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Chong X, Liu Y, Li P, Wang Y, Zhou T, Chen H, Wang H. Heterologous Expression of Chrysanthemum TCP Transcription Factor CmTCP13 Enhances Salinity Tolerance in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2024; 13:2118. [PMID: 39124235 PMCID: PMC11313808 DOI: 10.3390/plants13152118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024]
Abstract
Plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) proteins play critical roles in plant development and stress responses; however, their functions in chrysanthemum (Chrysanthemum morifolium) have not been well-studied. In this study, we isolated and characterized the chrysanthemum TCP transcription factor family gene CmTCP13, a homolog of AtTCP13. This gene encoded a protein harboring a conserved basic helix-loop-helix motif, and its expression was induced by salinity stress in chrysanthemum plants. Subcellular localization experiments showed that CmTCP13 localized in the nucleus. Sequence analysis revealed the presence of multiple stress- and hormone-responsive cis-elements in the promoter region of CmTCP13. The heterologous expression of CmTCP13 in Arabidopsis plants enhanced their tolerance to salinity stress. Under salinity stress, CmTCP13 transgenic plants exhibited enhanced germination, root length, seedling growth, and chlorophyll content and reduced relative electrical conductivity compared with those exhibited by wild-type (WT) plants. Moreover, the expression levels of stress-related genes, including AtSOS3, AtP5CS2, AtRD22, AtRD29A, and AtDREB2A, were upregulated in CmTCP13 transgenic plants than in WT plants under salt stress. Taken together, our results demonstrate that CmTCP13 is a critical regulator of salt stress tolerance in plants.
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Affiliation(s)
- Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Yanan Liu
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang 332005, China
| | - Peiling Li
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang 464000, China
| | - Yue Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ting Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Hong Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Li Y, Liu X, Xu X, Zhu G, Xiang D, Liu P. Identification and characterization of the RcTCP gene family and its expression in response to abiotic stresses in castor bean. BMC Genomics 2024; 25:670. [PMID: 38965476 PMCID: PMC11223397 DOI: 10.1186/s12864-024-10347-6] [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: 11/28/2023] [Accepted: 04/25/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND The TCP (teosinte branched1/cincinnata/proliferating cell factor) family plays a prominent role in plant development and stress responses. However, TCP family genes have thus far not been identified in castor bean, and therefore an understanding of the expression and functional aspects of castor bean TCP genes is lacking. To identify the potential biological functions of castor bean (RcTCP) TCP members, the composition of RcTCP family members, their basic physicochemical properties, subcellular localizations, interacting proteins, miRNA target sites, and gene expression patterns under stress were assessed. RESULTS The presence of 20 RcTCP genes on the nine chromosomes of castor bean was identified, all of which possess TCP domains. Phylogenetic analysis indicated a close relationship between RcTCP genes and Arabidopsis AtTCP genes, suggesting potential functional similarity. Subcellular localization experiments confirmed that RcTC01/02/03/10/16/18 are all localized in the nucleus. Protein interaction analysis revealed that the interaction quantity of RcTCP03/06/11 proteins is the highest, indicating a cascade response in the functional genes. Furthermore, it was found that the promoter region of RcTCP genes contains a large number of stress-responsive elements and hormone-induced elements, indicating a potential link between RcTCP genes and stress response functions. qRT-PCR showed that all RcTCP genes exhibit a distinct tissue-specific expression pattern and their expression is induced by abiotic stress (including low temperature, abscisic acid, drought, and high salt). Among them, RcTCP01/03/04/08/09/10/14/15/18/19 genes may be excellent stress-responsive genes. CONCLUSION We discovered that RcTCP genes play a crucial role in various activities, including growth and development, the stress response, and transcription. This study provides a basis for studying the function of RcTCP gene in castor.
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Affiliation(s)
- Yanxiao Li
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyang Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyuan Xu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Guishuang Zhu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Dianjun Xiang
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
| | - Peng Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
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3
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Liu S, An Z, Li Y, Yang R, Lai Z. Genome-Wide Identification of the Cation/Proton Antiporter (CPA) Gene Family and Functional Analysis of AtrNHX8 under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1701. [PMID: 38931134 PMCID: PMC11207833 DOI: 10.3390/plants13121701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024]
Abstract
Amaranthus tricolor is an important vegetable, and its quality is affected by salt stress. Cation/proton antiporters (CPA) contribute to plant development and tolerance to salt stress. In this study, 35 CPA genes were identified from a genome database for A. tricolor, including 9 NHX, 5 KEA, and 21 CPA2 genes. Furthermore, in A. tricolor, the expression levels of most AtrNHX genes were higher at a low salinity level (50 or 100 mM NaCl) than in the control or 200 mM NaCl treatment. Levels of most AtrNHX genes were elevated in the stem. Moreover, AtrNHX8 was homologous to AtNHX4, which is involved in the regulation of sodium homeostasis and salt stress response. After AtrNHX8 overexpression in Arabidopsis thaliana, seed germination was better, and the flowering time was earlier than that of wild-type plants. Additionally, the overexpression of AtrNHX8 in A. thaliana improved salt tolerance. These results reveal the roles of AtrNHX genes under salt stress and provide valuable information on this gene family in amaranth.
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Affiliation(s)
- Shengcai Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.A.); (Y.L.)
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zixian An
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.A.); (Y.L.)
| | - Yixuan Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.A.); (Y.L.)
| | - Rongzhi Yang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.A.); (Y.L.)
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.A.); (Y.L.)
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4
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Liu S, An Z, Lai Z. Amaranth's Growth and Physiological Responses to Salt Stress and the Functional Analysis of AtrTCP1 Gene. Int J Mol Sci 2024; 25:5437. [PMID: 38791475 PMCID: PMC11121779 DOI: 10.3390/ijms25105437] [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: 05/03/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Amaranth species are C4 plants that are rich in betalains, and they are tolerant to salinity stress. A small family of plant-specific TCP transcription factors are involved in the response to salt stress. However, it has not been investigated whether amaranth TCP1 is involved in salt stress. We elucidated that the growth and physiology of amaranth were affected by salt concentrations of 50-200 mmol·L-1 NaCl. The data showed that shoot and root growth was inhibited at 200 mmol·L-1, while it was promoted at 50 mmol·L-1. Meanwhile, the plants also showed physiological responses, which indicated salt-induced injuries and adaptation to the salt stress. Moreover, AtrTCP1 promoted Arabidopsis seed germination. The germination rate of wild-type (WT) and 35S::AtrTCP1-GUS Arabidopsis seeds reached around 92% by the seventh day and 94.5% by the second day under normal conditions, respectively. With 150 mmol·L-1 NaCl treatment, the germination rate of the WT and 35S::AtrTCP1-GUS plant seeds was 27.0% by the seventh day and 93.0% by the fourth day, respectively. Under salt stress, the transformed 35S::AtrTCP1 plants bloomed when they grew 21.8 leaves after 16.2 days of treatment, which was earlier than the WT plants. The transformed Arabidopsis plants flowered early to resist salt stress. These results reveal amaranth's growth and physiological responses to salt stress, and provide valuable information on the AtrTCP1 gene.
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Affiliation(s)
- Shengcai Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zixian An
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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Panzade KP, Vishwakarma H, Kharate PS, Azameti MK. Genome-wide analysis and expression profile of TCP gene family under drought and salinity stress condition in cowpea ( Vigna unguiculata (L.) Walp.). 3 Biotech 2024; 14:138. [PMID: 38682097 PMCID: PMC11052985 DOI: 10.1007/s13205-024-03976-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/13/2024] [Indexed: 05/01/2024] Open
Abstract
TCP transcription factors are known to regulate abiotic stress condition, but their role in V. unguiculata remains unexplored. So, in silico analysis and expression profile of the TCP gene family were performed in V. unguiculata to understand its role in response to heat and drought stress. A genome-wide search detected 28 TCPs (designated as VuTCPs) that were grouped into three subclasses by phylogenetic analysis. Gene structure, synteny, and phylogeny analyses of VuTCPs have shown a typical evolutionary path. One tandem and eight segmental duplication events were identified. Furthermore, identified duplicated, and orthologous VuTCP genes were under strong purifying selection pressure. A total of 15 SSRs were identified in the 12 VuTCPs, while 10 VuTCP genes were regulated by different miRNAs having a major role in abiotic stress tolerance. Analysed physicochemical properties, cis-acting elements, and gene ontology suggested that VuTCPs play various roles, including salinity and drought stress tolerance. qRT-PCR analysis showed that 11 and 15 VuTCPs were upregulated under drought and salinity stress conditions, respectively. Our findings provide comprehensive insights into the genomic characterization of the VuTCPs gene family in V. unguiculata, offering a foundation for understanding their structure, evolution, and role in abiotic stress tolerance. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03976-x.
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Affiliation(s)
- Kishor Prabhakar Panzade
- Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Chh. Sambhaji Nagar (Aurangabad), Maharashtra, 431002 India
| | - Harinder Vishwakarma
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012 India
| | - Pawankumar S. Kharate
- Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Chh. Sambhaji Nagar (Aurangabad), Maharashtra, 431002 India
| | - Mawuli K. Azameti
- Department of Applied Biology, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Upper East Region Ghana
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Carvalho P, Gomes C, Gonçalves I, Lourenço TF, Vlad D, Langdale JA, Saibo NJM. The bHLH transcription factor OsPRI1 activates the Setaria viridis PEPC1 promoter in rice. THE NEW PHYTOLOGIST 2024; 241:2495-2505. [PMID: 38323734 DOI: 10.1111/nph.19556] [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: 08/08/2023] [Accepted: 12/29/2023] [Indexed: 02/08/2024]
Abstract
Photosynthetic efficiency is reduced by the dual role of Rubisco, which acts either as a carboxylase or as an oxygenase, the latter leading to photorespiration. C4 photosynthesis evolved as a carbon-concentrating mechanism to reduce photorespiration. To engineer C4 into a C3 plant, it is essential to understand how C4 genes, such as phosphoenolpyruvate carboxylase (PEPC1), are regulated to be expressed at high levels and in a cell-specific manner. Yeast one-hybrid screening was used to show that OsPRI1, a rice bHLH transcription factor involved in iron homeostasis, binds to the Setaria viridis PEPC1 promoter. This promoter drives mesophyll-specific gene expression in rice. The role of OsPRI1 in planta was characterized using a rice line harbouring SvPEPC1pro ::GUS. We show that OsPRI1 activates the S. viridis PEPC1 promoter by binding to an N-box in the proximal promoter, and that GUS activity is highly reduced in SvPEPC1pro ::GUS lines when OsPRI1 is mutated. Cross-species comparisons showed that the SvPRI1 homolog binds to the SvPEPC1 promoter but the maize ZmPRI1 does not bind to the ZmPEPC1 promoter. Our results suggest that elements of the iron homeostasis pathway were co-opted to regulate PEPC1 gene expression during the evolution of some but not all C4 species.
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Affiliation(s)
- Pedro Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Célia Gomes
- Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Ivan Gonçalves
- Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Tiago F Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Daniela Vlad
- Department of Biology, University of Oxford, South Parks Rd, OX1 3RB, Oxford, UK
| | - Jane A Langdale
- Department of Biology, University of Oxford, South Parks Rd, OX1 3RB, Oxford, UK
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
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7
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Moulick D, Mukherjee A, Das A, Roy A, Majumdar A, Dhar A, Pattanaik BK, Chowardhara B, Ghosh D, Upadhyay MK, Yadav P, Hazra S, Sarkar S, Mahanta S, Santra SC, Choudhury S, Maitra S, Mishra UN, Bhutia KL, Skalicky M, Obročník O, Bárek V, Brestic M, Hossain A. Selenium - An environmentally friendly micronutrient in agroecosystem in the modern era: An overview of 50-year findings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 270:115832. [PMID: 38141336 DOI: 10.1016/j.ecoenv.2023.115832] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 12/25/2023]
Abstract
Agricultural productivity is constantly being forced to maintain yield stability to feed the enormously growing world population. However, shrinking arable and nutrient-deprived soil and abiotic and biotic stressor (s) in different magnitudes put additional challenges to achieving global food security. Though well-defined, the concept of macro, micronutrients, and beneficial elements is from a plant nutritional perspective. Among various micronutrients, selenium (Se) is essential in small amounts for the life cycle of organisms, including crops. Selenium has the potential to improve soil health, leading to the improvement of productivity and crop quality. However, Se possesses an immense encouraging phenomenon when supplied within the threshold limit, also having wide variations. The supplementation of Se has exhibited promising outcomes in lessening biotic and abiotic stress in various crops. Besides, bulk form, nano-Se, and biogenic-Se also revealed some merits and limitations. Literature suggests that the possibilities of biogenic-Se in stress alleviation and fortifying foods are encouraging. In this article, apart from adopting a combination of a conventional extensive review of the literature and bibliometric analysis, the authors have assessed the journey of Se in the "soil to spoon" perspective in a diverse agroecosystem to highlight the research gap area. There is no doubt that the time has come to seriously consider the tag of beneficial elements associated with Se, especially in the drastic global climate change era.
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Affiliation(s)
- Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India; Plant Stress Biology and Metabolomics Laboratory, Department of Life Science & Bioinformatics, H.G. Khorana School of Life Sciences, Assam University, Silchar 788011, India.
| | - Arkabanee Mukherjee
- Indian Institute of Tropical Meteorology, Dr Homi Bhabha Rd, Panchawati, Pashan, Pune, Maharashtra 411008, India.
| | - Anupam Das
- Department of Soil Science and Agricultural Chemistry, Bihar Agricultural University, Sabour, Bhagalpur, India.
| | - Anirban Roy
- School of Agriculture and Rural Development, Faculty Centre for IRDM, Ramakrishna Mission Vi-Vekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata 700103, India.
| | - Arnab Majumdar
- School of Environmental Studies, Jadavpur University, Kolkata 700032, India.
| | - Anannya Dhar
- School of Agriculture and Rural Development, Faculty Centre for IRDM, Ramakrishna Mission Vi-Vekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata 700103, India.
| | - Binaya Kumar Pattanaik
- Institute of Environment Education and Research, Bharati Vidyapeeth (Deemed to be University), Pune 411043, India.
| | - Bhaben Chowardhara
- Department of Botany, Faculty of Science and Technology, Arunachal University of Studies NH-52, Knowledge City, District- Namsai, Arunachal Pradesh 792103, India.
| | - Dibakar Ghosh
- Division of Agronomy, ICAR-Indian Institute of Water Management, Bhubaneswar 751023, Odisha, India.
| | - Munish Kumar Upadhyay
- Centre for Environmental Science & Engineering, Department of Civil Engineering, Indian Institute of Technology Kanpur, 208016, India.
| | - Poonam Yadav
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India.
| | - Swati Hazra
- School of Agricultural Sciences, Sharda University, Greater Noida, UP 201310, India.
| | - Sukamal Sarkar
- School of Agriculture and Rural Development, Faculty Centre for IRDM, Ramakrishna Mission Vi-Vekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata 700103, India.
| | - Subrata Mahanta
- Department of Chemistry, National Institute of Technology Jamshedpur, Adityapur, Jamshedpur, Jharkhand 831014, India.
| | - S C Santra
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | - Shuvasish Choudhury
- Plant Stress Biology and Metabolomics Laboratory, Department of Life Science & Bioinformatics, H.G. Khorana School of Life Sciences, Assam University, Silchar 788011, India.
| | - Sagar Maitra
- Department of Agronomy and Agroforestry, Centurion University of Technology and Management, Odisha 761211, India.
| | - Udit Nandan Mishra
- Department of Crop Physiology & Biochemistry, Faculty of Agriculture, Sri Sri University, Sri Sri Vihar, Bidyadharpur Arilo, Ward No-03, Cuttack, Odisha 754006, India.
| | - Karma L Bhutia
- Department of Agricultural Biotechnology & Molecular Biology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa (Samastipur), Bihar 848 125, India.
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czechia.
| | - Oliver Obročník
- Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia.
| | - Viliam Bárek
- Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia.
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czechia; Institute of Plant and Environmental Sciences, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovak.
| | - Akbar Hossain
- Division of Soil Science, Bangladesh Wheat and Maize Research Institute, Dinajpur 5200, Bangladesh.
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8
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Phan NTH, Van Pham C, Tang HT, Van Nguyen L, Nguyen LV, Bertin P. Integration of genome-wide association studies reveal loci associated with salt tolerance score of rice at the seedling stage. J Appl Genet 2023; 64:603-614. [PMID: 37555917 DOI: 10.1007/s13353-023-00775-7] [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: 03/29/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
Salt threatens rice cultivation in many countries. Hence, breeding new varieties with high salt tolerance is important.A panel of 2,391 rice accessions from the 3 K Rice Genome Project was selected to evaluate salt tolerance via the standard evaluation score (SES) in hydroponics under 60 mM NaCl at the seedling stage. Three sub-population panels including 1,332, 628, and 386 accessions from the original 2,391 ones were constructed based on low relatedness revealed by a phylogenetic tree generated by Archaeopteryx Tree. A genome-wide association study (GWAS) was conducted on the entire and sub-population panels using SES data and a selection of 5, 10, 20, and 40% of SNPs selected from the original 1,011,601 SNPs by filtering minor allele frequency > 5% and missing rate < 5%. To perform GWAS, three methods implemented in three different software packages were utilized.Using the integration of GWAS programs, a total of four QTLs associated with SES scores were identified in different panels. Some QTLs co-located with previously detected QTL-related traits. qSES1.1 was detected in three panels, qSES1.3 and qSES2.1 in two panels, and qSES3.1 in one panel through GWAS by all three methods used and selected SNPs. These four QTLs were selected to detect candidate genes. Combining gene-based association study plus haplotype analysis in the entire population and the three sub-populations let us shortlist three candidate genes, viz. LOC_Os01g23640 and LOC_Os01g23680 for qSES1.1, and LOC_Os01g71240 for qSES1.3 region affecting salt tolerance. The identified QTLs and candidate genes provided useful materials and genetic information for future functional characterization and genetic improvement of salt tolerance in rice.
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Affiliation(s)
- Nhung Thi Hong Phan
- Earth and Life Institute, Université Catholique de Louvain, 1348, Louvain la Neuve, Belgium.
- Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam.
| | - Cuong Van Pham
- Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Hanh Thi Tang
- Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Loc Van Nguyen
- Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Long Viet Nguyen
- Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Pierre Bertin
- Earth and Life Institute, Université Catholique de Louvain, 1348, Louvain la Neuve, Belgium
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9
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Jiang Y, Jiang D, Xia M, Gong M, Li H, Xing H, Zhu X, Li HL. Genome-Wide Identification and Expression Analysis of the TCP Gene Family Related to Developmental and Abiotic Stress in Ginger. PLANTS (BASEL, SWITZERLAND) 2023; 12:3389. [PMID: 37836129 PMCID: PMC10574737 DOI: 10.3390/plants12193389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Ginger (Zingiber officinale Roscoe), a widely consumed edible and medicinal plant, possesses significant nutritional and economic value. Abiotic stresses such as drought and low temperatures can impact the growth and development of ginger. The plant-specific transcription factor Teosinte branched1/cycloidea/proliferating cell factor (TCP) has progressively been identified in various plants for its role in regulating plant growth and development as well as conferring resistance to abiotic stresses. However, limited information on the TCP family is available in ginger. In this study, we identified 20 TCP members in the ginger genome, which were randomly distributed across 9 chromosomes. Based on phylogenetic analysis, these ginger TCP were classified into two subfamilies: Class I (PCF) and Class II (CIN, CYC/TB). The classification of the identified ginger TCPs was supported by a multi-species phylogenetic tree and motif structure analysis, suggesting that the amplification of the ginger TCP gene family occurred prior to the differentiation of angiosperms. The promoter region of ginger TCP genes was found to contain numerous cis-acting elements associated with plant growth, development, and abiotic stress response. Among these elements, the stress response element, anaerobic induction, and MYB binding site play a dominant role in drought responsiveness. Additionally, expression pattern analysis revealed variations in the expression of ginger TCP gene among different tissues and in response to diverse abiotic stresses (drought, low temperature, heat, and salt). Our research offers a thorough examination of TCP members within the ginger plant. This analysis greatly contributes to the understanding of how TCP genes regulate tissue development and response to stress, opening up new avenues for further exploration in this field.
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Affiliation(s)
- Yajun Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Dongzhu Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Maoqin Xia
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Min Gong
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Hui Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Haitao Xing
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Xuedong Zhu
- Yudongnan Academy of Agricultural Sciences, Chongqing 408000, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
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10
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Li Y, Li L, Yang J, Niu Z, Liu W, Lin Y, Xue Q, Ding X. Genome-Wide Identification and Analysis of TCP Gene Family among Three Dendrobium Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:3201. [PMID: 37765364 PMCID: PMC10538224 DOI: 10.3390/plants12183201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023]
Abstract
Dendrobium orchids, which are among the most well-known species of orchids, are appreciated for their aesthetic appeal across the globe. Furthermore, due to their strict living conditions, they have accumulated high levels of active ingredients, resulting not only in their medicinal value but also in their strong ability to respond to harsh environments. The TCP gene family plays an important role in plant growth and development, and signal transduction. However, these genes have not been systematically investigated in Dendrobium species. In this study, we detected a total of 24, 23, and 14 candidate TCP members in the genome sequences of D. officinale, D. nobile, and D. chrysotoxum, respectively. These genes were classified into three clades on the basis of a phylogenetic analysis. The TCP gene numbers among Dendrobium species were still highly variable due to the independent loss of genes in the CIN clade. However, only three gene duplication events were detected, with only one tandem duplication event (DcTCP9/DcTCP10) in D. chrysotoxum and two pairs of paralogous DoTCP gene duplication events (DoTCP1/DoTCP23 and DoTCP16/DoTCP24) in D. officinale. A total of 25 cis-acting elements of TCPs related to hormone/stress and light responses were detected. Among them, the proportions of hormone response, light response, and stress response elements in D. officinale (100/421, 127/421, and 171/421) were similar to those in D. nobile (83/352, 87/352, and 161/352). Using qRT-PCR to determine their expression patterns under MeJA treatment, four DoTCPs (DoTCP2, DoTCP4, DoTCP6, and DoTCP14) were significantly upregulated under MeJA treatment, which indicates that TCP genes may play important roles in responding to stress. Under ABA treatment, seven DoTCPs (DoTCP3, DoTCP7, DoTCP9, DoTCP11, DoTCP14, DoTCP15, and DoTCP21) were significantly upregulated, indicating that TCP genes may also play an important role in hormone response. Therefore, these results can provide useful information for studying the evolution and function of TCP genes in Dendrobium species.
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Affiliation(s)
- Yaoting Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (Y.L.); (Y.L.)
- School of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
| | - Lingli Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.L.); (J.Y.); (Z.N.); (W.L.)
| | - Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.L.); (J.Y.); (Z.N.); (W.L.)
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.L.); (J.Y.); (Z.N.); (W.L.)
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.L.); (J.Y.); (Z.N.); (W.L.)
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (Y.L.); (Y.L.)
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.L.); (J.Y.); (Z.N.); (W.L.)
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.L.); (J.Y.); (Z.N.); (W.L.)
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11
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Zhang M, Qin S, Yan J, Li L, Xu M, Liu Y, Zhang W. Genome-wide identification and analysis of TCP family genes in Medicago sativa reveal their critical roles in Na +/K + homeostasis. BMC PLANT BIOLOGY 2023; 23:301. [PMID: 37280506 DOI: 10.1186/s12870-023-04318-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND Medicago sativa is the most important forage world widely, and is characterized by high quality and large biomass. While abiotic factors such as salt stress can negatively impact the growth and productivity of alfalfa. Maintaining Na+/K+ homeostasis in the cytoplasm helps reduce cell damage and nutritional deprivation, which increases a salt-tolerance of plant. Teosinte Branched1/ Cycloidea/ Proliferating cell factors (TCP) family genes, a group of plant-specific transcription factors (TFs), involved in regulating plant growth and development and abiotic stresses. Recent studies have shown TCPs control the Na+/K+ concentration of plants during salt stress. In order to improve alfalfa salt tolerance, it is important to identify alfalfa TCP genes and investigate if and how they regulate alfalfa Na+/K+ homeostasis. RESULTS Seventy-one MsTCPs including 23 non-redundant TCP genes were identified in the database of alfalfa genome (C.V XinJiangDaYe), they were classified into class I PCF (37 members) and class II: CIN (28 members) and CYC/TB1 (9 members). Their distribution on chromosome were unequally. MsTCPs belonging to PCF were expressed specifically in different organs without regularity, which belonging to CIN class were mainly expressed in mature leaves. MsTCPs belongs to CYC/TB1 clade had the highest expression level at meristem. Cis-elements in the promoter of MsTCPs were also predicted, the results indicated that most of the MsTCPs will be induced by phytohormone and stress treatments, especially by ABA-related stimulus including salinity stress. We found 20 out of 23 MsTCPs were up-regulated in 200 mM NaCl treatment, and MsTCP3/14/15/18 were significantly induced by 10 μM KCl, a K+ deficiency treatment. Fourteen non-redundant MsTCPs contained miR319 target site, 11 of them were upregulated in MIM319 transgenic alfalfa, and among them four (MsTCP3/4/10A/B) genes were directly degraded by miR319. MIM319 transgene alfalfa plants showed a salt sensitive phenotype, which caused by a lower content of potassium in alfalfa at least partly. The expression of potassium transported related genes showed significantly higher expression in MIM319 plants. CONCLUSIONS We systematically analyzes the MsTCP gene family at a genome-wide level and reported that miR319-TCPs model played a function in K+ up-taking and/ or transportation especially in salt stress. The study provide valuable information for future study of TCP genes in alfalfa and supplies candidate genes for salt-tolerance alfalfa molecular-assisted breeding.
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Affiliation(s)
- Mingxiao Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shangqian Qin
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianping Yan
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lin Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mingzhi Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanrong Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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12
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Wang C, Feng G, Xu X, Huang L, Nie G, Li D, Zhang X. Genome-Wide Identification, Characterization, and Expression of TCP Genes Family in Orchardgrass. Genes (Basel) 2023; 14:genes14040925. [PMID: 37107682 PMCID: PMC10138293 DOI: 10.3390/genes14040925] [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: 03/29/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Plant-specific TCP transcription factors regulate several plant growth and development processes. Nevertheless, little information is available about the TCP family in orchardgrass (Dactylis glomerata L.). This study identified 22 DgTCP transcription factors in orchardgrass and determined their structure, phylogeny, and expression in different tissues and developmental stages. The phylogenetic tree classified the DgTCP gene family into two main subfamilies, including class I and II supported by the exon-intron structure and conserved motifs. The DgTCP promoter regions contained various cis-elements associated with hormones, growth and development, and stress responses, including MBS (drought inducibility), circadian (circadian rhythms), and TCA-element (salicylic acid responsiveness). Moreover, DgTCP9 possibly regulates tillering and flowering time. Additionally, several stress treatments upregulated DgTCP1, DgTCP2, DgTCP6, DgTCP12, and DgTCP17, indicting their potential effects regarding regulating responses to the respective stress. This research offers a valuable basis for further studies of the TCP gene family in other Gramineae and reveals new ideas for increasing gene utilization.
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Affiliation(s)
- Cheng Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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13
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Viola IL, Alem AL, Jure RM, Gonzalez DH. Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors. Int J Mol Sci 2023; 24:ijms24065437. [PMID: 36982512 PMCID: PMC10049435 DOI: 10.3390/ijms24065437] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 and 2 (TCP) proteins constitute a plant-specific transcription factors family exerting effects on multiple aspects of plant development, such as germination, embryogenesis, leaf and flower morphogenesis, and pollen development, through the recruitment of other factors and the modulation of different hormonal pathways. They are divided into two main classes, I and II. This review focuses on the function and regulation of class I TCP proteins (TCPs). We describe the role of class I TCPs in cell growth and proliferation and summarize recent progresses in understanding the function of class I TCPs in diverse developmental processes, defense, and abiotic stress responses. In addition, their function in redox signaling and the interplay between class I TCPs and proteins involved in immunity and transcriptional and posttranslational regulation is discussed.
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Affiliation(s)
- Ivana L. Viola
- Correspondence: (I.L.V.); (D.H.G.); Tel.: +54-342-4511370 (ext. 5021) (I.L.V.)
| | | | | | - Daniel H. Gonzalez
- Correspondence: (I.L.V.); (D.H.G.); Tel.: +54-342-4511370 (ext. 5021) (I.L.V.)
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14
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Urbanavičiūtė I, Bonfiglioli L, Pagnotta MA. Phenotypic and Genotypic Diversity of Roots Response to Salt in Durum Wheat Seedlings. PLANTS (BASEL, SWITZERLAND) 2023; 12:412. [PMID: 36679125 PMCID: PMC9865824 DOI: 10.3390/plants12020412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Soil salinity is a serious threat to food production now and in the near future. In this study, the root system of six durum wheat genotypes, including one highly salt-tolerant (J. Khetifa) used as a check genotype, was evaluated, by a high-throughput phenotyping system, under control and salt conditions at the seedling stage. Genotyping was performed using 11 SSR markers closely linked with genome regions associated with root traits. Based on phenotypic cluster analysis, genotypes were grouped differently under control and salt conditions. Under control conditions, genotypes were clustered mainly due to a root angle, while under salt stress, genotypes were grouped according to their capacity to maintain higher roots length, volume, and surface area, as J. Khetifa, Sebatel, and Azeghar. SSR analysis identified a total of 42 alleles, with an average of about three alleles per marker. Moreover, quite a high number of Private alleles in total, 18 were obtained. The UPGMA phenogram of the Nei (1972) genetic distance clusters for 11 SSR markers and all phenotypic data under control conditions discriminate genotypes almost into the same groups. The study revealed as the combination of high-throughput systems for phenotyping with SSR markers for genotyping it's a useful tool to provide important data for the selection of suitable parental lines for salt-tolerance breeding. Nevertheless, the narrow root angle, which is an important trait in drought tolerance, is not a good indicator of salt tolerance. Instated for salt tolerance is more important the amount of roots.
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Affiliation(s)
| | | | - Mario A. Pagnotta
- Department of Agricultural and Forest Sciences, Tuscia University, Via S. C. de Lellis, 01100 Viterbo, Italy
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15
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Genome-Wide Identification and Characterization of TCP Gene Family Members in Melastoma candidum. Molecules 2022; 27:molecules27249036. [PMID: 36558169 PMCID: PMC9787641 DOI: 10.3390/molecules27249036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
It has been confirmed that the plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) gene family plays a pivotal role during plant growth and development. M. candidum is a native ornamental species and has a wide range of pharmacodynamic effects. However, there is still a lack of research on TCP’s role in controlling M. candidum’s development, abiotic stress responses and hormone metabolism. A comprehensive description of the TCP gene family in M. candidum is urgently needed. In this study, we used the HMMER search method in conjunction with the BLASTp method to identify the members of the TCP gene family, and a total of 35 TCP genes were identified. A domain analysis further confirmed that all 35 TCPs contained a TCP superfamily, a characteristic involved in dimerization and DNA binding that can be found in most genes from this gene family, suggesting that our identification was effective. As a result of the domain conservation analysis, the 35 TCP genes could be classified into two classes, TCP-P and TCP-C, based on the conservative regions of 55 and 59 amino acids, respectively. Gene-duplication analysis revealed that most TCP genes were present in duplication events that eventually led to TCP gene expansion in M. candidum. All the detected gene pairs had a Ka/Ks value of less than one, suggesting that purification selection is the most important factor that influences the evolution of TCP genes. Phylogenetic analysis of three species displayed the evolutionary relationship of TCP genes across different species and further confirmed our results. The real-time quantitative PCR (qRT-PCR) results showed that McTCP2a, McTCP7a, McTCP10, McTCP11, McTCP12a, McTCP13, McTCP16, McTCP17, McTCP18, McTCP20 and McTCP21 may be involved in leaf development; McTCP4a, McTCP1, McTCP14, McTCP17, McTCP18, McTCP20, McTCP22 and McTCP24 may be involved in flower development; and McTCP2a, McTCP3, McTCP5a, McTCP6, McTCP7a, McTCP9, McTCP11, McTCP14 and McTCP16 may be involved in seed development. Our results dissect the TCP gene family across the genome of M. candidum and provide valuable information for exploring TCP genes to promote molecular breeding and property improvement of M. candidum in the future.
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16
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Li D, Tang X, Dong Y, Wang Y, Shi S, Li S, Liu Y, Ge H, Chen H. Comparative genomic investigation of TCP gene family in eggplant (Solanum melongena L.) and expression analysis under divergent treatments. PLANT CELL REPORTS 2022; 41:2213-2228. [PMID: 36001130 DOI: 10.1007/s00299-022-02918-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The putative TCP genes and their responses to abiotic stress in eggplant were comprehensively characterized, and SmTCP genes (Smechr0202855.1 and Smechr0602431.1) may be involved in anthocyanin synthesis. The Teosinte branched1/Cycloidea/Proliferating cell factors (TCPs), a family of plant-specific transcription factors, plays paramount roles in a plethora of developmental and physiological processes. We here systematically characterized putative TCP genes and their response to abiotic stress in eggplant. In total, 30 SmTCP genes were categorized into two subfamilies based on the classical TCP conserved domains. Chromosomal location analysis illustrated the random distribution of putative SmTCP genes along 12 eggplant chromosomes. Cis-acting elements and miRNA target prediction suggested that versatile and complicated regulatory mechanisms that control SmTCPs gene expression, and 3 miRNAs (miR319a, miR319b, and miR319c-3p) might act as major regulators targeting SmTCPs. Tissue expression profiles indicated divergent spatiotemporal expression patterns of SmTCPs. qRT-PCR assays demonstrated different expression profiles of SmTCP under 4 °C, drought and ABA treatment conditions, suggesting the possible participation of SmTCP genes in multiple signaling pathways. Furthermore, RNA-seq data of eggplant anthocyanin synthesis coupled with yeast one-hybrid and dual-luciferase assays suggested the involvement of SmTCP genes (Smechr0202855.1 and Smechr0602431.1) in the mediation of anthocyanin synthesis. Our study will facilitate further investigation on the putative functional characterization of eggplant TCP genes and lay a solid foundation for the in-depth study of the involvement of SmTCP genes in the regulation of anthocyanin synthesis.
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Affiliation(s)
- Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Xin Tang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yanxiao Dong
- Shanghai Agricultural Science and Technology Service Center, Shanghai, 200335, China
| | - Yingying Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Suli Shi
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Shaohang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Haiyan Ge
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
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17
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Wei N, Zhai Q, Li H, Zheng S, Zhang J, Liu W. Genome-Wide Identification of ERF Transcription Factor Family and Functional Analysis of the Drought Stress-Responsive Genes in Melilotus albus. Int J Mol Sci 2022; 23:ijms231912023. [PMID: 36233332 PMCID: PMC9570465 DOI: 10.3390/ijms231912023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
As an important forage legume with high values in feed and medicine, Melilotus albus has been widely cultivated. The AP2/ERF transcription factor has been shown to play an important regulatory role in plant drought resistance, but it has not been reported in the legume forage crop M. albus. To digger the genes of M. albus in response to drought stress, we identified and analyzed the ERF gene family of M. albus at the genome-wide level. A total of 100 MaERF genes containing a single AP2 domain sequence were identified in this study, named MaERF001 to MaERF100, and bioinformatics analysis was performed. Collinearity analysis indicated that segmental duplication may play a key role in the expansion of the M. albus ERF gene family. Cis-acting element predictions suggest that MaERF genes are involved in various hormonal responses and abiotic stresses. The expression patterns indicated that MaERFs responded to drought stress to varying degrees. Furthermore, four up-regulated ERFs (MaERF008, MaERF037, MaERF054 and MaERF058) under drought stress were overexpressed in yeast and indicated their biological functions to confer the tolerance to drought. This work will advance the understanding of the molecular mechanisms underlying the drought response in M. albus. Further study of the promising potential candidate genes identified in this study will provide a valuable resource as the next step in functional genomics studies and improve the possibility of improving drought tolerance in M. albus by transgenic approaches.
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18
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AlMulla AA, Dahlawi S, Randhawa MA, Zaman QU, Chen Y, Faraj TK. Toxic Metals and Metalloids in Hassawi Brown Rice: Fate during Cooking and Associated Health Risks. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12125. [PMID: 36231427 PMCID: PMC9566630 DOI: 10.3390/ijerph191912125] [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: 08/19/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Rice has been a dietary staple for centuries, providing vital nutrients to the human body. Brown rice is well known for its nutrient-dense food profile. However, owing to multiple causes (anthropogenic and non-anthropogenic), it can also be a potential source of toxic heavy metals in the diet. Brown Hassawi rice samples were collected from the Al-Ahsa region and analyzed for its content of toxic metals. The results reveal that all the tested metals varied significantly in the brown rice samples, while As and Pb in all three samples exceeded their respective maximum allowable limits (MALs), followed by Cd, which nearly approached the MAL in two samples out of three. Brown rice samples were cooked in rice:water systems, viz., low rice:water ratios (1:2.5, 1:3.5) and high rice:water ratios (1:5, 1:6), along with soaking as a pre-treatment. Soaking was unproductive in removing the heavy metals from the rice, whereas cooking dissipated all metals from the rice, except for Cd, which was statistically non-significant. The high-water cooking of the rice was more effective in the dissipation of metals from the rice as compared to low-water cooking conditions. Through the consumption of rice, the estimated daily intake (EDI) of heavy metals is 162 g per person per day for As, which is above the provisional maximum tolerable daily intake (PMTDI) regardless of cooking circumstances. The hazard risk index (HRI) also highlighted the fact that As can be a potential health hazard to rice consumers in the Al-Ahsa region of Saudi Arabia. These results indicate the potential health risks caused by the consumption of this rice by humans. Regular monitoring is recommended to manage and control elevated concentrations and related health hazards as a result of the use of Hassawi rice contaminated by the accumulation of metals and metalloids.
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Affiliation(s)
- Abdulaziz Abdulrahman AlMulla
- Department of Environmental Health, College of Public Health, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Saad Dahlawi
- Department of Environmental Health, College of Public Health, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Muhammad Atif Randhawa
- Department of Environmental Health, College of Public Health, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Qamar uz Zaman
- Department of Environmental Sciences, The University of Lahore, Punjab 54590, Pakistan
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Turki Kh. Faraj
- Department of Soil Science, College of Food and Agriculture Sciences, King Saud University, P.O. Box 145111, Riyadh 11362, Saudi Arabia
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19
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Rasheed A, Li H, Nawaz M, Mahmood A, Hassan MU, Shah AN, Hussain F, Azmat S, Gillani SFA, Majeed Y, Qari SH, Wu Z. Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective. FRONTIERS IN PLANT SCIENCE 2022; 13:966749. [PMID: 35968147 PMCID: PMC9366114 DOI: 10.3389/fpls.2022.966749] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 06/28/2022] [Indexed: 05/08/2023]
Abstract
Improvement of salinity tolerance in rice can minimize the stress-induced yield losses. Rice (Oryza sativa) is one of Asia's most widely consumed crops, native to the subtropical regions, and is generally associated with sensitivity to salinity stress episodes. Salt-tolerant rice genotypes have been developed using conventional breeding methods; however, the success ratio is limited because of the complex nature of the trait and the high cost of development. The narrow genetic base of rice limited the success of conventional breeding methods. Hence, it is critical to launch the molecular tools for screening rice novel germplasm for salt-tolerant genes. In this regard, the latest molecular techniques like quantitative trait loci (QTL) mapping, genetic engineering (GE), transcription factors (TFs) analysis, and clustered regularly interspaced short palindromic repeats (CRISPR) are reliable for incorporating the salt tolerance in rice at the molecular level. Large-scale use of these potent genetic approaches leads to identifying and editing several genes/alleles, and QTL/genes are accountable for holding the genetic mechanism of salinity tolerance in rice. Continuous breeding practices resulted in a huge decline in rice genetic diversity, which is a great worry for global food security. However, molecular breeding tools are the only way to conserve genetic diversity by exploring wild germplasm for desired genes in salt tolerance breeding programs. In this review, we have compiled the logical evidences of successful applications of potent molecular tools for boosting salinity tolerance in rice, their limitations, and future prospects. This well-organized information would assist future researchers in understanding the genetic improvement of salinity tolerance in rice.
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Affiliation(s)
- Adnan Rasheed
- Key Laboratory of Plant Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Huijie Li
- Key Laboratory of Plant Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- College of Humanity and Public Administration, Jiangxi Agricultural University, Nanchang, China
| | - Muhammad Nawaz
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, China
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Fiaz Hussain
- Directorate of Agronomy, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Saira Azmat
- Department of Agriculture, Agriculture Extension and Adaptive Research, Government of the Punjab, Lahore, Pakistan
| | | | - Yasir Majeed
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sameer H. Qari
- Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ziming Wu
- Key Laboratory of Plant Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, China
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Xu Y, Wang L, Liu H, He W, Jiang N, Wu M, Xiang Y. Identification of TCP family in moso bamboo (Phyllostachys edulis) and salt tolerance analysis of PheTCP9 in transgenic Arabidopsis. PLANTA 2022; 256:5. [PMID: 35670871 DOI: 10.1007/s00425-022-03917-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Bioinformatic analysis of moso bamboo TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors reveals their conservation and variation as well as the probable biological functions in abiotic stress response. Overexpressing PheTCP9 in Arabidopsis thaliana illustrates it may exhibit a new vision in different aspects of response to salt stress. Plant specific TCPs play important roles in plant growth, development and stress response, but studies of TCP in moso bamboo are limited. Therefore, in this study, a total of 40 TCP genes (PheTCP1 ~ 40) were identified and characterized from moso bamboo genome and divided into three different subfamilies, namely, 7 in TEOSINTE BRANCHED 1 / CYCLOIDEA (TB1/CYC), 14 in CINCINNATA (CIN) and 19 in PROLIFERATING CELL FACTOR (PCF). Subsequently, we analyzed the gene structures and conserved domain of these genes and found that the members from the same subfamilies exhibited similar exon/intron distribution patterns. Selection pressure and gene duplication analysis results indicated that PheTCP genes underwent strong purification selection during evolution. There were many cis-elements related to phytohermone and stress responsive existing in the upstream promoter regions of PheTCP genes, such as ABRE, CGTCA-motif and ARE. Subcellular localization experiments showed that PheTCP9 was a nuclear localized protein. As shown by β-glucuronidase (GUS) activity, the promoter of PheTCP9 was significantly indicated by salt stress. PheTCP9 was significantly induced in the roots, stems and leaves of moso bamboo. It was also significantly induced by NaCl solution. Overexpressing PheTCP9 increased the salt tolerance of transgenic Arabidopsis. Meanwhile, H2O2 and malondialdehyde (MDA) contents were significantly lower in PheTCP9 over expression (OE) transgenic Arabidopsis than WT. Catalase (CAT) activity, K+/Na+ ratio as well as CAT2 expression level was also much improved in transgenic Arabidopsis than WT under salt conditions. In addition, PheTCP9 OE transgenic Arabidopsis held higher survival rates of seedlings than WT under NaCl conditions. These results showed the positive regulation functions of PheTCP9 in plants under salt conditions.
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Affiliation(s)
- Yuzeng Xu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Linna Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Hongxia Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Wei He
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Nianqin Jiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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21
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Huang F, Shi C, Zhang Y, Hou X. Genome-Wide Identification and Characterization of TCP Family Genes in Pak-Choi [ Brassica campestris (syn. Brassica rapa) ssp. chinensis var. communis]. FRONTIERS IN PLANT SCIENCE 2022; 13:854171. [PMID: 35615139 PMCID: PMC9125175 DOI: 10.3389/fpls.2022.854171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/17/2022] [Indexed: 06/15/2023]
Abstract
The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) gene family, a kind of plant specific transcription factor, is essential for stress response, cell growth, and cell proliferation. However, the characterization of TCP family is still not clear in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis var. communis]. In this study, genome-wide analysis of TCP gene family was performed and 26 TCP genes were identified in Pak-choi. Phylogenetic analysis demonstrated that the 26 BcTCPs were divided into two classes: Class I and Class II. Class II was further classified into two subclasses, CIN and CYC/TB1. The qPCR results suggested that most BcTCPs respond to abiotic stresses. The expressions of BcTCP3, BcTCP12, BcTCP21, and BcTCP22 were significantly changed under ABA and cold treatment. BcTCP3 and BcTCP12 were also up-regulated under osmotic treatment. Subcellular localization showed that BcTCP3 and BcTCP21 were located in the nucleus. Our results will facilitate revealing the functions and regulatory mechanisms of BcTCPs.
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22
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Tang Y, Gao X, Cui Y, Xu H, Yu J. 植物TCP转录因子研究进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Nie YM, Han FX, Ma JJ, Chen X, Song YT, Niu SH, Wu HX. Genome-wide TCP transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in Pinus tabuliformis. BMC PLANT BIOLOGY 2022; 22:167. [PMID: 35366809 PMCID: PMC8976390 DOI: 10.1186/s12870-022-03554-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/23/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood. RESULTS In the present study, 43 TCP genes were identified from P. tabuliformis genome database. Based on the phylogeny tree and sequence similarity, the 43 TCP genes were classified into four groups. The motif results showed that different subfamilies indeed contained different motifs. Clade II genes contain motif 1, clade I genes contain motif 1, 8, 10 and clade III and IV contain more motifs, which is consistent with our grouping results. The structural analysis of PtTCP genes showed that most PtTCPs lacked introns. The distribution of clade I and clade II on the chromosome is relatively scattered, while clade III and clade IV is relatively concentrated. Co-expression network indicated that PtTCP2, PtTCP12, PtTCP36, PtTCP37, PtTCP38, PtTCP41 and PtTCP43 were co-expressed with clock genes in annual cycle and their annual cycle expression profiles both showed obvious seasonal oscillations. PtTCP2, PtTCP12, PtTCP37, PtTCP38, PtTCP40, PtTCP41, PtTCP42 and PtTCP43 were co-expressed with clock genes in diurnal cycle. Only the expression of PtTCP42 showed diurnal oscillation. CONCLUSIONS The TCP gene family, especially clade II, may play an important role in the regulation of the season and circadian rhythm of P. tabuliformis. In addition, the low temperature in winter may affect the diurnal oscillations.
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Affiliation(s)
- Yu-meng Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Fang-xu Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Jing-jing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Xi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Yi-tong Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Harry X. Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, SE-901 83 Umeå, Sweden
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Aazami MA, Mehrabani LV, Hashemi T, Hassanpouraghdam MB, Rasouli F. Soil-based nano-graphene oxide and foliar selenium and nano-Fe influence physiological responses of 'Sultana' grape under salinity. Sci Rep 2022; 12:4234. [PMID: 35273327 PMCID: PMC8913625 DOI: 10.1038/s41598-022-08251-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/25/2022] [Indexed: 11/17/2022] Open
Abstract
Salinity is a worldwide stressor that influences the growth and productivity of plants. Some novel compounds like; graphene oxide and nutrients such as Se and Fe especially as nano form may improve plant responses to the environmental stress factors. The soil-based graphene oxide (0, 50, and 100 g kg−1) and the foliar applications of Se and nano-Fe (control and 3 mg L−1) were assayed on grapevine cv. Sultana under salinity (0, 50, and 100 mM NaCl). The top flavonoids, chlorophyll b, and plant dry weight belonged to graphene oxide and nano-Fe applications. CAT activity was improved in response to Se, nano-Fe, and graphene oxide (50 g kg−1). The least Fe, K, Se, N, Mg, Mn, and Zn content was recorded for 100 mM NaCl. In contrast, the higher data for K, Se, Ca, Mg, Zn and Mn were acquired with graphene oxide × foliar treatments. In general, graphene oxide treatment (50 g kg−1) × nano-Fe and Se foliar use ameliorated the adverse salinity effects with the improved biochemical and physiological responses of Sultana grape.
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Affiliation(s)
- Mohammad Ali Aazami
- Department of Horticultural Science, Faculty of Agriculture, University of Maragheh, Maragheh, Iran.
| | - Lamia Vojodi Mehrabani
- Department of Agronomy and Plant Breeding, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Tahereh Hashemi
- Department of Horticultural Science, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | | | - Farzad Rasouli
- Department of Horticultural Science, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
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25
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Wang M, Hasegawa T, Beier M, Hayashi M, Ohmori Y, Yano K, Teramoto S, Kamiya T, Fujiwara T. Growth and Nitrate Reductase Activity Are Impaired in Rice Osnlp4 Mutants Supplied with Nitrate. PLANT & CELL PHYSIOLOGY 2021; 62:1156-1167. [PMID: 33693871 DOI: 10.1093/pcp/pcab035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 02/27/2021] [Indexed: 05/24/2023]
Abstract
Nitrate is an important nutrient and signaling molecule in plants, which modulates the expression of many genes and regulates plant growth. In paddy-grown rice (Oryza sativa), nitrogen is mostly supplied in the form of ammonium but can also be supplied in the form of nitrate. Several nitrogen transporters and nitrate assimilation enzymes have been identified and functionally characterized in rice. However, little is known regarding the nitrate sensing system in rice, and the regulatory mechanisms of nitrate-related genes remain to be elucidated. In recent years, NIN-like proteins (NLPs) have been described as key transcription factors of nitrogen responses in Arabidopsis thaliana, which implies that OsNLP4 is involved in the regulation of nitrate assimilation and nitrogen use efficiency in rice. Here, we show that OsNLP4 can influence plant growth by affecting nitrate reductase (NR) activity. The growth of OsNLP4 knockdown mutants was reduced when nitrate was supplied, but not when ammonium was supplied. The nitrate concentration was significantly reduced in osnlp4 mutants. Furthermore, the concentrations of iron and molybdenum, essential elements for NR activity, were reduced in OsNLP4 knockdown mutants. We propose that, in addition to the regulation of gene expression within the nitrate signaling pathway, OsNLP4 can affect the NR activity and nitrate-dependent growth of rice. Our results support a working model for the role of OsNLP4 in the nitrate signaling pathway.
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Affiliation(s)
- Mengyao Wang
- The Laboratory of Plant Nutrition and Fertilizers, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 1138657 Japan
| | - Takahiro Hasegawa
- The Laboratory of Plant Nutrition and Fertilizers, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 1138657 Japan
| | - Marcel Beier
- The Laboratory of Plant Nutrition and Fertilizers, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 1138657 Japan
| | - Makoto Hayashi
- RIKEN Center for Sustainable Resource Science, Kanagawa, 2300045 Japan
| | - Yoshihiro Ohmori
- The Laboratory of Plant Nutrition and Fertilizers, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 1138657 Japan
| | - Kenji Yano
- The Laboratory of Plant Nutrition and Fertilizers, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 1138657 Japan
| | - Shota Teramoto
- The Laboratory of Plant Nutrition and Fertilizers, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 1138657 Japan
| | - Takehiro Kamiya
- The Laboratory of Plant Nutrition and Fertilizers, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 1138657 Japan
| | - Toru Fujiwara
- The Laboratory of Plant Nutrition and Fertilizers, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 1138657 Japan
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26
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Li T, Zhu D, Han Z, Zhang J, Zhang M, Yan Y. Label-Free Quantitative Proteome Analysis Reveals the Underlying Mechanisms of Grain Nuclear Proteins Involved in Wheat Water-Deficit Response. FRONTIERS IN PLANT SCIENCE 2021; 12:748487. [PMID: 34759942 PMCID: PMC8572964 DOI: 10.3389/fpls.2021.748487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
In this study, we performed the first nuclear proteome analysis of wheat developing grains under water deficit by using a label-free based quantitative proteomic approach. In total, we identified 625 unique proteins as differentially accumulated proteins (DAPs), of which 398 DAPs were predicted to be localized in nucleus. Under water deficit, 146 DAPs were up-regulated and mainly involved in the stress response and oxidation-reduction process, while 252 were down-regulated and mainly participated in translation, the cellular amino metabolic process, and the oxidation-reduction process. The cis-acting elements analysis of the key nuclear DAPs encoding genes demonstrated that most of these genes contained the same cis-acting elements in the promoter region, mainly including ABRE involved in abscisic acid response, antioxidant response element, MYB responsive to drought regulation and MYC responsive to early drought. The cis-acting elements related to environmental stress and hormones response were relatively abundant. The transcription expression profiling of the nuclear up-regulated DAPs encoding genes under different organs, developmental stages and abiotic stresses was further detected by RNA-seq and Real-time quantitative polymerase chain reaction, and more than 50% of these genes showed consistency between transcription and translation expression. Finally, we proposed a putative synergistic responsive network of wheat nuclear proteome to water deficit, revealing the underlying mechanisms of wheat grain nuclear proteome in response to water deficit.
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Affiliation(s)
- Tingting Li
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Dong Zhu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhisheng Han
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Junwei Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Ming Zhang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Yueming Yan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
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Xu Y, Liu H, Gao Y, Xiong R, Wu M, Zhang K, Xiang Y. The TCP transcription factor PeTCP10 modulates salt tolerance in transgenic Arabidopsis. PLANT CELL REPORTS 2021; 40:1971-1987. [PMID: 34392380 DOI: 10.1007/s00299-021-02765-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
PeTCP10 can be induced by salt stresses and play important regulation roles in salt stresses response in transgenic Arabidopsis. Salt stress is one of the major adverse environmental factors that affect normal plant development and growth. PeTCP10, a Class I TCP member, was markedly expressed in moso bamboo mature leaf, root and stem under normal conditions and also induced by salt stress. Overexpressed PeTCP10 was found to enhance salt tolerance of transgenic Arabidopsis at the vegetative growth stage. It was also found capable to increase relative water content, while decreasing relative electrolyte leakage and Na+ accumulation of transgenic Arabidopsis versus wild-type (WT) plants at high-salt conditions. In addition, it improved antioxidant capacity of transgenic Arabidopsis plants by promoting catalase activity and enhanced their H2O2 tolerance. In contrast to WT plants, transcriptome analysis demonstrated that multiple genes related to abscisic acid, salt and H2O2 response were induced after NaCl treatment in transgenic plants. Meanwhile, overexpressed PeTCP10 improved the tolerance of abscisic acid. Moreover, luciferase reporter assay results showed that PeTCP10 is able to directly activate the expression of BT2 in transgenic plants. In contrary, the germination rates of transgenic plants were significantly lower than those of WT plants under high-NaCl conditions. Both primary root length and survival rate at the seedling stage are also found lower in transgenic plants than in WT plants. It is concluded that overexpressed PeTCP10 enhances salt stress tolerance of transgenic plants at the vegetative growth stage, and it also improves salt sensitiveness in both germination and seedling stages. These research results will contribute to further understand the functions of TCPs in abiotic stress response.
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Affiliation(s)
- Yuzeng Xu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Huanlong Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yameng Gao
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Rui Xiong
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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28
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Khan MA, Hamayun M, Asaf S, Khan M, Yun BW, Kang SM, Lee IJ. Rhizospheric Bacillus spp. Rescues Plant Growth Under Salinity Stress via Regulating Gene Expression, Endogenous Hormones, and Antioxidant System of Oryza sativa L. FRONTIERS IN PLANT SCIENCE 2021; 12:665590. [PMID: 34177981 PMCID: PMC8226221 DOI: 10.3389/fpls.2021.665590] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/19/2021] [Indexed: 05/27/2023]
Abstract
Salinity has drastically reduced crop yields and harmed the global agricultural industry. We isolated 55 bacterial strains from plants inhabiting the coastal sand dunes of Pohang, Korea. A screening bioassay showed that 14 of the bacterial isolates secreted indole-3-acetic acid (IAA), 12 isolates were capable of exopolysaccharide (EPS) production and phosphate solubilization, and 10 isolates secreted siderophores. Based on our preliminary screening, 11 bacterial isolates were tested for salinity tolerance on Luria-Bertani (LB) media supplemented with 0, 50, 100, and 150 mM of NaCl. Three bacterial isolates, ALT11, ALT12, and ALT30, had the best tolerance against elevated NaCl levels and were selected for further study. Inoculation of the selected bacterial isolates significantly enhanced rice growth attributes, viz., shoot length (22.8-42.2%), root length (28.18-59%), fresh biomass (44.7-66.41%), dry biomass (85-90%), chlorophyll content (18.30-36.15%), Chl a (29.02-60.87%), Chl b (30.86-64.51%), and carotenoid content (26.86-70%), under elevated salt stress of 70 and 140 mM. Furthermore, a decrease in the endogenous abscisic acid (ABA) content (27.9-23%) and endogenous salicylic acid (SA) levels (11.70-69.19%) was observed in inoculated plants. Antioxidant analysis revealed an increase in total protein (TP) levels (42.57-68.26%), whereas it revealed a decrease in polyphenol peroxidase (PPO) (24.63-34.57%), glutathione (GSH) (25.53-24.91%), SOA (13.88-18.67%), and LPO levels (15.96-26.06%) of bacterial-inoculated plants. Moreover, an increase in catalase (CAT) (26-33.04%), peroxidase (POD) (59.55-78%), superoxide dismutase (SOD) (13.58-27.77%), and ascorbic peroxidase (APX) (5.76-22.74%) activity was observed. Additionally, inductively coupled plasma mass spectrometry (ICP-MS) analysis showed a decline in Na+ content (24.11 and 30.60%) and an increase in K+ (23.14 and 15.45%) and Mg+ (2.82 and 18.74%) under elevated salt stress. OsNHX1 gene expression was downregulated (0.3 and 4.1-folds), whereas the gene expression of OsPIN1A, OsCATA, and OsAPX1 was upregulated by a 7-17-fold in bacterial-inoculated rice plants. It was concluded that the selected bacterial isolates, ALT11, ALT12, and ALT30, mitigated the adverse effects of salt stress on rice growth and can be used as climate smart agricultural tools in ecofriendly agricultural practices.
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Affiliation(s)
- Muhammad Aaqil Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Muhammad Hamayun
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, Nizwa, Oman
| | - Murtaza Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Byung-Wook Yun
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
| | - Sang-Mo Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
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Foliar Nourishment with Nano-Selenium Dioxide Promotes Physiology, Biochemistry, Antioxidant Defenses, and Salt Tolerance in Phaseolus vulgaris. PLANTS 2021; 10:plants10061189. [PMID: 34207988 PMCID: PMC8230738 DOI: 10.3390/plants10061189] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023]
Abstract
Novel strategic green approaches are urgently needed to raise the performance of plants subjected to stress. Two field-level experimental attempts were implemented during two (2019 and 2020) growing seasons to study the possible effects of exogenous nourishment with selenium dioxide nanoparticles (Se-NPs) on growth, physio-biochemical ingredients, antioxidant defenses, and yield of Phaseolus vulgaris (L.) plant growing on a salt-affected soil (EC = 7.55–7.61 dS m−1). At 20, 30, and 40 days from seeding, three foliar sprays were applied to plants with Se-NPs at a rate of 0.5, 1.0, or 1.5 mM. The experimental design was accomplished in randomized complete plots. The data indicate noteworthy elevations in indicators related to growth and yield; pigments related to effective photosynthesis, osmoprotectant (free proline and soluble sugars), nutrient and Se contents, K+/Na+ ratio, cell integrity (water content and stability of membranes), all enzyme activities; and all features related to leaf anatomy induced by Se-NPs foliar spray. Conversely, marked lowering in markers of Na+ content-induced oxidative stress (superoxide radical and hydrogen peroxide) and their outcomes in terms of ionic leakage and malondialdehyde were reported by foliar nourishment with Se-NPS compared to spraying leaves with water as an implemented control. The best results were recorded with Se-NPs applied at 1.0 mM, which mitigated the negative effects of soil salinity (control results). Therefore, the outcomes of this successful study recommend the use of Se-NPs at a rate of 1.0 mM as a foliar spray to grow common beans on saline soils with EC up to 7.55–7.61 dS m−1.
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30
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Górska AM, Gouveia P, Borba AR, Zimmermann A, Serra TS, Carvalho P, Lourenço TF, Oliveira MM, Peterhänsel C, Saibo NJM. ZmOrphan94 Transcription Factor Downregulates ZmPEPC1 Gene Expression in Maize Bundle Sheath Cells. FRONTIERS IN PLANT SCIENCE 2021; 12:559967. [PMID: 33897718 PMCID: PMC8062929 DOI: 10.3389/fpls.2021.559967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Spatial separation of the photosynthetic reactions is a key feature of C4 metabolism. In most C4 plants, this separation requires compartmentation of photosynthetic enzymes between mesophyll (M) and bundle sheath (BS) cells. The upstream region of the gene encoding the maize PHOSPHOENOLPYRUVATE CARBOXYLASE 1 (ZmPEPC1) has been shown sufficient to drive M-specific ZmPEPC1 gene expression. Although this region has been well characterized, to date, only few trans-factors involved in the ZmPEPC1 gene regulation were identified. Here, using a yeast one-hybrid approach, we have identified three novel maize transcription factors ZmHB87, ZmCPP8, and ZmOrphan94 as binding to the ZmPEPC1 upstream region. Bimolecular fluorescence complementation assays in maize M protoplasts unveiled that ZmOrphan94 forms homodimers and interacts with ZmCPP8 and with two other ZmPEPC1 regulators previously reported, ZmbHLH80 and ZmbHLH90. Trans-activation assays in maize M protoplasts unveiled that ZmHB87 does not have a clear transcriptional activity, whereas ZmCPP8 and ZmOrphan94 act as activator and repressor, respectively. Moreover, we observed that ZmOrphan94 reduces the trans-activation activity of both activators ZmCPP8 and ZmbHLH90. Using the electromobility shift assay, we showed that ZmOrphan94 binds to several cis-elements present in the ZmPEPC1 upstream region and one of these cis-elements overlaps with the ZmbHLH90 binding site. Gene expression analysis revealed that ZmOrphan94 is preferentially expressed in the BS cells, suggesting that ZmOrphan94 is part of a transcriptional regulatory network downregulating ZmPEPC1 transcript level in the BS cells. Based on both this and our previous work, we propose a model underpinning the importance of a regulatory mechanism within BS cells that contributes to the M-specific ZmPEPC1 gene expression.
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Affiliation(s)
- Alicja M. Górska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Paulo Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Ana Rita Borba
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Anna Zimmermann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Institut für Botanik, Leibniz Universität Hannover, Hannover, Germany
| | - Tânia S. Serra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Pedro Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tiago F. Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | | | - Nelson J. M. Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
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Ponce KS, Guo L, Leng Y, Meng L, Ye G. Advances in Sensing, Response and Regulation Mechanism of Salt Tolerance in Rice. Int J Mol Sci 2021; 22:ijms22052254. [PMID: 33668247 PMCID: PMC7956267 DOI: 10.3390/ijms22052254] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 01/06/2023] Open
Abstract
Soil salinity is a serious menace in rice production threatening global food security. Rice responses to salt stress involve a series of biological processes, including antioxidation, osmoregulation or osmoprotection, and ion homeostasis, which are regulated by different genes. Understanding these adaptive mechanisms and the key genes involved are crucial in developing highly salt-tolerant cultivars. In this review, we discuss the molecular mechanisms of salt tolerance in rice—from sensing to transcriptional regulation of key genes—based on the current knowledge. Furthermore, we highlight the functionally validated salt-responsive genes in rice.
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Affiliation(s)
- Kimberly S. Ponce
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China;
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China;
- Correspondence: (Y.L.); (L.G.); Tel.: +86-514-8797-4757 (Y.L.); +86-571-6337-0136 (L.G.)
| | - Yujia Leng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou 225009, China
- Correspondence: (Y.L.); (L.G.); Tel.: +86-514-8797-4757 (Y.L.); +86-571-6337-0136 (L.G.)
| | - Lijun Meng
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (L.M.); (G.Y.)
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (L.M.); (G.Y.)
- Strategic Innovation Platform, International Rice Research Institute, DAPO BOX 7777, Metro Manila 1301, Philippines
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32
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Kandpal M, Vishwakarma C, Krishnan K, Chinnusamy V, Pareek A, Sharma MK, Sharma R. Gene Expression Dynamics in Rice Peduncles at the Heading Stage. Front Genet 2020; 11:584678. [PMID: 33343630 PMCID: PMC7744745 DOI: 10.3389/fgene.2020.584678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022] Open
Abstract
Improving grain yield in the staple food crop rice has been long sought goal of plant biotechnology. One of the traits with significant impact on rice breeding programs is peduncle elongation at the time of heading failing which leads to significant reduction in grain yield due to incomplete panicle exsertion. To decipher transcriptional dynamics and molecular players underlying peduncle elongation, we performed RNA sequencing analysis of elongating and non-elongating peduncles in two Indian cultivars, Swarna and Pokkali, at the time of heading. Along with genes associated with cell division and cell wall biosynthesis, we observed significant enrichment of genes associated with auxins, gibberellins, and brassinosteroid biosynthesis/signaling in the elongating peduncles before heading in both the genotypes. Similarly, genes associated with carbohydrate metabolism and mobilization, abiotic stress response along with cytokinin, abscisic acid, jasmonic acid, and ethylene biosynthesis/signaling were enriched in non-elongating peduncles post heading. Significant enrichment of genes belonging to key transcription factor families highlights their specialized roles in peduncle elongation and grain filling before and after heading, respectively. A comparison with anther/pollen development-related genes provided 76 candidates with overlapping roles in anther/pollen development and peduncle elongation. Some of these are important for carbohydrate remobilization to the developing grains. These can be engineered to combat with incomplete panicle exsertion in male sterile lines and manipulate carbohydrate dynamics in grasses. Overall, this study provides baseline information about potential target genes for engineering peduncle elongation with implications on plant height, biomass composition and grain yields in rice.
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Affiliation(s)
- Manu Kandpal
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Chandrapal Vishwakarma
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kushagra Krishnan
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ashwani Pareek
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manoj K. Sharma
- Grass Genetics and Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rita Sharma
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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33
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He C, Zhang HY, Zhang YX, Fu P, You LL, Xiao WB, Wang ZH, Song HY, Huang YJ, Liao JL. Cytosine methylations in the promoter regions of genes involved in the cellular oxidation equilibrium pathways affect rice heat tolerance. BMC Genomics 2020; 21:560. [PMID: 32799794 PMCID: PMC7430847 DOI: 10.1186/s12864-020-06975-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 08/06/2020] [Indexed: 11/15/2022] Open
Abstract
Background High temperatures, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that tolerate HNTs. DNA methylation may represent a potential avenue for HNT-tolerant rice strain development, as this mechanism regulates gene activity and cellular phenotype in response to adverse environmental conditions without changing the nucleotide sequence. Results After HNT exposure, the methylation patterns of cytosines in the CHH context differed noticeably between two coisogenic rice strains with significantly different levels in heat tolerance. Methylation differences between strains were primarily observed on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, the regions 358–359 bp and 2–60 bp downstream of two basal transcriptional factors (TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31, respectively) were fully demethylated in the heat-tolerant strain after HNT exposure. In the heat-tolerant strain, HNTs reversed the methylation patterns of successive cytosines in the promoter regions of various genes involved in abscisic acid (ABA)-related reactive oxygen species (ROS) equilibrium pathways, including the pentatricopeptide repeat domain gene PPR (LOC_Os07g28900) and the homeobox domain gene homeobox (LOC_Os01g19694). Indeed, PRR expression was inhibited in heat-sensitive rice strains, and the methylation rates of the cytosines in the promoter region of PRR were greater in heat-sensitive strains as compared to heat-tolerant strains. Conclusions After HNT exposure, cytosines in the CHH context were more likely than cytosines in other contexts to be methylated differently between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes associated with ABA-related oxidation and ROS scavenging improved heat tolerance in rice. Our results help to clarify the molecular mechanisms underlying rice heat tolerance.
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Affiliation(s)
- Chao He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Hong-Yu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Yong-Xin Zhang
- South Zhejiang Key Laboratory of Crop Breeding, Institute of Crop Research, Wenzhou Academy of Agricultural Sciences, Wenzhou, 325006, China
| | - Pei Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Li-Li You
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Wen-Bo Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Zhao-Hai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Hai-Yan Song
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China
| | - Ying-Jin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China. .,Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China.
| | - Jiang-Lin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang, 330045, China. .,Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China.
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Parvathaneni RK, Bertolini E, Shamimuzzaman M, Vera DL, Lung PY, Rice BR, Zhang J, Brown PJ, Lipka AE, Bass HW, Eveland AL. The regulatory landscape of early maize inflorescence development. Genome Biol 2020; 21:165. [PMID: 32631399 PMCID: PMC7336428 DOI: 10.1186/s13059-020-02070-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. RESULT Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen- and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6% of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3' ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates. CONCLUSIONS These analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.
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Affiliation(s)
| | | | - Md Shamimuzzaman
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
- Current address: USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND 58102 USA
| | - Daniel L. Vera
- The Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL 32306 USA
- Current address: Department of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL 32306 USA
| | - Brian R. Rice
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306 USA
| | - Patrick J. Brown
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306 USA
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35
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Lilay GH, Castro PH, Guedes JG, Almeida DM, Campilho A, Azevedo H, Aarts MGM, Saibo NJM, Assunção AGL. Rice F-bZIP transcription factors regulate the zinc deficiency response. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3664-3677. [PMID: 32133499 PMCID: PMC7307843 DOI: 10.1093/jxb/eraa115] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/02/2020] [Indexed: 05/07/2023]
Abstract
The F-bZIP transcription factors bZIP19 and bZIP23 are the central regulators of the zinc deficiency response in Arabidopsis, and phylogenetic analysis of F-bZIP homologs across land plants indicates that the regulatory mechanism of the zinc deficiency response may be conserved. Here, we identified the rice F-bZIP homologs and investigated their function. OsbZIP48 and OsbZIP50, but not OsbZIP49, complement the zinc deficiency-hypersensitive Arabidopsis bzip19bzip23 double mutant. Ectopic expression of OsbZIP50 in Arabidopsis significantly increases plant zinc accumulation under control zinc supply, suggesting an altered Zn sensing in OsbZIP50. In addition, we performed a phylogenetic analysis of F-bZIP homologs from representative monocot species that supports the branching of plant F-bZIPs into Group 1 and Group 2. Our results suggest that regulation of the zinc deficiency response in rice is conserved, with OsbZIP48 being a functional homolog of AtbZIP19 and AtbZIP23. A better understanding of the mechanisms behind the Zn deficiency response in rice and other important crops will contribute to develop plant-based strategies to address the problems of Zn deficiency in soils, crops, and cereal-based human diets.
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Affiliation(s)
- Grmay H Lilay
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg-C, Denmark
| | - Pedro Humberto Castro
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
| | - Joana G Guedes
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
| | - Diego M Almeida
- Genomics of Plant Stress Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, New University of Lisbon, Oeiras, Portugal
| | - Ana Campilho
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Herlander Azevedo
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University& Research, Wageningen, The Netherlands
| | - Nelson J M Saibo
- Genomics of Plant Stress Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, New University of Lisbon, Oeiras, Portugal
| | - Ana G L Assunção
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg-C, Denmark
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
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36
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Ling L, Zhang W, An Y, Du B, Wang D, Guo C. Genome-wide analysis of the TCP transcription factor genes in five legume genomes and their response to salt and drought stresses. Funct Integr Genomics 2020; 20:537-550. [PMID: 32034565 DOI: 10.1007/s10142-020-00733-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/28/2019] [Accepted: 01/27/2020] [Indexed: 01/17/2023]
Abstract
The teosinte branched1, cycloidea, and proliferating cell factor family (TCP) proteins, plant-specific transcription factors, are involved in the regulation of plant development; however, the TCP gene family of legumes has been based primarily on a single crop. Here, a total of 55, 22, 26, 21, and 25 genes containing the VQ motif were identified from the genomes of Glycine max, Cicer arietinum, Phaseolus vulgaris, Medicago truncatula, and Lotus japonicus, respectively. Based on the phylogenetic analysis, we divided these TCP genes into three distinct subfamilies: PCF, CYC/TB1, and CIN. The conserved domain analysis indicated that the TCP gene family members contain the bHLH and R domains. The TCP genes from the same evolutionary branches of legumes shared similar motifs and structures. The promoter analysis revealed that cis-elements were related to stress responses, phytohormone responses, and physical and reproductive growth regulation. In addition, the TCP genes presented different expression patterns in the five legumes. Most of them showed specific expression patterns during development. The results of qRT-PCR indicated that the TCP genes played regulatory roles in both salt and drought stresses. The present study provides novel and detailed information regarding the legume TCP gene family, which aids in functional characterisation of the TCP genes in other plants.
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Affiliation(s)
- Lei Ling
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 of Shida Road, Limin Development Zone, Harbin, 150025, China
| | - Wenrui Zhang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 of Shida Road, Limin Development Zone, Harbin, 150025, China
| | - Yimin An
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 of Shida Road, Limin Development Zone, Harbin, 150025, China
| | - Binghao Du
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 of Shida Road, Limin Development Zone, Harbin, 150025, China
| | - Dan Wang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 of Shida Road, Limin Development Zone, Harbin, 150025, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 of Shida Road, Limin Development Zone, Harbin, 150025, China.
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37
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Kamran M, Parveen A, Ahmar S, Malik Z, Hussain S, Chattha MS, Saleem MH, Adil M, Heidari P, Chen JT. An Overview of Hazardous Impacts of Soil Salinity in Crops, Tolerance Mechanisms, and Amelioration through Selenium Supplementation. Int J Mol Sci 2019; 21:E148. [PMID: 31878296 PMCID: PMC6981449 DOI: 10.3390/ijms21010148] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 02/05/2023] Open
Abstract
Soil salinization is one of the major environmental stressors hampering the growth and yield of crops all over the world. A wide spectrum of physiological and biochemical alterations of plants are induced by salinity, which causes lowered water potential in the soil solution, ionic disequilibrium, specific ion effects, and a higher accumulation of reactive oxygen species (ROS). For many years, numerous investigations have been made into salinity stresses and attempts to minimize the losses of plant productivity, including the effects of phytohormones, osmoprotectants, antioxidants, polyamines, and trace elements. One of the protectants, selenium (Se), has been found to be effective in improving growth and inducing tolerance against excessive soil salinity. However, the in-depth mechanisms of Se-induced salinity tolerance are still unclear. This review refines the knowledge involved in Se-mediated improvements of plant growth when subjected to salinity and suggests future perspectives as well as several research limitations in this field.
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Affiliation(s)
- Muhammad Kamran
- Key Laboratory of Arable Land Conservation, Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China;
| | - Aasma Parveen
- Department of Soil Science, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Punjab, Pakistan; (A.P.); (Z.M.)
| | - Sunny Ahmar
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.S.C.); (M.H.S.)
| | - Zaffar Malik
- Department of Soil Science, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Punjab, Pakistan; (A.P.); (Z.M.)
| | - Sajid Hussain
- Stat Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China;
| | - Muhammad Sohaib Chattha
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.S.C.); (M.H.S.)
| | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.S.C.); (M.H.S.)
| | - Muhammad Adil
- College of Urban and Environmental Sciences, Northwest University, Xi’an 710127, China;
| | - Parviz Heidari
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran;
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
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38
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Krishnamurthy P, Vishal B, Khoo K, Rajappa S, Loh CS, Kumar PP. Expression of AoNHX1 increases salt tolerance of rice and Arabidopsis, and bHLH transcription factors regulate AtNHX1 and AtNHX6 in Arabidopsis. PLANT CELL REPORTS 2019; 38:1299-1315. [PMID: 31350571 DOI: 10.1007/s00299-019-02450-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/22/2019] [Indexed: 05/17/2023]
Abstract
Expression of AoNHX1 from the mangrove Avicennia increases salt tolerance of rice and Arabidopsis, and specific bHLH transcription factors regulate AtNHX1 and AtNHX6 in Arabidopsis to mediate the salinity response. Improving crop plants to better tolerate soil salinity is a challenging task. Mangrove trees such as Avicennia officinalis have special adaptations to thrive in high salt conditions, which include subcellular compartmentalization of ions facilitated by specialized ion transporters. We identified and characterized two genes encoding Na+/H+ exchangers AoNHX1 and AoNHX6 from Avicennia. AoNHX1 was present in the tonoplast, while, AoNHX6 was localized to the ER and Golgi. Both NHXs were induced by NaCl treatment, with AoNHX1 showing high expression levels in the leaves and AoNHX6 in the seedling roots. Yeast deletion mutants (ena1-5Δ nha1Δ nhx1Δ and ena1-5Δ nha1Δ vnx1Δ) complemented with AoNHX1 and AoNHX6 showed increased tolerance to both NaCl and KCl. Expression of AoNHX1 and AoNHX6 in the corresponding Arabidopsis mutants conferred enhanced NaCl tolerance. The underlying molecular regulatory mechanism was investigated using AtNHX1 and AtNHX6 in Arabidopsis. We identified two basic helix-loop-helix (bHLH) transcription factors AtMYC2 and AtbHLH122 as the ABA-mediated upstream regulators of AtNHX1 and AtNHX6 by chromatin immunoprecipitation. Furthermore, expression of AtNHX1 and AtNHX6 transcripts was reduced in the atmyc2 and atbhlh122 mutants. Lastly, transgenic rice seedlings harboring pUBI::AoNHX1 showed enhanced salt tolerance, suggesting that this gene can be exploited for developing salt-tolerant crops.
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Affiliation(s)
- Pannaga Krishnamurthy
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
- NUS Environmental Research Institute (NERI), National University of Singapore, #02-01, T-Lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Bhushan Vishal
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Kaijie Khoo
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Sivamathini Rajappa
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Chiang-Shiong Loh
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
- NUS Environmental Research Institute (NERI), National University of Singapore, #02-01, T-Lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Prakash P Kumar
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
- NUS Environmental Research Institute (NERI), National University of Singapore, #02-01, T-Lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore.
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Comparative Proteomics of Salt-Tolerant and Salt-Sensitive Maize Inbred Lines to Reveal the Molecular Mechanism of Salt Tolerance. Int J Mol Sci 2019; 20:ijms20194725. [PMID: 31554168 PMCID: PMC6801879 DOI: 10.3390/ijms20194725] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/31/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022] Open
Abstract
Salt stress is one of the key abiotic stresses that causes great loss of yield and serious decrease in quality in maize (Zea mays L.). Therefore, it is very important to reveal the molecular mechanism of salt tolerance in maize. To acknowledge the molecular mechanisms underlying maize salt tolerance, two maize inbred lines, including salt-tolerant 8723 and salt-sensitive P138, were used in this study. Comparative proteomics of seedling roots from two maize inbred lines under 180 mM salt stress for 10 days were performed by the isobaric tags for relative and absolute quantitation (iTRAQ) approach. A total of 1056 differentially expressed proteins (DEPs) were identified. In total, 626 DEPs were identified in line 8723 under salt stress, among them, 378 up-regulated and 248 down-regulated. There were 473 DEPs identified in P138, of which 212 were up-regulated and 261 were down-regulated. Venn diagram analysis showed that 17 DEPs were up-regulated and 12 DEPs were down-regulated in the two inbred lines. In addition, 8 DEPs were up-regulated in line 8723 but down-regulated in P138, 6 DEPs were down-regulated in line 8723 but up-regulated in P138. In salt-stressed 8723, the DEPs were primarily associated with phenylpropanoid biosynthesis, starch and sucrose metabolism, and the mitogen-activated protein kinase (MAPK) signaling pathway. Intriguingly, the DEPs were only associated with the nitrogen metabolism pathway in P138. Compared to P138, the root response to salt stress in 8723 could maintain stronger water retention capacity, osmotic regulation ability, synergistic effects of antioxidant enzymes, energy supply capacity, signal transduction, ammonia detoxification ability, lipid metabolism, and nucleic acid synthesis. Based on the proteome sequencing information, changes of 8 DEPs abundance were related to the corresponding mRNA levels by quantitative real-time PCR (qRT-PCR). Our results from this study may elucidate some details of salt tolerance mechanisms and salt tolerance breeding of maize.
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Liu MM, Wang MM, Yang J, Wen J, Guo PC, Wu YW, Ke YZ, Li PF, Li JN, Du H. Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants. Int J Mol Sci 2019; 20:E3591. [PMID: 31340456 PMCID: PMC6679135 DOI: 10.3390/ijms20143591] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants' development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.
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Affiliation(s)
- Ming-Ming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Mang-Mang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Cheng Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Wen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Zhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Feng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jia-Na Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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Characteristics and Expression Analysis of FmTCP15 under Abiotic Stresses and Hormones and Interact with DELLA Protein in Fraxinus mandshurica Rupr. FORESTS 2019. [DOI: 10.3390/f10040343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The TEOSINTE BRANCHED1, CYCLOIDEA, and PROLIFERATION CELL FACTOR (TCP) transcription factor is a plant-specific gene family and acts on multiple functional genes in controlling growth, development, stress response, and the circadian clock. In this study, a class I member of the TCP family from Fraxinus mandshurica Rupr. was isolated and named FmTCP15, which encoded a protein of 362 amino acids. Protein structures were analyzed and five ligand binding sites were predicted. The phylogenetic relationship showed that FmTCP15 was most closely related to Solanaceae and Plantaginaceae. FmTCP15 was localized in the nuclei of F. mandshurica protoplast cells and highly expressed in cotyledons. The expression pattern revealed the FmTCP15 response to multiple abiotic stresses and hormone signals. Downstream genes for transient overexpression of FmTCP15 in seedlings were also investigated. A yeast two-hybrid assay confirmed that FmTCP15 could interact with DELLA proteins. FmTCP15 participated in the GA-signaling pathway, responded to abiotic stresses and hormone signals, and regulated multiple genes in these biological processes. Our study revealed the potential value of FmTCP15 for understanding the molecular mechanisms of stress and hormone signal responses.
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Subramanyam K, Du Laing G, Van Damme EJM. Sodium Selenate Treatment Using a Combination of Seed Priming and Foliar Spray Alleviates Salinity Stress in Rice. FRONTIERS IN PLANT SCIENCE 2019; 10:116. [PMID: 30804974 PMCID: PMC6378292 DOI: 10.3389/fpls.2019.00116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 01/23/2019] [Indexed: 05/21/2023]
Abstract
Soil salinity is one of the important abiotic stress factors that affect rice productivity and quality. Research with several dicotyledonous plants indicated that the detrimental effects associated with salinity stress can (partly) be overcome by the external application of antioxidative substances. For instance, sodium selenate (Na2SeO4) significantly improved the growth and productivity of several crops under various abiotic stress conditions. At present there is no report describing the impact of Na2SeO4 on salinity stressed cereals such as rice. Rice cultivation is threatened by increasing salinity stress, and in future this problem will further be aggravated by global warming and sea level rise, impacting coastal areas. The current study reports on the effect of Na2SeO4 in alleviating salinity stress in rice plants. The optimal concentration of Na2SeO4 and the most efficient mode of selenium application were investigated. Selenium, sodium, and potassium contents in leaves were determined. Antioxidant enzyme activities as well as proline, hydrogen peroxide (H2O2), and malondialdehyde (MDA) concentrations were analyzed. In addition, the transcript levels for OsNHX1, an important Na+/H+ antiporter, were quantified. Treatment of 2-week-old rice plants under 150 mM NaCl stress with 6 mg l-1 Na2SeO4 improved the total biomass. A significantly higher biomass was observed for the plants that received Na2SeO4 by a combination of seed priming and foliar spray compared to the individual treatments. The Na2SeO4 application enhanced the activity of antioxidant enzymes (SOD, APX, CAT, and GSH-Px), increased the proline content, and reduced H2O2 and MDA concentrations in plants under NaCl stress. These biochemical changes were accompanied by increased transcript levels for OsNHX1 resulting in a higher K+/Na+ ratio in the rice plants under NaCl stress. The results suggest that Na2SeO4 treatment alleviates the adverse effect of salinity on rice plant growth through enhancing the antioxidant defense system and increase of OsNHX1 transcript levels.
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Affiliation(s)
- Kondeti Subramanyam
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Gijs Du Laing
- Laboratory of Analytical Chemistry and Applied Ecochemistry, Department of Green Chemistry and Technology, Ghent University, Ghent, Belgium
| | - Els J. M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Ghent, Belgium
- *Correspondence: Els J. M. Van Damme,
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Liu HL, Wu M, Li F, Gao YM, Chen F, Xiang Y. TCP Transcription Factors in Moso Bamboo ( Phyllostachys edulis): Genome-Wide Identification and Expression Analysis. FRONTIERS IN PLANT SCIENCE 2018; 9:1263. [PMID: 30344527 PMCID: PMC6182085 DOI: 10.3389/fpls.2018.01263] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 08/10/2018] [Indexed: 05/18/2023]
Abstract
TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (T), members of a plant-specific gene family, play significant roles during plant growth and development, as well as in response to environmental stress. However, knowledge about this family in moso bamboo (Phyllostachys edulis) is limited. Therefore, in this study, the first genome-wide identification, classification, characterization, and expression pattern analysis of the TCP transcription factor family in moso bamboo was performed. Sixteen TCP members were identified from the moso bamboo genome using a BLASTP algorithm-based method and verified using the Pfam database. Based on a multiple-sequence alignment, the members were divided into two subfamilies, and members of the same family shared highly conserved motif structures. Subcellular localization and transactivation activity analyses of four selected genes revealed that they were nuclear localized and had self-activation activities. Additionally, the expression levels of several PeTCP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating that they play crucial plant hormone transduction roles in the processes of plant growth and development, as well as in responses to environmental stresses. Thus, the current study provides previously lacking information on the TCP family in moso bamboo and reveals the potential functions of this gene family in growth and development.
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Affiliation(s)
- Huan-Long Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Min Wu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Fei Li
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Ya-Meng Gao
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Feng Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yan Xiang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
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Zhao J, Zhai Z, Li Y, Geng S, Song G, Guan J, Jia M, Wang F, Sun G, Feng N, Kong X, Chen L, Mao L, Li A. Genome-Wide Identification and Expression Profiling of the TCP Family Genes in Spike and Grain Development of Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1282. [PMID: 30298074 PMCID: PMC6160802 DOI: 10.3389/fpls.2018.01282] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
The TCP family genes are plant-specific transcription factors and play important roles in plant development. TCPs have been evolutionarily and functionally studied in several plants. Although common wheat (Triticum aestivum L.) is a major staple crop worldwide, no systematic analysis of TCPs in this important crop has been conducted. Here, we performed a genome-wide survey in wheat and found 66 TCP genes that belonged to 22 homoeologous groups. We then mapped these genes on wheat chromosomes and found that several TCP genes were duplicated in wheat including the ortholog of the maize TEOSINTE BRANCHED 1. Expression study using both RT-PCR and in situ hybridization assay showed that most wheat TCP genes were expressed throughout development of young spike and immature seed. Cis-acting element survey along promoter regions suggests that subfunctionalization may have occurred for homoeologous genes. Moreover, protein-protein interaction experiments of three TCP proteins showed that they can form either homodimers or heterodimers. Finally, we characterized two TaTCP9 mutants from tetraploid wheat. Each of these two mutant lines contained a premature stop codon in the A subgenome homoeolog that was dominantly expressed over the B subgenome homoeolog. We observed that mutation caused increased spike and grain lengths. Together, our analysis of the wheat TCP gene family provides a start point for further functional study of these important transcription factors in wheat.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Long Mao
- *Correspondence: Long Mao, Aili Li,
| | - Aili Li
- *Correspondence: Long Mao, Aili Li,
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Andrés-Colás N, Carrió-Seguí A, Abdel-Ghany SE, Pilon M, Peñarrubia L. Expression of the Intracellular COPT3-Mediated Cu Transport Is Temporally Regulated by the TCP16 Transcription Factor. FRONTIERS IN PLANT SCIENCE 2018; 9:910. [PMID: 30018625 PMCID: PMC6037871 DOI: 10.3389/fpls.2018.00910] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/08/2018] [Indexed: 05/23/2023]
Abstract
Copper is an essential element in plants. When scarce, copper is acquired from extracellular environment or remobilized from intracellular sites, through members of the high affinity copper transporters family COPT located at the plasma membrane and internal membrane, respectively. Here, we show that COPT3 is an intracellular copper transporter, located at a compartment of the secretory pathway, that is mainly expressed in pollen grains and vascular bundles. Contrary to the COPT1 plasma membrane member, the expression of the internal COPT3 membrane transporter was higher at 12 h than at 0 h of a neutral photoperiod day under copper deficiency. The screening of a library of conditionally overexpressed transcription factors implicated members of the TCP family in the COPT3 differential temporal expression pattern. Particularly, in vitro, TCP16 was found to bind to the COPT3 promoter and down-regulated its expression. Accordingly, TCP16 was mainly expressed at 0 h under copper deficiency and induced at 12 h by copper excess. Moreover, TCP16 overexpression resulted in increased sensitivity to copper deficiency, whereas the tcp16 mutant was sensitive to copper excess. Both copper content and the expression of particular copper status markers were altered in plants with modified levels of TCP16. Consistent with TCP16 affecting pollen development, the lack of COPT3 function led to altered pollen morphology. Furthermore, analysis of copt3 and COPT3 overexpressing plants revealed that COPT3 function exerted a negative effect on TCP16 expression. Taken together, these results suggest a differential daily regulation of copper uptake depending on the external and internal copper pools, in which TCP16 inhibits copper remobilization at dawn through repression of intracellular transporters.
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Affiliation(s)
- Nuria Andrés-Colás
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina, Universitat de València, Valencia, Spain
| | - Angela Carrió-Seguí
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina, Universitat de València, Valencia, Spain
| | - Salah E. Abdel-Ghany
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Marinus Pilon
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Lola Peñarrubia
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina, Universitat de València, Valencia, Spain
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Song CB, Shan W, Yang YY, Tan XL, Fan ZQ, Chen JY, Lu WJ, Kuang JF. Heterodimerization of MaTCP proteins modulates the transcription of MaXTH10/11 genes during banana fruit ripening. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:613-622. [PMID: 29935343 DOI: 10.1016/j.bbagrm.2018.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/10/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022]
Abstract
The biological processes involved in banana fruit ripening are extremely complex and modulated by a number of genes such as transcription factors (TFs). Although TFs like MADS, ERF and NAC are implicated in controlling banana ripening, little is known about other TFs such as TCP in this process. In this work, 25 MaTCPs named MaTCP1 to MaTCP25 were characterized from our previously reported transcriptomes related to banana ripening. Expression analysis revealed that these MaTCPs displayed differential expression patterns during the progression of banana ripening. Particularly, MaTCP5, MaTCP19 and MaTCP20 were ethylene-inducible and nuclear-localized, with MaTCP5 and MaTCP20 acting as transcriptional activators while MaTCP19 being a transcriptional inhibitor. Moreover, MaTCP5 and MaTCP20 promoted the transcription of MaXTH10/11 that may play a role in fruit softening during banana ripening, whereas MaTCP19 repressed their transcription, by directly binding to their promoters. Importantly, protein-protein interaction assays demonstrated that MaTCP20 physically interacts with MaTCP5 and MaTCP19 to form heterodimers in vitro and in vivo, and these protein complexes affects their transcriptional activities in regulating the target genes. Taken together, our results provide an overview of the interactions between MaTCPs in controlling the ripening-associated genes and lay a foundation for further investigation of MaTCP gene family in regulating banana fruit ripening.
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Affiliation(s)
- Chun-Bo Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Xiao-Li Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Zhong-Qi Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China.
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Genome-Wide Identification and Analysis of TCP Transcription Factors Involved in the Formation of Leafy Head in Chinese Cabbage. Int J Mol Sci 2018. [PMID: 29538304 PMCID: PMC5877708 DOI: 10.3390/ijms19030847] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a widely cultivated and economically important vegetable crop with typical leaf curvature. The TCP (Teosinte branched1, Cycloidea, Proliferating cell factor) family proteins are plant-specific transcription factors (TFs) and play important roles in many plant biological processes, especially in the regulation of leaf curvature. In this study, 39 genes encoding TCP TFs are detected on the whole genome of B. rapa. Based on the phylogenetic analysis of TCPs between Arabidopsis thaliana and Brassica rapa, TCP genes of Chinese cabbage are named from BrTCP1a to BrTCP24b. Moreover, the chromosomal location; phylogenetic relationships among B. rapa, A. thaliana, and rice; gene structures and protein conserved sequence alignment; and conserved domains are analyzed. The expression profiles of BrTCPs are analyzed in different tissues. To understand the role of Chinese cabbage TCP members in regulating the curvature of leaves, the expression patterns of all BrTCP genes are detected at three development stages essential for leafy head formation. Our results provide information on the classification and details of BrTCPs and allow us to better understand the function of TCPs involved in leaf curvature of Chinese cabbage.
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Dhaka N, Bhardwaj V, Sharma MK, Sharma R. Evolving Tale of TCPs: New Paradigms and Old Lacunae. FRONTIERS IN PLANT SCIENCE 2017; 8:479. [PMID: 28421104 PMCID: PMC5376618 DOI: 10.3389/fpls.2017.00479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 03/20/2017] [Indexed: 05/03/2023]
Abstract
Teosinte Branched1/Cycloidea/Proliferating cell factors (TCP) genes are key mediators of genetic innovations underlying morphological novelties, stress adaptation, and evolution of immune response in plants. They have a remarkable ability to integrate and translate diverse endogenous, and environmental signals with high fidelity. Compilation of studies, aimed at elucidating the mechanism of TCP functions, shows that it takes an amalgamation and interplay of several different factors, regulatory processes and pathways, instead of individual components, to achieve the incredible functional diversity and specificity, demonstrated by TCP proteins. Through this minireview, we provide a brief description of key structural features and molecular components, known so far, that operate this conglomerate, and highlight the important conceptual challenges and lacunae in TCP research.
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Affiliation(s)
- Namrata Dhaka
- Crop Genetics & Informatics Group, School of Computational and Integrative SciencesJawaharlal Nehru University, New Delhi, India
| | - Vasudha Bhardwaj
- Crop Genetics & Informatics Group, School of BiotechnologyJawaharlal Nehru University, New Delhi, India
| | - Manoj K. Sharma
- Crop Genetics & Informatics Group, School of BiotechnologyJawaharlal Nehru University, New Delhi, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative SciencesJawaharlal Nehru University, New Delhi, India
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