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Chen R, Gu G, Zhang B, Du C, Lin X, Cai W, Zheng Y, Li T, Wang R, Xie X. Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to bacterial wilt resistance in tobacco ( Nicotiana tabacum L.) and eggplant ( Solanum melongena L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1425651. [PMID: 39139726 PMCID: PMC11319268 DOI: 10.3389/fpls.2024.1425651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024]
Abstract
The E3 enzyme in the UPS pathway is a crucial factor for inhibiting substrate specificity. In Solanaceae, the U-box E3 ubiquitin ligase has a complex relationship with plant growth and development, and plays a pivotal role in responding to various biotic and abiotic stresses. The analysis of the U-box gene family in Solanaceae and its expression profile under different stresses holds significant implications. A total of 116 tobacco NtU-boxs and 56 eggplant SmU-boxs were identified based on their respective genome sequences. Phylogenetic analysis of U-box genes in tobacco, eggplant, tomato, Arabidopsis, pepper, and potato revealed five distinct subgroups (I-V). Gene structure and protein motifs analysis found a high degree of conservation in both exon/intron organization and protein motifs among tobacco and eggplant U-box genes especially the members within the same subfamily. A total of 15 pairs of segmental duplication and 1 gene pair of tandem duplication were identified in tobacco based on the analysis of gene duplication events, while 10 pairs of segmental duplication in eggplant. It is speculated that segmental duplication events are the primary driver for the expansion of the U-box gene family in both tobacco and eggplant. The promoters of NtU-box and SmU-box genes contained cis-regulatory elements associated with cellular development, phytohormones, environment stress, and photoresponsive elements. Transcriptomic data analysis shows that the expression levels of the tobacco and eggplant U-box genes in different tissues and various abiotic stress conditions. Using cultivar Hongda of tobacco and cultivar Yanzhi of eggplant as materials, qRT-PCR analysis has revealed that 15 selected NtU-box genes and 8 SmU-box may play important roles in response to pathogen Ras invasion both in tobacco and eggplant.
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Affiliation(s)
- Rui Chen
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Gang Gu
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, China
| | - Binghui Zhang
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, China
| | | | | | | | - Yan Zheng
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Tong Li
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Ruiqi Wang
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou, China
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Mei J, Che J, Shi Y, Fang Y, Wu R, Zhu X. Mapping the Influence of Light Intensity on the Transgenerational Genetic Architecture of Arabidopsis thaliana. Curr Issues Mol Biol 2024; 46:8148-8169. [PMID: 39194699 DOI: 10.3390/cimb46080482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
Light is a crucial environmental factor that influences the phenotypic development of plants. Despite extensive studies on the physiological, biochemical, and molecular mechanisms of the impact of light on phenotypes, genetic investigations regarding light-induced transgenerational plasticity in Arabidopsis thaliana remain incomplete. In this study, we used thaliana as the material, then gathered phenotypic data regarding leaf number and plant height under high- and low-light conditions from two generations. In addition to the developed genotype data, a functional mapping model was used to locate a series of significant single-nucleotide polymorphisms (SNPs). Under low-light conditions, a noticeable adaptive change in the phenotype of leaf number in the second generation suggests the presence of transgenerational genetic effects in thaliana under environmental stress. Under different lighting treatments, 33 and 13 significant genes associated with transgenerational inheritance were identified, respectively. These genes are largely involved in signal transduction, technical hormone pathways, light responses, and the regulation of organ development. Notably, genes identified under high-light conditions more significantly influence plant development, whereas those identified under low-light conditions focus more on responding to external environmental stimuli.
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Affiliation(s)
- Jie Mei
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jincan Che
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yunzhu Shi
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yudian Fang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
| | - Xuli Zhu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China
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Su Y, Ngea GLN, Wang K, Lu Y, Godana EA, Ackah M, Yang Q, Zhang H. Deciphering the mechanism of E3 ubiquitin ligases in plant responses to abiotic and biotic stresses and perspectives on PROTACs for crop resistance. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38864414 DOI: 10.1111/pbi.14407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/12/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024]
Abstract
With global climate change, it is essential to find strategies to make crops more resistant to different stresses and guarantee food security worldwide. E3 ubiquitin ligases are critical regulatory elements that are gaining importance due to their role in selecting proteins for degradation in the ubiquitin-proteasome proteolysis pathway. The role of E3 Ub ligases has been demonstrated in numerous cellular processes in plants responding to biotic and abiotic stresses. E3 Ub ligases are considered a class of proteins that are difficult to control by conventional inhibitors, as they lack a standard active site with pocket, and their biological activity is mainly due to protein-protein interactions with transient conformational changes. Proteolysis-targeted chimeras (PROTACs) are a new class of heterobifunctional molecules that have emerged in recent years as relevant alternatives for incurable human diseases like cancer because they can target recalcitrant proteins for destruction. PROTACs interact with the ubiquitin-proteasome system, principally the E3 Ub ligase in the cell, and facilitate proteasome turnover of the proteins of interest. PROTAC strategies harness the essential functions of E3 Ub ligases for proteasomal degradation of proteins involved in dysfunction. This review examines critical advances in E3 Ub ligase research in plant responses to biotic and abiotic stresses. It highlights how PROTACs can be applied to target proteins involved in plant stress response to mitigate pathogenic agents and environmental adversities.
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Affiliation(s)
- Yingying Su
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Guillaume Legrand Ngolong Ngea
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Fisheries Sciences, University of Douala, Douala, Cameroon
| | - Kaili Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yuchun Lu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Esa Abiso Godana
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Michael Ackah
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
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Wu S, Hu C, Zhu C, Fan Y, Zhou J, Xia X, Shi K, Zhou Y, Foyer CH, Yu J. The MYC2-PUB22-JAZ4 module plays a crucial role in jasmonate signaling in tomato. MOLECULAR PLANT 2024; 17:598-613. [PMID: 38341757 DOI: 10.1016/j.molp.2024.02.006] [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: 08/03/2023] [Revised: 12/06/2023] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
Jasmonates (JAs), a class of lipid-derived stress hormones, play a crucial role across an array of plant physiological processes and stress responses. Although JA signaling is thought to rely predominantly on the degradation of specific JAZ proteins by SCFCOI1, it remains unclear whether other pathways are involved in the regulation of JAZ protein stability. Here, we report that PUB22, a plant U-box type E3 ubiquitin ligase, plays a critical role in the regulation of plant resistance against Helicoverpa armigera and other JA responses in tomato. Whereas COI1 physically interacts with JAZ1/2/5/7, PUB22 physically interacts with JAZ1/3/4/6. PUB22 ubiquitinates JAZ4 to promote its degradation via the 26S proteasome pathway. Importantly, we observed that pub22 mutants showreduced resistance to H. armigera, whereas jaz4 single mutants and jaz1 jaz3 jaz4 jaz6 quadruple mutants have enhanced resistance. The hypersensitivity of pub22 mutants to herbivores could be partially rescued by JAZ4 mutation. Moreover, we found that expression of PUB22 can be transcriptionally activated by MYC2, thus forming a positive feedback circuit in JA signaling. We noticed that the PUB22-JAZ4 module also regulates other JA responses, including defense against B. cinerea, inhibition of root elongation, and anthocyanin accumulation. Taken together, these results indicate that PUB22 plays a crucial role in plant growth and defense responses, together with COI1-regulated JA signaling, by targeting specific JAZs.
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Affiliation(s)
- Shaofang Wu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Chaoyi Hu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China
| | - Changan Zhu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yanfen Fan
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Horticulture, Northwest Agriculture & Forestry University, Xianyang 712100, China
| | - Jie Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Xiaojia Xia
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Kai Shi
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yanhong Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Jingquan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China; Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Zhejiang University, Hangzhou 310058, China.
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Zhou X, Li Y, Wang J, Zhao Y, Wang H, Han Y, Lin X. Genome-wide identification of U-box gene family and expression analysis in response to saline-alkali stress in foxtail millet ( Setaria italica L. Beauv). Front Genet 2024; 15:1356807. [PMID: 38435060 PMCID: PMC10904469 DOI: 10.3389/fgene.2024.1356807] [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: 12/16/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
E3 ubiquitin ligases are central modifiers of plant signaling pathways that regulate protein function, localization, degradation, and other biological processes by linking ubiquitin to target proteins. E3 ubiquitin ligases include proteins with the U-box domain. However, there has been no report about the foxtail millet (Setaria italica L. Beauv) U-box gene family (SiPUB) to date. To explore the function of SiPUBs, this study performed genome-wide identification of SiPUBs and expression analysis of them in response to saline-alkali stress. A total of 70 SiPUBs were identified, which were unevenly distributed on eight chromosomes. Phylogenetic and conserved motif analysis demonstrated that SiPUBs could be clustered into six subfamilies (I-VI), and most SiPUBs were closely related to the homologues in rice. Twenty-eight types of cis-acting elements were identified in SiPUBs, most of which contained many light-responsive elements and plant hormone-responsive elements. Foxtail millet had 19, 78, 85, 18, and 89 collinear U-box gene pairs with Arabidopsis, rice, sorghum, tomato, and maize, respectively. Tissue specific expression analysis revealed great variations in SiPUB expression among different tissues, and most SiPUBs were relatively highly expressed in roots, indicating that SiPUBs may play important roles in root development or other growth and development processes of foxtail millet. Furthermore, the responses of 15 SiPUBs to saline-alkali stress were detected by qRT-PCR. The results showed that saline-alkali stress led to significantly differential expression of these 15 SiPUBs, and SiPUB20/48/70 may play important roles in the response mechanism against saline-alkali stress. Overall, this study provides important information for further exploration of the biological function of U-box genes.
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Affiliation(s)
- Xiaoke Zhou
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yun Li
- Research Center of Rural Vitalization, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jian Wang
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuxue Zhao
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Huimin Wang
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yucui Han
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xiaohu Lin
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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Leon RG, Bassham DC. PROTAC for agriculture: learning from human medicine to generate new biotechnological weed control solutions. PEST MANAGEMENT SCIENCE 2024; 80:262-266. [PMID: 37612249 DOI: 10.1002/ps.7741] [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: 07/13/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 08/25/2023]
Abstract
Weed control has relied on the use of organic and inorganic molecules that interfere with druggable targets, especially enzymes, for almost a century. This approach, although effective, has resulted in multiple cases of herbicide resistance. Furthermore, the rate of discovery of new druggable targets that are selective and with favorable environmental profiles has slowed down, highlighting the need for innovative control tools. The arrival of the biotechnology and genomics era gave hope to many that all sorts of new control tools would be developed. However, the reality is that most efforts have been limited to the development of transgenic crops with resistance to a few existing herbicides, which in fact is just another form of selectivity. Proteolysis-targeting chimera (PROTAC) is a new technology developed to treat human diseases but that has potential for multiple applications in agriculture. This technology uses a small bait molecule linked to an E3 ligand. The 3-dimensional structure of the bait favors physical interaction with a binding site in the target protein in a manner that allows E3 recruitment, ubiquitination and then proteasome-mediated degradation. This system makes it possible to circumvent the need to find druggable targets because it can degrade structural proteins, transporters, transcription factors, and enzymes without the need to interact with the active site. PROTAC can help control herbicide-resistant weeds as well as expand the number of biochemical targets that can be used for weed control. In the present article, we provide an overview of how PROTAC works and describe the possible applications for weed control as well as the challenges that this technology might face during development and implementation for field uses. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ramon G Leon
- Professor and University Faculty Scholar, Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA
| | - Diane C Bassham
- Distinguished Professor and Walter E. and Helen Parke Loomis Professor of Plant Physiology, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
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Kohli M, Bansal H, Mishra GP, Dikshit HK, Reddappa SB, Roy A, Sinha SK, Shivaprasad K, Kumari N, Kumar A, Kumar RR, Nair RM, Aski M. Genome-wide association studies for earliness, MYMIV resistance, and other associated traits in mungbean ( Vigna radiata L. Wilczek) using genotyping by sequencing approach. PeerJ 2024; 12:e16653. [PMID: 38288464 PMCID: PMC10823994 DOI: 10.7717/peerj.16653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
Yellow mosaic disease (YMD) remains a major constraint in mungbean (Vigna radiata (L.)) production; while short-duration genotypes offer multiple crop cycles per year and help in escaping terminal heat stress, especially during summer cultivation. A comprehensive genotyping by sequencing (GBS)-based genome-wide association studies (GWAS) analysis was conducted using 132 diverse mungbean genotypes for traits like flowering time, YMD resistance, soil plant analysis development (SPAD) value, trichome density, and leaf area. The frequency distribution revealed a wide range of values for all the traits. GBS studies identified 31,953 high-quality single nucleotide polymorphism (SNPs) across all 11 mungbean chromosomes and were used for GWAS. Structure analysis revealed the presence of two genetically distinct populations based on ΔK. The linkage disequilibrium (LD) varied throughout the chromosomes and at r2 = 0.2, the mean LD decay was estimated as 39.59 kb. Two statistical models, mixed linear model (MLM) and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) identified 44 shared SNPs linked with various candidate genes. Notable candidate genes identified include FPA for flowering time (VRADI10G01470; chr. 10), TIR-NBS-LRR for mungbean yellow mosaic India virus (MYMIV) resistance (VRADI09G06940; chr. 9), E3 ubiquitin-protein ligase RIE1 for SPAD value (VRADI07G28100; chr. 11), WRKY family transcription factor for leaf area (VRADI03G06560; chr. 3), and LOB domain-containing protein 21 for trichomes (VRADI06G04290; chr. 6). In-silico validation of candidate genes was done through digital gene expression analysis using Arabidopsis orthologous (compared with Vigna radiata genome). The findings provided valuable insight for marker-assisted breeding aiming for the development of YMD-resistant and early-maturing mungbean varieties.
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Affiliation(s)
- Manju Kohli
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
| | - Hina Bansal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | | | | | | | - Anirban Roy
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Subodh Kumar Sinha
- Biotechnology, National Institute of Plant Biotechnology, New Delhi, Delhi, India
| | - K.M. Shivaprasad
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
| | - Nikki Kumari
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
| | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Ranjeet R. Kumar
- Biochemistry, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | | | - Muraleedhar Aski
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
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Liu Z, Wang L, Li Y, Zhu J, Li Z, Chen L, Li H, Shi T, Yao P, Bi Z, Sun C, Bai J, Zhang J, Liu Y. Genome-wide analysis of the U-box E3 ligases gene family in potato (Solanum tuberosum L.) and overexpress StPUB25 enhance drought tolerance in transgenic Arabidopsis. BMC Genomics 2024; 25:10. [PMID: 38166714 PMCID: PMC10759479 DOI: 10.1186/s12864-023-09890-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Plant U-box (PUB) E3 ubiquitin ligases have vital effects on various biological processes. Therefore, a comprehensive and systematic identification of the members of the U-box gene family in potato will help to understand the evolution and function of U-box E3 ubiquitin ligases in plants. RESULTS This work identified altogether 74 PUBs in the potato (StPUBs) and examined their gene structures, chromosomal distributions, and conserved motifs. There were seventy-four StPUB genes on ten chromosomes with diverse densities. As revealed by phylogenetic analysis on PUBs within potato, Arabidopsis, tomato (Solanum lycopersicum), cabbage (Brassica oleracea), rice (Oryza sativa), and corn (Zea mays), were clustered into eight subclasses (C1-C8). According to synteny analysis, there were 40 orthologous StPUB genes to Arabidopsis, 58 to tomato, 28 to cabbage, 7 to rice, and 8 to corn. In addition, RNA-seq data downloaded from PGSC were utilized to reveal StPUBs' abiotic stress responses and tissue-specific expression in the doubled-monoploid potato (DM). Inaddition, we performed RNA-seq on the 'Atlantic' (drought-sensitive cultivar, DS) and the 'Qingshu NO.9' (drought-tolerant cultivar, DT) in early flowering, full-blooming, along with flower-falling stages to detect genes that might be involved in response to drought stress. Finally, quantitative real-time PCR (qPCR) was carried out to analyze three candidate genes for their expression levels within 100 mM NaCl- and 10% PEG 6000 (w/v)-treated potato plantlets for a 24-h period. Furthermore, we analyzed the drought tolerance of StPUB25 transgenic plants and found that overexpression of StPUB25 significantly increased peroxidase (POD) activity, reduced ROS (reactive oxygen species) and MDA (malondialdehyde) accumulation compared with wild-type (WT) plants, and enhancing drought tolerance of the transgenic plants. CONCLUSION In this study, three candidate genes related to drought tolerance in potato were excavated, and the function of StPUB25 under drought stress was verified. These results should provide valuable information to understand the potato StPUB gene family and investigate the molecular mechanisms of StPUBs regulating potato drought tolerance.
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Affiliation(s)
- Zhen Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lei Wang
- Hebei North University, Zhangjiakou, 075000, China
| | - Yuanming Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jinyong Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhitao Li
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Limin Chen
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Hongyang Li
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Tianbin Shi
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhenzhen Bi
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chao Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jiangping Bai
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Junlian Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
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Zhu P, Fan Y, Xu P, Fan G. Bioinformatic Analysis of the BTB Gene Family in Paulownia fortunei and Functional Characterization in Response to Abiotic and Biotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:4144. [PMID: 38140471 PMCID: PMC10747981 DOI: 10.3390/plants12244144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
To learn about the gene structure, phylogenetic evolution, and function under biotic and abiotic stresses of BTB (Bric-a-Brac/Tramtrack/Broad Complex) genes in Paulownia fortunei, a whole-genome sequence evaluation was carried out, and a total of 62 PfBTB genes were identified. The phylogenetic analysis showed that PfBTB proteins are divided into eight groups, and these proteins are highly conserved. PfBTB genes were unevenly distributed on 17 chromosomes. The colinearity analysis found that fragment replication and tandem replication are the main modes of gene amplification in the PfBTB family. The analysis of cis-acting elements suggests that PfBTB genes may be involved in a variety of biological processes. The transcriptomic analysis results showed that PfBTB3/12/14/16/19/36/44 responded to Paulownia witches' broom (PaWB), while PfBTB1/4/17/43 responded to drought stress, and the RT-qPCR results further support the reliability of transcriptome data. In addition, the association analysis between miRNA and transcriptome revealed a 91-pair targeting relationship between miRNAs and PfBTBs. In conclusion, the BTB genes in Paulownia are systematically identified in this research. This work provides useful knowledge to more fully appreciate the potential functions of these genes and their possible roles in the occurrence of PaWB and in response to stress.
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Affiliation(s)
- Peipei Zhu
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (P.Z.); (Y.F.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Yujie Fan
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (P.Z.); (Y.F.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Pingluo Xu
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (P.Z.); (Y.F.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Guoqiang Fan
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (P.Z.); (Y.F.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
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Hu Z, Fang H, Zhu C, Gu S, Ding S, Yu J, Shi K. Ubiquitylation of PHYTOSULFOKINE RECEPTOR 1 modulates the defense response in tomato. PLANT PHYSIOLOGY 2023; 192:2507-2522. [PMID: 36946197 PMCID: PMC10315268 DOI: 10.1093/plphys/kiad188] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Phytosulfokine (PSK) is a danger-associated molecular pattern recognized by PHYTOSULFOKINE RECEPTOR 1 (PSKR1) and initiates intercellular signaling to coordinate different physiological processes, especially in the defense response to the necrotrophic fungus Botrytis cinerea. The activity of peptide receptors is largely influenced by different posttranslational modifications, which determine intercellular peptide signal outputs. To date, the posttranslational modification to PHYTOSULFOKINE RECEPTOR 1 (PSKR1) remains largely unknown. Here, we show that tomato (Solanum lycopersicum) PSKR1 is regulated by the ubiquitin/proteasome degradation pathway. Using multiple protein-protein interactions and ubiquitylation analyses, we identified that plant U-box E3 ligases PUB12 and PUB13 interacted with PSKR1, among which PUB13 caused PSKR1 ubiquitylation at Lys-748 and Lys-905 sites to control PSKR1 abundance. However, this posttranslational modification was attenuated upon addition of PSK. Moreover, the disease symptoms observed in PUB13 knock-down and overexpression lines demonstrated that PUB13 significantly suppressed the PSK-initiated defense response. This highlights an important regulatory function for the turnover of a peptide receptor by E3 ligase-mediated ubiquitylation in the plant defense response.
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Affiliation(s)
- Zhangjian Hu
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China
| | - Hanmo Fang
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Changan Zhu
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Shaohan Gu
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Shuting Ding
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Jingquan Yu
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China
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11
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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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12
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Wang P, Zhu L, Li Z, Cheng M, Chen X, Wang A, Wang C, Zhang X. Genome-Wide Identification of the U-Box E3 Ubiquitin Ligase Gene Family in Cabbage ( Brassica oleracea var. capitata) and Its Expression Analysis in Response to Cold Stress and Pathogen Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:1437. [PMID: 37050063 PMCID: PMC10097260 DOI: 10.3390/plants12071437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Plant U-box E3 ubiquitin ligases (PUBs) play an important role in growth, development, and stress responses in many species. However, the characteristics of U-box E3 ubiquitin ligase genes in cabbage (Brassica oleracea var. capitata) are still unclear. Here, we carry out the genome-wide analysis of U-box E3 ubiquitin ligase genes in cabbage and identify 65 Brassica oleracea var. capitata U-box E3 ubiquitin ligase (BoPUB) genes in the cabbage genome. Phylogenetic analysis indicates that all 65 BoPUB genes are grouped into six subfamilies, whose members are relatively conserved in the protein domain and exon-intron structure. Chromosomal localization and synteny analyses show that segmental and tandem duplication events contribute to the expansion of the U-box E3 ubiquitin ligase gene family in cabbage. Protein interaction prediction presents that heterodimerization may occur in BoPUB proteins. In silico promoter analysis and spatio-temporal expression profiling of BoPUB genes reveal their involvement in light response, phytohormone response, and growth and development. Furthermore, we find that BoPUB genes participate in the biosynthesis of cuticular wax and in response to cold stress and pathogenic attack. Our findings provide a deep insight into the U-box E3 ubiquitin ligase gene family in cabbage and lay a foundation for the further functional analysis of BoPUB genes in different biological processes.
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Affiliation(s)
- Peiwen Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Lin Zhu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Ziheng Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Mozhen Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Xiuling Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Aoxue Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Chao Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Xiaoxuan Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
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Jiang L, Lin Y, Wang L, Peng Y, Yang M, Jiang Y, Hou G, Liu X, Li M, Zhang Y, Zhang Y, Chen Q, Wang Y, He W, Wang X, Tang H, Luo Y. Genome-wide identification and expression profiling reveal the regulatory role of U-box E3 ubiquitin ligase genes in strawberry fruit ripening and abiotic stresses resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1171056. [PMID: 37035055 PMCID: PMC10078948 DOI: 10.3389/fpls.2023.1171056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
The plant U-box (PUB) proteins are a type of E3 ubiquitin ligases well known for their functions in response to various stresses. They are also related to fruit development and ripening. However, PUB members possess such roles that remain unclear in strawberry. In this study, 155 PUB genes were identified in octoploid strawberry and classified into four groups. Their promoters possessed a variety of cis-acting elements, most of which are associated with abiotic stresses, followed by phytohormones response and development. Protein-protein interaction analysis suggested that FaU-box members could interact with each other as well as other proteins involved in hormone signaling and stress resistance. Transcriptome-based and RT-qPCR expression analysis revealed the potential involvement of FaU-box genes in resistance to stresses and fruit ripening. Of these, FaU-box98 and FaU-box136 were positively while FaU-box52 was negatively related to strawberry ripening. FaU-box98 comprehensively participated in resistance of ABA, cold, and salt, while FaU-box83 and FaU-box136 were broadly associated with drought and salt stresses. FaU-box18 and FaU-box52 were ABA-specific; FaU-box3 was specific to salt stress. In addition, the functional analysis of a randomly selected FaU-box (FaU-box127) showed that the transient overexpression of FaU-box127 promoted the ripening of strawberry fruit, along with significant changes in the expression levels of some ripening-related genes and the content of organic acid and soluble sugar. Overall, these findings provided comprehensive information about the FaU-box gene family and identified the potential FaU-box members participating in stress resistance and strawberry fruit ripening regulation.
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Affiliation(s)
- Leiyu Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Liangxin Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yuting Peng
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Min Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yuyan Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Guoyan Hou
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyang Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
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14
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Yao S, Xie M, Hu M, Cui X, Wu H, Li X, Hu P, Tong C, Yu X. Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1118339. [PMID: 37021309 PMCID: PMC10067767 DOI: 10.3389/fpls.2023.1118339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin-proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although UBC genes have been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in Brassica napus. In the present study, 200 putative BnUBCs were identified in B. napus, which were clustered into 18 subgroups based on phylogenetic analysis. BnUBCs within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of cis-acting regulatory elements in BnUBC promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three BnUBCs were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the UBC family in B. napus and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of B. napus.
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Affiliation(s)
- Shengli Yao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - XiaoBo Cui
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Haoming Wu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Xiaohua Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Peng Hu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoli Yu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
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15
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Cui J, Ren G, Bai Y, Gao Y, Yang P, Chang J. Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to salt tolerance in sorghum ( Sorghum bicolor L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1141617. [PMID: 37008506 PMCID: PMC10063820 DOI: 10.3389/fpls.2023.1141617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Plant U-box (PUB) E3 ubiquitin ligases play essential roles in many biological processes and stress responses, but little is known about their functions in sorghum (Sorghum bicolor L.). In the present study, 59 SbPUB genes were identified in the sorghum genome. Based on the phylogenetic analysis, the 59 SbPUB genes were clustered into five groups, which were also supported by the conserved motifs and structures of these genes. SbPUB genes were found to be unevenly distributed on the 10 chromosomes of sorghum. Most PUB genes (16) were found on chromosome 4, but there were no PUB genes on chromosome 5. Analysis of cis-acting elements showed that SbPUB genes were involved in many important biological processes, particularly in response to salt stress. From proteomic and transcriptomic data, we found that several SbPUB genes had diverse expressions under different salt treatments. To verify the expression of SbPUBs, qRT-PCR analyses also were conducted under salt stress, and the result was consistent with the expression analysis. Furthermore, 12 SbPUB genes were found to contain MYB-related elements, which are important regulators of flavonoid biosynthesis. These results, which were consistent with our previous multi-omics analysis of sorghum salt stress, laid a solid foundation for further mechanistic study of salt tolerance in sorghum. Our study showed that PUB genes play a crucial role in regulating salt stress, and might serve as promising targets for the breeding of salt-tolerant sorghum in the future.
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Affiliation(s)
- Jianghui Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Genzeng Ren
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Yuzhe Bai
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Yukun Gao
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Puyuan Yang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
| | - Jinhua Chang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Baoding, China
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16
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Zizelski Valenci G, Raveh D, Bar-Zvi D. The activity of the stress modulated Arabidopsis ubiquitin ligases PUB46 and PUB48 is partially redundant. PLANT SIGNALING & BEHAVIOR 2022; 17:2072111. [PMID: 35546519 PMCID: PMC9116408 DOI: 10.1080/15592324.2022.2072111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
The Arabidopsis ubiquitin ligases PUB46, PUB47 and PUB48 are encoded by paralogus genes. Single gene pub46 and pub48 mutants display increased drought sensitivity compared to wild type (WT) suggesting that each has specific biological activity. The high sequence homology between PUB46 and PUB48 activity suggested that they may also share some aspects of their activity. Unfortunately, the close proximity of the PUB46 and PUB48 gene loci precludes obtaining a double mutant required to study if they are partially redundant by crossing the available single mutants. We thus applied microRNA technology to reduce the activity of all three gene products of the PUB46-48 subfamily by constructing an artificial microRNA (aMIR) targeted to this subfamily. Expressing aMIR46-48 in WT plants resulted in increased drought-sensitivity, a phenotype resembling that of each of the single pub46 and pub48 mutants, and enhanced sensitivity to methyl viologen, similar to that observed for the pub46 mutant. The WT plants expressing aMIR46-48 plants also revealed reduced inhibition by ABA at seed germination, a phenotype not evident in the single mutants. Expressing aMIR46-48 in pub46 and pub48 mutants further enhanced the drought sensitivity of each parental single mutant and of WT expressing aMIR46-48. These results suggest that the biological activities of PUB46 and PUB48 in abiotic stress response are partially redundant.
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Affiliation(s)
- Gal Zizelski Valenci
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dina Raveh
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dudy Bar-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the NegevThe Doris and Bertie I. , Beer-Sheva, Israel
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17
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Gao X, Li X, Chen C, Wang C, Fu Y, Zheng Z, Shi M, Hao X, Zhao L, Qiu M, Kai G, Zhou W. Mining of the CULLIN E3 ubiquitin ligase genes in the whole genome of Salvia miltiorrhiza. Curr Res Food Sci 2022; 5:1760-1768. [PMID: 36268136 PMCID: PMC9576582 DOI: 10.1016/j.crfs.2022.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/01/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
CULLIN (CUL) proteins are E3 ubiquitin ligases that are involved in a wide variety of biological processes as well as in response to stress in plants. In Salvia miltiorrhiza, CUL genes have not been characterized and its role in plant development, stress response and secondary metabolite synthesis have not been studied. In this study, genome-wide analyses were performed to identify and to predict the structure and function of CUL of S. miltiorrhiza. Eight CUL genes were identified from the genome of S. miltiorrhiza. The CUL genes were clustered into four subgroups according to phylogenetic relationships. The CUL domain was highly conserved across the family of CUL genes. Analysis of cis-acting elements suggested that CUL genes might play important roles in a variety of biological processes, including abscission reaction acid (ABA) processing. To investigate this hypothesis, we treated hairy roots of S. miltiorrhiza with ABA. The expression of CUL genes varied obviously after ABA treatment. Co-expression network results indicated that three CUL genes might be involved in the biosynthesis of phenolic acid or tanshinone. In summary, the mining of the CUL genes in the whole genome of S. miltiorrhiza contribute novel information to the understanding of the CUL genes and its functional roles in plant secondary metabolites, growth and development.
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Affiliation(s)
- Xiankui Gao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Xiujuan Li
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Chengan Chen
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Can Wang
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Yuqi Fu
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - ZiZhen Zheng
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Min Shi
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Xiaolong Hao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Limei Zhao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Minghua Qiu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Guoyin Kai
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Wei Zhou
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
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18
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The Ubiquitin–Proteasome System (UPS) and Viral Infection in Plants. PLANTS 2022; 11:plants11192476. [PMID: 36235343 PMCID: PMC9572368 DOI: 10.3390/plants11192476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022]
Abstract
The ubiquitin–proteasome system (UPS) is crucial in maintaining cellular physiological balance. The UPS performs quality control and degrades proteins that have already fulfilled their regulatory purpose. The UPS is essential for cellular and organic homeostasis, and its functions regulate DNA repair, gene transcription, protein activation, and receptor trafficking. Besides that, the UPS protects cellular immunity and acts on the host’s defense system. In order to produce successful infections, viruses frequently need to manipulate the UPS to maintain the proper level of viral proteins and hijack defense mechanisms. This review highlights and updates the mechanisms and strategies used by plant viruses to subvert the defenses of their hosts. Proteins involved in these mechanisms are important clues for biotechnological approaches in viral resistance.
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Classification and Expression Profile of the U-Box E3 Ubiquitin Ligase Enzyme Gene Family in Maize (Zea mays L.). PLANTS 2022; 11:plants11192459. [PMID: 36235327 PMCID: PMC9573083 DOI: 10.3390/plants11192459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022]
Abstract
The U-box E3 (PUB) family genes encode the E3 ubiquitin ligase enzyme, which determines substrate specific recognition during protein ubiquitination. 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 characteristic of PUB gene family in the important staple crop, maize (Zea mays L.). In this study, the PUB gene in maize was aimed to identify and classify through whole-genome screening. Phylogenetic tree, gene structure, conserved motif, chromosome location, gene duplication (GD), synteny, and cis-acting regulatory element of PUB member were analyzed. The expression profiles of ZmPUB gene family in maize during development and under abiotic stress and hormones treatment were analyzed by the RNA-seq data. A total of 79 PUB genes were identified in maize genome, and they were stratified into seven categories. There were 25 pairs of segmental duplications (SD) and 1 pair of tandem duplication (TD) identified in the maize PUB gene family. A close relationship was observed between the monocot plant maize and rice in PUB gene family. There were 94 kinds of cis-acting elements identified in the maize PUB gene family, which included 46 biotic- and abiotic-responsive elements, 19 hormone-responsive elements, 13 metabolic and growth-related elements. The expression profiles of maize PUB gene family showed characteristics of tissue specificity and response to abiotic stress and hormones treatment. These results provided an extensive overview of the maize PUB gene family.
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20
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Fang Y, Du Q, Yang Q, Jiang J, Hou X, Yang Z, Zhao D, Li X, Xie X. Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor. Front Microbiol 2022; 13:942302. [PMID: 36187972 PMCID: PMC9520534 DOI: 10.3389/fmicb.2022.942302] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
The U-box family is one of the main E3 ubiquitin ligase families in plants. The U-box family has been characterized in several species. However, genome-wide gene identification and expression profiling of the U-box family in response to abiotic stress in Sorghum bicolor remain unclear. In this study, we broadly identified 68 U-box genes in the sorghum genome, including 2 CHIP genes, and 1 typical UFD2 (Ub fusion degradation 2) gene. The U-box gene family was divided into eight subclasses based on homology and conserved domain characteristics. Evolutionary analysis identified 14, 66, and 82 U-box collinear gene pairs in sorghum compared with arabidopsis, rice, and maize, respectively, and a unique tandem repeat pair (SbPUB26/SbPUB27) is present in the sorghum genome. Gene Ontology (GO) enrichment analysis showed that U-box proteins were mainly related to ubiquitination and modification, and various stress responses. Comprehensive analysis of promoters, expression profiling, and gene co-regulation networks also revealed that many sorghum U-box genes may be correlated with multiple stress responses. In summary, our results showed that sorghum contains 68 U-box genes, which may be involved in multiple abiotic stress responses. The findings will support future gene functional studies related to ubiquitination in sorghum.
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Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Qiaoli Du
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Qian Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Zaifu Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Degang Zhao
- College of Life Sciences, Ministry of Education, Institute of Agricultural Bioengineering, Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Guizhou University, Guiyang, China
- Guizhou Academy of Agricultural Sciences, Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture, Guizhou Institute of Biotechnology, Guiyang, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Academy of Agricultural Sciences, Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture, Guizhou Institute of Biotechnology, Guiyang, China
- *Correspondence: Xin Xie,
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21
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Yuan J, Liu Y, Wang Z, Lei T, Hu Y, Zhang L, Yuan M, Wang J, Li Y. Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato. Life (Basel) 2022; 12:1236. [PMID: 36013415 PMCID: PMC9410287 DOI: 10.3390/life12081236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/06/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
NAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (S. lycopersicum) and 88 (S. pennellii) members of the NAC family were present in two tomatoes, and most of them were amplified from two paleohexaploidizations. We differentiated NAC family members from the different paleohexaploidizations and found that the SWGT-derived NAC genes had more rearrangement events, so it was different from the DWGT-derived NAC genes in terms of physicochemical properties, phylogeny, and gene location. The results of selection pressure show that DWGT-derived NAC genes tended to be positively selected in S. lycopersicum and negatively selected in S. pennellii. A comprehensive analysis of paleopolyploidization and expression reveals that DWGT-derived NAC genes tend to promote fruit ripening, and are expressed at the early and middle stages, whereas SWGT-derived NAC genes tend to terminate fruit growth and are expressed at the late stages of fruit ripening. This study obtained NAC genes from different sources that can be used as materials for tomato fruit development, and the method in the study can be extended to the study of other plants.
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Affiliation(s)
- Jiale Yuan
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Ying Liu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Zhenyi Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Tianyu Lei
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanfang Hu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Lan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Min Yuan
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxian Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
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22
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Trenner J, Monaghan J, Saeed B, Quint M, Shabek N, Trujillo M. Evolution and Functions of Plant U-Box Proteins: From Protein Quality Control to Signaling. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:93-121. [PMID: 35226816 DOI: 10.1146/annurev-arplant-102720-012310] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Posttranslational modifications add complexity and diversity to cellular proteomes. One of the most prevalent modifications across eukaryotes is ubiquitination, which is orchestrated by E3 ubiquitin ligases. U-box-containing E3 ligases have massively expanded in the plant kingdom and have diversified into plant U-box proteins (PUBs). PUBs likely originated from two or three ancestral forms, fusing with diverse functional subdomains that resulted in neofunctionalization. Their emergence and diversification may reflect adaptations to stress during plant evolution, reflecting changes in the needs of plant proteomes to maintain cellular homeostasis. Through their close association with protein kinases, they are physically linked to cell signaling hubs and activate feedback loops by dynamically pairing with E2-ubiquitin-conjugating enzymes to generate distinct ubiquitin polymers that themselves act as signals. Here, we complement current knowledgewith comparative genomics to gain a deeper understanding of PUB function, focusing on their evolution and structural adaptations of key U-box residues, as well as their various roles in plant cells.
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Affiliation(s)
- Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany; ,
| | | | - Bushra Saeed
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany; ,
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany; ,
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA;
| | - Marco Trujillo
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany; ,
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23
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Zhang H, Zheng D, Song F, Jiang M. Expression Patterns and Functional Analysis of 11 E3 Ubiquitin Ligase Genes in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:840360. [PMID: 35310657 PMCID: PMC8924586 DOI: 10.3389/fpls.2022.840360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/10/2022] [Indexed: 05/27/2023]
Abstract
E3 ubiquitin ligases are involved in many processes, regulating the response to biotic and abiotic stresses. In this study, 11 E3 ubiquitin ligase genes from Arabidopsis, which were hypothesized to function in response to biotic or abiotic stresses were selected, and the homologous genes in rice were found. Their functions were analyzed in rice. These 11 E3 ubiquitin ligase genes showed different patterns of expression under different treatments. The BMV:OsPUB39-infiltrated seedlings showed decreased resistance to Magnaporthe grisea (M. grisea) when compared with BMV:00-infiltrated seedlings, whereas the BMV:OsPUB34- and BMV:OsPUB33-infiltrated seedlings showed increased resistance. The involvement of these genes in the resistance against M. grisea may be attributed to the regulation of the accumulation of reactive oxygen species (ROS) and expression levels of defense-related genes. Seedlings infiltrated by BMV:OsATL69 showed decreased tolerance to drought stress, whereas BMV:OsPUB33-infiltraed seedlings showed increased tolerance, possibly through the regulation of proline content, sugar content, and expression of drought-responsive genes. BMV:OsATL32-infiltrated seedlings showed decreased tolerance to cold stress by regulating malondialdehyde (MDA) content and the expression of cold-responsive genes.
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Affiliation(s)
- Huijuan Zhang
- College of Life Science, Taizhou University, Taizhou, China
| | - Dewei Zheng
- College of Life Science, Taizhou University, Taizhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ming Jiang
- College of Life Science, Taizhou University, Taizhou, China
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24
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How Many Faces Does the Plant U-Box E3 Ligase Have? Int J Mol Sci 2022; 23:ijms23042285. [PMID: 35216399 PMCID: PMC8875423 DOI: 10.3390/ijms23042285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Ubiquitination is a major type of post-translational modification of proteins in eukaryotes. The plant U-Box (PUB) E3 ligase is the smallest family in the E3 ligase superfamily, but plays a variety of essential roles in plant growth, development and response to diverse environmental stresses. Hence, PUBs are potential gene resources for developing climate-resilient crops. However, there is a lack of review of the latest advances to fully understand the powerful gene family. To bridge the gap and facilitate its use in future crop breeding, we comprehensively summarize the recent progress of the PUB family, including gene evolution, classification, biological functions, and multifarious regulatory mechanisms in plants.
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25
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Chen C, Wang C, Li J, Gao X, Huang Q, Gong Y, Hao X, Maoz I, Kai G, Zhou W. Genome-Wide Analysis of U-box E3 Ubiquitin Ligase Family in Response to ABA Treatment in Salvia miltiorrhiza. FRONTIERS IN PLANT SCIENCE 2022; 13:829447. [PMID: 35222487 PMCID: PMC8863962 DOI: 10.3389/fpls.2022.829447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Plant U-box (PUB) proteins are ubiquitin ligases (E3) involved in multiple biological processes and in response to plant stress. However, the various aspects of the genome and the differences in functions between the U-box E3 (UBE3) ubiquitin ligases remain quite obscure in Salvia miltiorrhiza. The 60 UBE3 genes in the S. miltiorrhiza genome were recognized in the present study. The phylogenetic analysis, gene structure, motifs, promoters, and physical and chemical properties of the genes were also examined. Based on the phylogenetic relationship, the 60 UBE3 genes were categorized under six different groups. The U-box domain was highly conserved across the family of UBE3 genes. Analysis of the cis-acting element revealed that the UBE3 genes might play an important role in a variety of biological processes, including a reaction to the abscisic acid (ABA) treatment. To investigate this hypothesis, an ABA treatment was developed for the hairy roots of S. miltiorrhiza. Thirteen out of the UBE3 genes significantly increased after the ABA treatment. The co-expression network revealed that nine UBE3 genes might be associated with phenolic acids or tanshinone biosynthesis. The findings of the present study brought fresh and new understanding to the participation of the UBE3 gene family in plants, specifically in their biological responses mediated by the ABA. In S. miltiorrhiza, this gene family may be crucial during the ABA treatment. Significantly, the results of this study contribute novel information to the understanding of the ubiquitin ligase gene and its role in plant growth.
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Affiliation(s)
- Chengan Chen
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Can Wang
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Junbo Li
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiankui Gao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qikai Huang
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yifu Gong
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaolong Hao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Itay Maoz
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Guoyin Kai
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wei Zhou
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
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26
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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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27
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Li F, Han Z, Qiao W, Wang J, Song Y, Cui Y, Li J, Ge J, Lou D, Fan W, Li D, Nong B, Zhang Z, Cheng Y, Zhang L, Zheng X, Yang Q. High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:775051. [PMID: 34868173 PMCID: PMC8639688 DOI: 10.3389/fpls.2021.775051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.
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Affiliation(s)
- Fei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenyun Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junrui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Yue Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxia Cui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jiaqi Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Little Berry Research Room, Liaoning Institute of Fruit Science, Yingkou, China
| | - Jinyue Ge
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danjing Lou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiya Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yunlian Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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28
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Jia B, Wang Y, Zhang D, Li W, Cui H, Jin J, Cai X, Shen Y, Wu S, Guo Y, Sun M, Sun X. Genome-Wide Identification, Characterization and Expression Analysis of Soybean CHYR Gene Family. Int J Mol Sci 2021; 22:12192. [PMID: 34830077 PMCID: PMC8625759 DOI: 10.3390/ijms222212192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/16/2022] Open
Abstract
The CHYR (CHY ZINC-FINGER AND RING FINGER PROTEIN) proteins have been functionally characterized in iron regulation and stress response in Arabidopsis, rice and Populus. However, their roles in soybean have not yet been systematically investigated. Here, in this study, 16 GmCHYR genes with conserved Zinc_ribbon, CHY zinc finger and Ring finger domains were obtained and divided into three groups. Moreover, additional 2-3 hemerythrin domains could be found in the N terminus of Group III. Phylogenetic and homology analysis of CHYRs in green plants indicated that three groups might originate from different ancestors. Expectedly, GmCHYR genes shared similar conserved domains/motifs distribution within the same group. Gene expression analysis uncovered their special expression patterns in different soybean tissues/organs and under various abiotic stresses. Group I and II members were mainly involved in salt and alkaline stresses. The expression of Group III members was induced/repressed by dehydration, salt and alkaline stresses, indicating their diverse roles in response to abiotic stress. In conclusion, our work will benefit for further revealing the biological roles of GmCHYRs.
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Affiliation(s)
- Bowei Jia
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
| | - Yan Wang
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
| | - Dajian Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China;
| | - Wanhong Li
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
| | - Hongli Cui
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
| | - Jun Jin
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
| | - Xiaoxi Cai
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
| | - Yang Shen
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
| | - Shengyang Wu
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
| | - Yongxia Guo
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
| | - Mingzhe Sun
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (B.J.); (Y.W.); (W.L.); (H.C.); (J.J.); (X.C.); (Y.S.); (S.W.); (Y.G.)
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Sharma B, Saxena H, Negi H. Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum. Sci Rep 2021; 11:15891. [PMID: 34354159 PMCID: PMC8342558 DOI: 10.1038/s41598-021-95436-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
The E3 ubiquitin ligases have been known to intrigue many researchers to date, due to their heterogenicity and substrate mediation for ubiquitin transfer to the protein. HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ligases are spatially and temporally regulated for substrate specificity, E2 ubiquitin-conjugating enzyme interaction, and chain specificity during ubiquitylation. However, the role of the HECT E3 ubiquitin ligase in plant development and stress responses was rarely explored. We have conducted an in-silico genome-wide analysis to identify and predict the structural and functional aspects of HECT E3 ligase members in tomato. Fourteen members of HECT E3 ligases were identified and analyzed for the physicochemical parameters, phylogenetic relations, structural organizations, tissue-specific gene expression patterns, and protein interaction networks. Our comprehensive analysis revealed the HECT domain conservation throughout the gene family, close evolutionary relationship with different plant species, and active involvement of HECT E3 ubiquitin ligases in tomato plant development and stress responses. We speculate an indispensable biological significance of the HECT gene family through extensive participation in several plant cellular and molecular pathways.
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Affiliation(s)
- Bhaskar Sharma
- School of Life and Environmental Sciences, Faculty of Science, Engineering, and Built Environment, Deakin University, Geelong, VIC, 3220, Australia.
- Structural and Molecular Biology Laboratory, Department of Biotechnology, TERI School of Advanced Studies, New Delhi, 110070, India.
| | - Harshita Saxena
- Structural and Molecular Biology Laboratory, Department of Biotechnology, TERI School of Advanced Studies, New Delhi, 110070, India
| | - Harshita Negi
- Structural and Molecular Biology Laboratory, Department of Biotechnology, TERI School of Advanced Studies, New Delhi, 110070, India
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Wang C, Song B, Dai Y, Zhang S, Huang X. Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri). BMC PLANT BIOLOGY 2021; 21:235. [PMID: 34039263 PMCID: PMC8152096 DOI: 10.1186/s12870-021-03024-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The plant U-box (PUB) proteins are a family of ubiquitin ligases (E3) enzymes that involved in diverse biological processes, as well as in responses to plant stress response. However, the characteristics and functional divergence of the PUB gene family have not yet been previously studied in the Chinese white pear (Pyrus bretschneideri). RESULTS In the present study, we identified 62 PbrPUBs in Chinese white pear genome. Based on the phylogenetic relationship, 62 PUB genes were clustered into five groups. The results of conserved motif and gene structure analysis supported the classification phylogenetic tree. The PbrPUB genes were unevenly distribution on 17 pear chromosomes, chromosome 15 housed most member of PUB family, with eight PUB genes. Cis-acting element analysis indicated that PUB genes might participate in diverse biological processes, especially in the response to abiotic stresses. Based on RNA-data from 'Dangshansuli' at seven tissues, we found that PUB genes exhibited diverse of expression level in seven tissues, and qRT-PCR experiment further supported the reliable of RNA-Seq data. To identify candidate genes associated with resistance, we conducted qRT-PCR experiment the expression level of pear seed plant under four abiotic stresses, including: ABA, dehydration, salt and cold treatment. One candidate PUB gene associated with dehydration stress was selected to conduct further functional experiment. Subcellular localization revealed PbrPUB18 protein was located on cell nucleus. Furthermore, heterologous over-expression of PbrPUB18 in Arabidopsis indicated that the over-expression of PbrPUB18 could enhance resistance in drought treatment. In conclusions, we systematically identified the PUB genes in pear, and provided useful knowledge for functional identification of PUB genes in pear.
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Affiliation(s)
- Chunmeng Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Bobo Song
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuqin Dai
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xiaosan Huang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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Doroodian P, Hua Z. The Ubiquitin Switch in Plant Stress Response. PLANTS (BASEL, SWITZERLAND) 2021; 10:246. [PMID: 33514032 PMCID: PMC7911189 DOI: 10.3390/plants10020246] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/20/2022]
Abstract
Ubiquitin is a 76 amino acid polypeptide common to all eukaryotic organisms. It functions as a post-translationally modifying mark covalently linked to a large cohort of yet poorly defined protein substrates. The resulting ubiquitylated proteins can rapidly change their activities, cellular localization, or turnover through the 26S proteasome if they are no longer needed or are abnormal. Such a selective modification is essential to many signal transduction pathways particularly in those related to stress responses by rapidly enhancing or quenching output. Hence, this modification system, the so-called ubiquitin-26S proteasome system (UPS), has caught the attention in the plant research community over the last two decades for its roles in plant abiotic and biotic stress responses. Through direct or indirect mediation of plant hormones, the UPS selectively degrades key components in stress signaling to either negatively or positively regulate plant response to a given stimulus. As a result, a tightly regulated signaling network has become of much interest over the years. The ever-increasing changes of the global climate require both the development of new crops to cope with rapid changing environment and new knowledge to survey the dynamics of ecosystem. This review examines how the ubiquitin can switch and tune plant stress response and poses potential avenues to further explore this system.
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Affiliation(s)
- Paymon Doroodian
- Department of Environment and Plant Biology, Ohio University, Athens, OH 45701, USA;
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
| | - Zhihua Hua
- Department of Environment and Plant Biology, Ohio University, Athens, OH 45701, USA;
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
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