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Luo C, Akhtar M, Min W, Bai X, Ma T, Liu C. Domain of unknown function (DUF) proteins in plants: function and perspective. PROTOPLASMA 2024; 261:397-410. [PMID: 38158398 DOI: 10.1007/s00709-023-01917-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Domains of unknown function (DUFs), which are deposited in the protein family database (Pfam), are protein domains with conserved amino acid sequences and uncharacterized functions. Proteins with the same DUF were classified as DUF families. Although DUF families are generally not essential for the survival of plants, they play roles in plant development and adaptation. Characterizing the functions of DUFs is important for deciphering biological puzzles. DUFs were generally studied through forward and reverse genetics. Some novelty approaches, especially the determination of crystal structures and interaction partners of the DUFs, should attract more attention. This review described the identification of DUF genes by genome-wide and transcriptome-wide analyses, summarized the function of DUF-containing proteins, and addressed the prospects for future studies in DUFs in plants.
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Affiliation(s)
- Chengke Luo
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Maryam Akhtar
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
| | - Weifang Min
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Xiaorong Bai
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Tianli Ma
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Caixia Liu
- School of Agriculture, Ningxia University, Yinchuan, 750021, China.
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2
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Yao X, Chen H, Ai A, Wang F, Lian S, Tang H, Jiang Y, Jiao Y, He Y, Li T, Lu L. The transcription factor CsS40 negatively regulates TCS1 expression and caffeine biosynthesis in connection to leaf senescence in Camellia sinensis. HORTICULTURE RESEARCH 2023; 10:uhad162. [PMID: 37731861 PMCID: PMC10508035 DOI: 10.1093/hr/uhad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/30/2023] [Indexed: 09/22/2023]
Abstract
Caffeine is considered as one of the most important bioactive components in the popular plant beverages tea, cacao, and coffee, but as a wide-spread plant secondary metabolite its biosynthetic regulation at transcription level remains largely unclear. Here, we report a novel transcription factor Camellia sinensis Senescnece 40 (CsS40) as a caffeine biosynthesis regulator, which was discovered during screening a yeast expression library constructed from tea leaf cDNAs for activation of tea caffeine synthase (TCS1) promoter. Besides multiple hits of the non-self-activation CsS40 clones that bound to and activated TCS1 promoter in yeast-one-hybrid assays, a split-luciferase complementation assay demonstrated that CsS40 acts as a transcription factor to activate the CsTCS1 gene and EMSA assay also demonstrated that CsS40 bound to the TCS1 gene promoter. Consistently, immunofluorescence data indicated that CsS40-GFP fusion was localized in the nuclei of tobacco epidermal cells. The expression pattern of CsS40 in 'Fuding Dabai' developing leaves was opposite to that of TCS1; and knockdown and overexpression of CsS40 in tea leaf calli significantly increased and decreased TCS1 expression levels, respectively. The expression levels of CsS40 were also negatively correlated to caffeine accumulation in developing leaves and transgenic calli of 'Fuding Dabai'. Furthermore, overexpression of CsS40 reduced the accumulation of xanthine and hypoxanthine in tobacco plants, meanwhile, increased their susceptibility to aging. CsS40 expression in tea leaves was also induced by senescence-promoting hormones and environmental factors. Taken together, we showed that a novel senescence-related factor CsS40 negatively regulates TCS1 and represses caffeine accumulation in tea cultivar 'Fuding Dabai'. The study provides new insights into caffeine biosynthesis regulation by a plant-specific senescence regulator in tea plants in connection to leaf senescence and hormone signaling.
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Affiliation(s)
- Xinzhuan Yao
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Hufang Chen
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Antao Ai
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Fen Wang
- School of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Shanshan Lian
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Hu Tang
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Yihe Jiang
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Yujie Jiao
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Yumei He
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Tong Li
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Litang Lu
- College of Tea Sciences, Institute of Plant Health & Medicine, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
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Yang T, Zhang M, Yang Q, Liu K, Cui J, Chen J, Ren Y, Shao Y, Wang R, Li G. The S40 family members delay leaf senescence by promoting cytokinin synthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 191:99-109. [PMID: 36201884 DOI: 10.1016/j.plaphy.2022.09.017] [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: 07/16/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Leaf senescence is regulated by both endogenous hormones and environmental stimuli in a programmed and concerted way. The members of the S40 family have been reported to play roles in leaf senescence. Here we identified an S40 family member, CiS40-11, from Caragana intermedia. Phylogenetic analysis revealed that the CiS40-11 protein had the highest identity with AtS40-5 (AT1G11700) and AtS40-6 (AT1G61930) of Arabidopsis thaliana. CiS40-11 was highly expressed in leaves and was down-regulated after dark treatment. The subcellular localization analysis showed that CiS40-11 was a cytoplasm-nucleus dual-localized protein. Leaf senescence was delayed in both the CiS40-11 overexpressed A. thaliana and its transiently expressed C. intermedia. Transcriptomic analysis and endogenous hormones assay revealed that CiS40-11 inhibited leaf senescence via promoting the biosynthesis of cytokinins by blocking AtMYB2 expression in the CiS40-11 overexpression lines. Furthermore, overexpression of either AtS40-5 or AtS40-6 showed similar phenotype as the CiS40-11 overexpressing lines, while in the ats40-5a or ats40-6a mutants, the AtMYB2 expression was increased and their leaves exhibited a premature senescence phenotype. These results provide a new molecular mechanism of the S40 family in leaf senescence regulation of plants.
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Affiliation(s)
- Tianrui Yang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Minna Zhang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Qi Yang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Kun Liu
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Jiaming Cui
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Jia Chen
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Yufan Ren
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Yunjie Shao
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Ruigang Wang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China; Inner Mongolia Enterprise Key Laboratory of Tree Breeding, Mengshu Ecological Construction Group Co., Ltd., Hohhot, 011517, PR China
| | - Guojing Li
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, 010018, PR China; Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010021, PR China; Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010021, PR China.
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Wang Y, Li Y, Tian H, Wang W, Wang X, Hussain S, Yuan Y, Lin R, Hussain H, Wang T, Wang S. AtS40-1, a group I DUF584 protein positively regulates ABA response and salt tolerance in Arabidopsis. Gene 2022; 846:146846. [PMID: 36044943 DOI: 10.1016/j.gene.2022.146846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/06/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022]
Abstract
Abiotic stresses such as salt and drought affect plants growth and development, whereas the plant hormone ABA is able to regulate plant responses to abiotic stresses by regulating downstream gene expression. Therefore characterization of unknown function ABA responsive genes is able to identify novel regulators of plant abiotic stress responses. We report here the characterization of AtS40-1, a Group I DUF584 protein in the regulation of ABA and salt responses in Arabidopsis. RT-PCR results show that the expression of AtS40-1 was dramatically induced by ABA, but only slightly increase, if any, was observed for other three Group I DUF584 genes including AtS40-1L, AtS40-2 and AtS40-3. Transfection assays in Arabidopsis protoplasts show that all the four Group I DUF584 proteins were predominately localized in nucleus and were able to repress the expression of the co-transfected reporter gene. The roles of AtS40-1 in regulating plant response to ABA and abiotic stress responses were analyzed, by using transgenic plants and inactivation mutants. The results show that the ABA responses were increased in the 35S:AtS40-1 transgenic plants, but decreased in the ats40-1 mutants. Similar to AtS40-1, the results indicate that AtS40-1L, the most closely related DUF584 protein to AtS40-1, positively regulates ABA responses in Arabidopsis. However, further decreased ABA responses were not observed in the ats40-1 ats40-1l double mutants. On the other hand, salt tolerance was increased in the transgenic plants overexpressing AtS40-1 or AtS40-1L, but decreased in the ats40-1 and ats40-1l mutants. Quantitative RT-PCR results show that the ABA induced expression of the ABA signaling regulator genes ABI3, ABI4 and ABA responsive gene RAB18 was decreased, where as ABA signaling gene ABI1 was increased in the ats40-1 mutants. These results suggest that AtS40-1 regulates ABA and salt responses in Arabidopsis, possibly by affecting ABA induced expression of some ABA signaling regulator genes.
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Affiliation(s)
- Yating Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024 China
| | - Yingying Li
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024 China
| | - Hainan Tian
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024 China
| | - Wei Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China
| | - Xutong Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China
| | - Saddam Hussain
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024 China
| | - Yuan Yuan
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024 China
| | - Rao Lin
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024 China
| | - Hadia Hussain
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024 China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024 China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024 China; Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China.
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Xu J, Gad AG, Luo Y, Fan C, Uddin JBG, ul Ain N, Huang C, Zhang Y, Miao Y, Zheng X. Five OsS40 Family Members Are Identified as Senescence-Related Genes in Rice by Reverse Genetics Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:701529. [PMID: 34539694 PMCID: PMC8446524 DOI: 10.3389/fpls.2021.701529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/09/2021] [Indexed: 05/30/2023]
Abstract
A total of 16 OsS40 genes of Oryza sativa were identified in our previous work, but their functions remain unclear. In this study, 13 OsS40 members were knocked out using the CRISPR/cas9 gene-editing technology. After screening phenotype characterization of CRISPR/Cas9 mutants compared to WT, five oss40s mutants exhibited a stay-green phenotype at 30 days after heading. Moreover, increased grain size and grain weight occurred in the oss40-1, oss40-12, and oss40-14 lines, while declined grain weight appeared in the oss40-7 and oss40-13 mutants. The transcript levels of several senescence-associated genes (SAGs), chlorophyll degradation-related genes (CDGs), as well as WRKY members were differentially decreased in the five stay-green oss40s mutants compared to WT. Five oss40 mutants also exhibited a stay-green phenotype when the detached leaves were incubated under darkness for 4 days. OsSWEET4 and OsSWEET1b were significantly upregulated, while OsSWEET1a and OsSWEET13 were significantly downregulated in both oss40-7 and oss40-14 compared to WT. Furthermore, these five OsS40 displayed strong transcriptional activation activity and were located in the nucleus. Most of the OsS40 genes were downregulated in the oss40-1, oss40-7, and oss40-12 mutants, but upregulated in the oss40-13 and oss40-14 mutants, indicating coordinated regulation among OsS40 members. These results suggest that OsS40-1, OsS40-7, OsS40-12, OsS40-13, and OsS40-14 are senescence-associated genes, involved in the senescence and carbon allocation network by modulating other OsS40 members, SWEET member genes, and senescence-related gene expression.
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