock at high temperatures redundantly with UCH1 and UCH2. Whereas single uch1, uch2 and uch3 mutants have weak circadian phenotypes, the triple uch mutant displays a drastic lengthening of period at high temperatures that is more extreme than the uch1 uch2 double mutant. UCH3 also possesses a broad deubiquitylation activity against a range of substrates that link ubiquitin via peptide and isopeptide linkages. While the protein target(s) of UCH1-3 are not yet known, we propose that these DUBs act on one or more factors that control period length of the circadian clock through removal of their bound ubiquitin moieties, thus ensuring that the clock oscillates with a proper period even at elevated temperatures.
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Affiliation(s)
- Ryosuke Hayama
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829, Cologne, Germany. .,Department of Natural Sciences, International Christian University, 3-10-2 Osawa, Mitaka, 181-8585, Tokyo, Japan.
| | - Peizhen Yang
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,, Bayer Crop Science, 800 N Lindbergh Blvd, St Louis, Missouri, 63146, USA
| | - Federico Valverde
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829, Cologne, Germany.,Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 49th Américo Vespucio Avenue, Sevilla, 41092, Spain
| | - Tsuyoshi Mizoguchi
- Department of Natural Sciences, International Christian University, 3-10-2 Osawa, Mitaka, 181-8585, Tokyo, Japan
| | - Ikuyo Furutani-Hayama
- Department of Natural Sciences, International Christian University, 3-10-2 Osawa, Mitaka, 181-8585, Tokyo, Japan
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri, 63130, USA
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829, Cologne, Germany.
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36
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Wu R, Shi Y, Zhang Q, Zheng W, Chen S, Du L, Lu C. Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo ( Phyllostachys edulis). Int J Mol Sci 2019; 20:E4309. [PMID: 31484390 PMCID: PMC6747111 DOI: 10.3390/ijms20174309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 02/02/2023] Open
Abstract
The largest group of deubiquitinases-ubiquitin-specific proteases (UBPs)-perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study has been conducted in moso bamboo (Phyllostachys edulis). In this study, the genome-wide identification, classification, gene, protein, promoter region characterization, divergence time, and expression pattern analyses of the UBPs in moso bamboo were conducted. In total, 48 putative UBP genes were identified in moso bamboo, which were divided into 14 distinct subfamilies in accordance with a comparative phylogenetic analysis using 132 full-length protein sequences, including 48, 27, 25, and 32 sequences from moso bamboo, A. thaliana, rice (Oryza sativa), and purple false brome (Brachypodium distachyon), respectively. Analyses of the evolutionary patterns and divergence levels revealed that the PeUBP genes experienced a duplication event approximately 15 million years ago and that the divergence between PeUBP and OsUBP occurred approximately 27 million years ago. Additionally, several PeUBP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating their potential roles in abiotic stress responses in plants.
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Affiliation(s)
- Ruihua Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yanrong Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qian Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wenqing Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shaoliang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Liang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Cunfu Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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37
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Lee CM, Li MW, Feke A, Liu W, Saffer AM, Gendron JM. GIGANTEA recruits the UBP12 and UBP13 deubiquitylases to regulate accumulation of the ZTL photoreceptor complex. Nat Commun 2019; 10:3750. [PMID: 31434902 PMCID: PMC6704089 DOI: 10.1038/s41467-019-11769-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/29/2019] [Indexed: 01/01/2023] Open
Abstract
ZEITLUPE (ZTL), a photoreceptor with E3 ubiquitin ligase activity, communicates end-of-day light conditions to the plant circadian clock. It still remains unclear how ZTL protein accumulates in the light but does not destabilize target proteins before dusk. Two deubiquitylating enzymes, UBIQUITIN-SPECIFIC PROTEASE 12 and 13 (UBP12 and UBP13), which regulate clock period and protein ubiquitylation in a manner opposite to ZTL, associate with the ZTL protein complex. Here we demonstrate that the ZTL interacting partner, GIGANTEA (GI), recruits UBP12 and UBP13 to the ZTL photoreceptor complex. We show that loss of UBP12 and UBP13 reduces ZTL and GI protein levels through a post-transcriptional mechanism. Furthermore, a ZTL target protein is unable to accumulate to normal levels in ubp mutants. This demonstrates that the ZTL photoreceptor complex contains both ubiquitin-conjugating and -deconjugating enzymes, and that these two opposing enzyme types are necessary for circadian clock pacing. This shows that deubiquitylating enzymes are a core element of circadian clocks, conserved from plants to animals. The daily accumulation of the ZEITLUPE (ZTL) photoreceptor/E3 ubiquitin ligase relies on a light-dependent interaction with GIGANTEA (GI). Here the authors show that GI recruits two deubiquitylases to help stabilize the ZTL-GI complex during the day and likely counterbalance the activity of ZTL.
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Affiliation(s)
- Chin-Mei Lee
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Man-Wah Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Ann Feke
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Wei Liu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Adam M Saffer
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Joshua M Gendron
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA.
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38
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Pan W, Wu Y, Xie Q. Regulation of Ubiquitination Is Central to the Phosphate Starvation Response. TRENDS IN PLANT SCIENCE 2019; 24:755-769. [PMID: 31176527 DOI: 10.1016/j.tplants.2019.05.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 05/22/2023]
Abstract
As sessile organisms, plants have developed numerous strategies to overcome the limiting availability of the essential nutrient phosphate in nature. Recent studies reveal that post-translational modification (PTM) by ubiquitination is an important and central regulation mechanism in the plant phosphate starvation response (PSR). Ubiquitination precisely modulates the stability and trafficking of proteins in response to the heterogeneous phosphate supplement. Induction of autophagy provides novel insights into the molecular mechanisms under phosphate starvation. In this review, we present and discuss novel findings on the regulation of diverse PSRs through ubiquitination. Resolving these regulation mechanisms will pave the way to improve phosphate acquisition and utilization efficiency in crops.
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Affiliation(s)
- Wenbo Pan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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39
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Park SH, Jeong JS, Seo JS, Park BS, Chua NH. Arabidopsis ubiquitin-specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency. THE NEW PHYTOLOGIST 2019; 223:1447-1460. [PMID: 31050353 DOI: 10.1111/nph.15879] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/18/2019] [Indexed: 05/09/2023]
Abstract
Nitrogen deficiency (-N) in plants triggers leaf senescence which is regulated by the transcription factor ORE1. Little is known about post-translational regulation of ORE1 in this process. Here, we show that UBP12/UBP13 (ubiquitin-specific protease 12/13) antagonize the action of NLA (nitrogen limitation adaptation) E3 ligase to maintain ORE1 homeostasis. In vitro pull-down and in vivo co-immunoprecipitation assays demonstrated specific binding between UBP12/UBP13 and ORE1. We further analyzed in various genotypes total Chl content and expression levels of senescence-related genes under -N conditions. We found that UBP12/UBP13 can deubiquitinate polyubiquitinated ORE1 in vitro and increase the stability of ORE1 in vivo in MG132/cycloheximide-chase experiments. Plants overexpressing UBP12/UBP13 display accelerated leaf senescence which is reversed by the ore1 mutation. By contrast, the senescence phenotype of plants overexpressing ORE1 is exacerbated by UBP12/UBP13 overexpression. The expression of senescence-related genes tracks the senescence phenotype. ORE1 protein levels can be elevated by UBP12/UBP13 overexpression but decreased in ubp12-2w/13-3. In conclusion, UBP12/UBP13 deubiquitinate ORE1 to stabilize this transcription factor and promote its activity as a positive regulator for leaf senescence under -N conditions. Our study shows that UBP12/UBP13 counteracts the effect of NLA E3 ligase to accelerate leaf senescence under nitrogen starvation.
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Affiliation(s)
- Su-Hyun Park
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jin Seo Jeong
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jun Sung Seo
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Bong Soo Park
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
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40
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Yang X, Guo W, Li F, Sunter G, Zhou X. Geminivirus-Associated Betasatellites: Exploiting Chinks in the Antiviral Arsenal of Plants. TRENDS IN PLANT SCIENCE 2019; 24:519-529. [PMID: 31003895 DOI: 10.1016/j.tplants.2019.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/21/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
Betasatellites are a diverse group of circular single-stranded DNA satellites frequently associated with begomoviruses belonging to the family Geminiviridae. Challenged with a geminivirus-betasatellite infection, plants have employed sophisticated defense mechanisms to protect themselves. Betasatellites, in turn, employ mechanisms to antagonize these plant antiviral pathways. In this review, we focus on the anti-geminiviral immune pathways present both in plants and whiteflies. We also outline the counter-defensive strategies deployed by betasatellites to overcome the host defenses and initiate a successful infection. Finally, we discuss the outcomes of the opposing forces of plant immunity and betasatellite-mediated antagonism in the context of an evolutionary arms race. Understanding of the molecular dialog between plants and betasatellites will likely allow for the development of novel antiviral strategies.
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Affiliation(s)
- Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wei Guo
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Garry Sunter
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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41
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Liu H, Li X, Yan G, Lun R. Knockdown of USP14 inhibits PDGF-BB-induced vascular smooth muscle cell dedifferentiation via inhibiting mTOR/P70S6K signaling pathway. RSC Adv 2019; 9:36649-36657. [PMID: 35539036 PMCID: PMC9075170 DOI: 10.1039/c9ra04726c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/30/2019] [Indexed: 12/18/2022] Open
Abstract
Atherosclerosis is a chronic progressive cardiovascular disease, which may result in many clinical consequences. Ubiquitin-specific protease 14 (USP14), a member of the USP family, has been found to be involved in cardiovascular disease. In the present study, we aimed to explore the role of USP14 in atherosclerosis. The results showed that USP14 expression was markedly increased in atherosclerotic tissues as compared to control tissues. Then we next examined the role of USP14 in primary human aortic smooth muscle cells (HASMCs) in response to PDGF-BB stimulation. The results demonstrated that PDGF-BB induced the USP14 expression in a dose- and time-dependent manner. Knockdown of USP14 in HASMCs suppressed PDGF-BB-induced proliferation and migration of HASMCs. The expressions of VSMCs markers including α-SMA, calponin and SM-MHC were markedly increased by knockdown of USP14, indicating that USP14 knockdown suppressed phenotypic modulation of HASMCs. However, USP14 overexpression exhibited the opposite effects. Furthermore, PDGF-BB-induced phosphorylation of mTOR and P70S6K in HASMCs was prevented by knockdown of USP14. In addition, MHY-1485, an activator of mTOR signaling, reversed the effects of USP14 knockdown on PDGF-BB-induced HASMCs. These data suggested that knockdown of USP14 prevented PDGF-BB-induced proliferation, migration, and phenotypic modulation of HASMCs via inhibiting the mTOR/P70S6K signaling pathway. Atherosclerosis is a chronic progressive cardiovascular disease, which may result in many clinical consequences.![]()
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Affiliation(s)
- Hongbin Liu
- Department of Laboratory
- The First Affiliated Hospital of Henan Polytechnic University
- The Second People's Hospital of Jiaozuo
- Jiaozuo 454001
- P. R. China
| | - Xiaoliang Li
- Department of Laboratory
- The First Affiliated Hospital of Henan Polytechnic University
- The Second People's Hospital of Jiaozuo
- Jiaozuo 454001
- P. R. China
| | - Guobei Yan
- Department of Laboratory
- The First Affiliated Hospital of Henan Polytechnic University
- The Second People's Hospital of Jiaozuo
- Jiaozuo 454001
- P. R. China
| | - Ruihua Lun
- Department of Laboratory
- Jiaozuo Maternal and Children's Hospital
- Jiaozuo 454001
- P. R. China
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42
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Al Khateeb WM, Sher AA, Marcus JM, Schroeder DF. UVSSA, UBP12, and RDO2/TFIIS Contribute to Arabidopsis UV Tolerance. FRONTIERS IN PLANT SCIENCE 2019; 10:516. [PMID: 31105721 PMCID: PMC6492544 DOI: 10.3389/fpls.2019.00516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/03/2019] [Indexed: 05/03/2023]
Abstract
Plant DNA is damaged by exposure to solar radiation, which includes ultraviolet (UV) rays. UV damaged DNA is repaired either by photolyases, using visible light energy, or by nucleotide excision repair (NER), also known as dark repair. NER consists of two subpathways: global genomic repair (GGR), which repairs untranscribed DNA throughout the genome, and transcription-coupled repair (TCR), which repairs transcribed DNA. In mammals, CSA, CSB, UVSSA, USP7, and TFIIS have been implicated in TCR. Arabidopsis homologs of CSA (AtCSA-1/2) and CSB (CHR8) have previously been shown to contribute to UV tolerance. Here we examine the role of Arabidopsis homologs of UVSSA, USP7 (UBP12/13), and TFIIS (RDO2) in UV tolerance. We find that loss of function alleles of UVSSA, UBP12, and RDO2 exhibit increased UV sensitivity in both seedlings and adults. UV sensitivity in atcsa-1, uvssa, and ubp12 mutants is specific to dark conditions, consistent with a role in NER. Interestingly, chr8 mutants exhibit UV sensitivity in both light and dark conditions, suggesting that the Arabidopsis CSB homolog may play a role in both NER and light repair. Overall our results indicate a conserved role for UVSSA, USP7 (UBP12), and TFIIS (RDO2) in TCR.
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Affiliation(s)
| | - Annan A Sher
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Jeffery M Marcus
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Dana F Schroeder
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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Vu LD, Gevaert K, De Smet I. Protein Language: Post-Translational Modifications Talking to Each Other. TRENDS IN PLANT SCIENCE 2018; 23:1068-1080. [PMID: 30279071 DOI: 10.1016/j.tplants.2018.09.004] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/31/2018] [Accepted: 09/10/2018] [Indexed: 05/21/2023]
Abstract
Post-translational modifications (PTMs) are at the heart of many cellular signaling events. Apart from a single regulatory PTM, there are also PTMs that function in orchestrated manners. Such PTM crosstalk usually serves as a fine-tuning mechanism to adjust cellular responses to the slightest changes in the environment. While PTM crosstalk has been studied in depth in various species; in plants, this field is just emerging. In this review, we discuss recent studies on crosstalk between three of the most common protein PTMs in plant cells, being phosphorylation, ubiquitination, and sumoylation, and we highlight the diverse underlying mechanisms as well as signaling outputs of such crosstalk.
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Affiliation(s)
- Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium; These authors contributed equally. https://twitter.com/KrisGevaert_VIB
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium; These authors contributed equally.
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The cloak, dagger, and shield: proteases in plant-pathogen interactions. Biochem J 2018; 475:2491-2509. [PMID: 30115747 DOI: 10.1042/bcj20170781] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 01/03/2023]
Abstract
Plants sense the presence of pathogens or pests through the recognition of evolutionarily conserved microbe- or herbivore-associated molecular patterns or specific pathogen effectors, as well as plant endogenous danger-associated molecular patterns. This sensory capacity is largely mediated through plasma membrane and cytosol-localized receptors which trigger complex downstream immune signaling cascades. As immune signaling outputs are often associated with a high fitness cost, precise regulation of this signaling is critical. Protease-mediated proteolysis represents an important form of pathway regulation in this context. Proteases have been widely implicated in plant-pathogen interactions, and their biochemical mechanisms and targets continue to be elucidated. During the plant and pathogen arms race, specific proteases are employed from both the plant and the pathogen sides to contribute to either defend or invade. Several pathogen effectors have been identified as proteases or protease inhibitors which act to functionally defend or camouflage the pathogens from plant proteases and immune receptors. In this review, we discuss known protease functions and protease-regulated signaling processes involved in both sides of plant-pathogen interactions.
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March E, Farrona S. Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones. FRONTIERS IN PLANT SCIENCE 2017; 8:2274. [PMID: 29387079 PMCID: PMC5776116 DOI: 10.3389/fpls.2017.02274] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/29/2017] [Indexed: 05/11/2023]
Abstract
Selective degradation of proteins in the cell occurs through ubiquitination, which consists of post-translational deposition of ubiquitin on proteins to target them for degradation by proteases. However, ubiquitination does not only impact on protein stability, but promotes changes in their functions. Whereas the deposition of ubiquitin has been amply studied and discussed, the antagonistic activity, deubiquitination, is just emerging and the full model and players involved in this mechanism are far from being completely understood. Nevertheless, it is the dynamic balance between ubiquitination and deubiquitination that is essential for the development and homeostasis of organisms. In this review, we present a detailed analysis of the members of the deubiquitinase (DUB) superfamily in plants and its division in different clades. We describe current knowledge in the molecular and functional characterisation of DUB proteins, focusing primarily on Arabidopsis thaliana. In addition, the striking function of the duality between ubiquitination and deubiquitination in the control of gene expression through the modification of chromatin is discussed and, using the available information of the activities of the DUB superfamily in yeast and animals as scaffold, we propose possible scenarios for the role of these proteins in plants.
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