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Peng Y, Cui L, Wang Y, Wei L, Geng S, Chen H, Chen G, Yang L, Bie Z. Pumpkin CmoDREB2A enhances salt tolerance of grafted cucumber through interaction with CmoNAC1 to regulate H 2O 2 and ABA signaling and K +/Na + homeostasis. HORTICULTURE RESEARCH 2024; 11:uhae057. [PMID: 38720932 PMCID: PMC11077054 DOI: 10.1093/hr/uhae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 05/12/2024]
Abstract
Pumpkin CmoNAC1 enhances salt tolerance in grafted cucumbers. However, the potential interactions with other proteins that may co-regulate salt tolerance alongside CmoNAC1 have yet to be explored. In this study, we identified pumpkin CmoDREB2A as a pivotal transcription factor that interacts synergistically with CmoNAC1 in the co-regulation of salt tolerance. Both transcription factors were observed to bind to each other's promoters, forming a positive regulatory loop of their transcription. Knockout of CmoDREB2A in the root resulted in reduced salt tolerance in grafted cucumbers, whereas overexpression demonstrated the opposite effect. Multiple assays in our study provided evidence of the protein interaction between CmoDREB2A and CmoNAC1. Exploiting this interaction, CmoDREB2A facilitated the binding of CmoNAC1 to the promoters of CmoRBOHD1, CmoNCED6, CmoAKT1;2, and CmoHKT1;1, inducing H2O2 and ABA synthesis and increasing the K+/Na+ ratio in grafted cucumbers under salt stress. Additionally, CmoNAC1 also promoted the binding of CmoDREB2A to CmoHAK5;1/CmoHAK5;2 promoters, further contributing to the K+/Na+ homeostasis. In summary, these findings reveal a crucial mechanism of CmoNAC1 and CmoDREB2A forming a complex enhancing salt tolerance in grafted cucumbers.
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Affiliation(s)
- Yuquan Peng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Lvjun Cui
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ying Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Lanxing Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Shouyu Geng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Hui Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Guoyu Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Li Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhilong Bie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
- Hubei Hongshan Laboratory, Department of Science and Technology of Hubei Province, 430070 Wuhan, China
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Liang X, Li J, Yang Y, Jiang C, Guo Y. Designing salt stress-resilient crops: Current progress and future challenges. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:303-329. [PMID: 38108117 DOI: 10.1111/jipb.13599] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Excess soil salinity affects large regions of land and is a major hindrance to crop production worldwide. Therefore, understanding the molecular mechanisms of plant salt tolerance has scientific importance and practical significance. In recent decades, studies have characterized hundreds of genes associated with plant responses to salt stress in different plant species. These studies have substantially advanced our molecular and genetic understanding of salt tolerance in plants and have introduced an era of molecular design breeding of salt-tolerant crops. This review summarizes our current knowledge of plant salt tolerance, emphasizing advances in elucidating the molecular mechanisms of osmotic stress tolerance, salt-ion transport and compartmentalization, oxidative stress tolerance, alkaline stress tolerance, and the trade-off between growth and salt tolerance. We also examine recent advances in understanding natural variation in the salt tolerance of crops and discuss possible strategies and challenges for designing salt stress-resilient crops. We focus on the model plant Arabidopsis (Arabidopsis thaliana) and the four most-studied crops: rice (Oryza sativa), wheat (Triticum aestivum), maize (Zea mays), and soybean (Glycine max).
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Affiliation(s)
- Xiaoyan Liang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Jianfang Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100194, China
| | - Yongqing Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Caifu Jiang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
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Almeida-Silva F, Pedrosa-Silva F, Venancio TM. The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1041-1051. [PMID: 37681739 DOI: 10.1111/tpj.16459] [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: 04/28/2023] [Revised: 07/04/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
Soybean is a crucial crop worldwide, used as a source of food, feed, and industrial products due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA-seq data in public databases and the computational challenges of processing raw RNA-seq data motivated us to develop the Soybean Expression Atlas, a gene expression database of over a thousand RNA-seq samples. Over the past few years, our database has allowed researchers to explore the expression profiles of important gene families, discover genes associated with agronomic traits, and understand the transcriptional dynamics of cellular processes. Here, we present the Soybean Expression Atlas v2, an updated version of our database with a fourfold increase in the number of samples, featuring transcript- and gene-level transcript abundance matrices for 5481 publicly available RNA-seq samples. New features in our database include the availability of transcript-level abundance estimates and equivalence classes to explore differential transcript usage, abundance estimates in bias-corrected counts to increase the accuracy of differential gene expression analyses, a new web interface with improved data visualization and user experience, and a reproducible and scalable pipeline available as an R package. The Soybean Expression Atlas v2 is available at https://soyatlas.venanciogroup.uenf.br/, and it will accelerate soybean research, empowering researchers with high-quality and easily accessible gene expression data.
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Affiliation(s)
- Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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Zhang Y, Xia P. The DREB transcription factor, a biomacromolecule, responds to abiotic stress by regulating the expression of stress-related genes. Int J Biol Macromol 2023:125231. [PMID: 37301338 DOI: 10.1016/j.ijbiomac.2023.125231] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/23/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
Abiotic stress is a crucial factor that affects plant survival and growth and even leads to plant death in severe cases. Transcription factors can enhance the ability of plants to fight against various stresses by controlling the expression of downstream genes. The dehydration response element binding protein (DREB) is the most extensive subfamily of AP2/ERF transcription factors involved in abiotic stress. However, insufficient research on the signal network of DREB transcription factors has limited plant growth and reproduction. Furthermore, field planting of DREB transcription factors and their roles under multiple stress also require extensive research. Previous reports on DREB transcription factors have focused on the regulation of DREB expression and its roles in plant abiotic stress. In recent years, there has been new progress in DREB transcription factors. Here, the structure and classification, evolution and regulation, role in abiotic stress, and application in crops of DREB transcription factors were reviewed. And this paper highlighted the evolution of DREB1/CBF, as well as the regulation of DREB transcription factors under the participation of plant hormone signals and the roles of subgroups in abiotic stress. In the future, it will lay a solid foundation for further study of DREB transcription factors and pave the way for the cultivation of resistant plants.
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Affiliation(s)
- Yan Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pengguo Xia
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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Su J, Song S, Wang Y, Zeng Y, Dong T, Ge X, Duan H. Genome-wide identification and expression analysis of DREB family genes in cotton. BMC PLANT BIOLOGY 2023; 23:169. [PMID: 36997878 PMCID: PMC10061749 DOI: 10.1186/s12870-023-04180-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Dehydration responsive element-binding (DREB) transcription factors are widely present in plants, and involve in signalling transduction, plant growth and development, and stress response. DREB genes have been characterized in multiple species. However, only a few DREB genes have been studied in cotton, one of the most important fibre crops. Herein, the genome‑wide identification, phylogeny, and expression analysis of DREB family genes are performed in diploid and tetraploid cotton species. RESULTS In total, 193, 183, 80, and 79 putative genes containing the AP2 domain were identified using bioinformatics approaches in G. barbadense, G. hirsutum, G. arboretum, and G. raimondii, respectively. Phylogenetic analysis showed that based on the categorization of Arabidopsis DREB genes, 535 DREB genes were divided into six subgroups (A1-A6) by using MEGA 7.0. The identified DREB genes were distributed unevenly across 13/26 chromosomes of A and/or D genomes. Synteny and collinearity analysis confirmed that during the evolution, the whole genome duplications, segmental duplications, and/or tandem duplications occurred in cotton DREB genes, and then DREB gene family was further expanded. Further, the evolutionary trees with conserved motifs, cis-acting elements, and gene structure of cotton DREB gene family were predicted, and these results suggested that DREB genes might be involved in the hormone and abiotic stresses responses. The subcellular localization showed that in four cotton species, DREB proteins were predominantly located in the nucleus. Further, the analysis of DREB gene expression was carried out by real-time quantitative PCR, confirming that the identified DREB genes of cotton were involved in response to early salinity and osmotic stress. CONCLUSIONS Collectively, our results presented a comprehensive and systematic understanding in the evolution of cotton DREB genes, and demonstrated the potential roles of DREB family genes in stress and hormone response.
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Affiliation(s)
- Jiuchang Su
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shanglin Song
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yiting Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yunpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Tianyu Dong
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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Feng C, Gao H, Zhou Y, Jing Y, Li S, Yan Z, Xu K, Zhou F, Zhang W, Yang X, Hussain MA, Li H. Unfolding molecular switches for salt stress resilience in soybean: recent advances and prospects for salt-tolerant smart plant production. FRONTIERS IN PLANT SCIENCE 2023; 14:1162014. [PMID: 37152141 PMCID: PMC10154572 DOI: 10.3389/fpls.2023.1162014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023]
Abstract
The increasing sodium salts (NaCl, NaHCO3, NaSO4 etc.) in agricultural soil is a serious global concern for sustainable agricultural production and food security. Soybean is an important food crop, and their cultivation is severely challenged by high salt concentration in soils. Classical transgenic and innovative breeding technologies are immediately needed to engineer salt tolerant soybean plants. Additionally, unfolding the molecular switches and the key components of the soybean salt tolerance network are crucial for soybean salt tolerance improvement. Here we review our understandings of the core salt stress response mechanism in soybean. Recent findings described that salt stress sensing, signalling, ionic homeostasis (Na+/K+) and osmotic stress adjustment might be important in regulating the soybean salinity stress response. We also evaluated the importance of antiporters and transporters such as Arabidopsis K+ Transporter 1 (AKT1) potassium channel and the impact of epigenetic modification on soybean salt tolerance. We also review key phytohormones, and osmo-protectants and their role in salt tolerance in soybean. In addition, we discuss the progress of omics technologies for identifying salt stress responsive molecular switches and their targeted engineering for salt tolerance in soybean. This review summarizes recent progress in soybean salt stress functional genomics and way forward for molecular breeding for developing salt-tolerant soybean plant.
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Affiliation(s)
- Chen Feng
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Hongtao Gao
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yonggang Zhou
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yan Jing
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Senquan Li
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhao Yan
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Keheng Xu
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Fangxue Zhou
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Wenping Zhang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xinquan Yang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, China
| | - Muhammad Azhar Hussain
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Muhammad Azhar Hussain, ; Haiyan Li,
| | - Haiyan Li
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Muhammad Azhar Hussain, ; Haiyan Li,
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Maqsood H, Munir F, Amir R, Gul A. Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 13:1031679. [PMID: 36507398 PMCID: PMC9731513 DOI: 10.3389/fpls.2022.1031679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/25/2022] [Indexed: 06/12/2023]
Abstract
Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.
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Affiliation(s)
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Cai X, Jia B, Sun M, Sun X. Insights into the regulation of wild soybean tolerance to salt-alkaline stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1002302. [PMID: 36340388 PMCID: PMC9627173 DOI: 10.3389/fpls.2022.1002302] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 05/24/2023]
Abstract
Soybean is an important grain and oil crop. In China, there is a great contradiction between soybean supply and demand. China has around 100 million ha of salt-alkaline soil, and at least 10 million could be potentially developed for cultivated land. Therefore, it is an effective way to improve soybean production by breeding salt-alkaline-tolerant soybean cultivars. Compared with wild soybean, cultivated soybean has lost a large number of important genes related to environmental adaptation during the long-term domestication and improvement process. Therefore, it is greatly important to identify the salt-alkaline tolerant genes in wild soybean, and investigate the molecular basis of wild soybean tolerance to salt-alkaline stress. In this review, we summarized the current research regarding the salt-alkaline stress response in wild soybean. The genes involved in the ion balance and ROS scavenging in wild soybean were summarized. Meanwhile, we also introduce key protein kinases and transcription factors that were reported to mediate the salt-alkaline stress response in wild soybean. The findings summarized here will facilitate the molecular breeding of salt-alkaline tolerant soybean cultivars.
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Affiliation(s)
| | | | | | - Xiaoli Sun
- *Correspondence: Mingzhe Sun, ; Xiaoli Sun,
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