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Wu L, Cao L, Tao Y, Zhatova H, Hu H, Li C. Identification of the succinate-CoA ligase protein gene family reveals that TaSUCL1-1 positively regulate cadmium resistance in wheat. Int J Biol Macromol 2024; 268:131693. [PMID: 38657916 DOI: 10.1016/j.ijbiomac.2024.131693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
The Succinate-CoA ligase (SUCL1) gene family is involved in energy metabolism, phytohormone signaling, and plant growth, development, and tolerance to stress. This is the first study to analyze the SUCL1 gene family in wheat (Triticum aestivum). 17 TaSUCL1 genes were identified in the complete genome sequence and classified into five subfamilies based on related genes found in three other species. The 17 TaSUCL1 genes were unevenly distributed across 11 chromosomes, and the collinearity of these genes was further investigated. Through using real-time qPCR (RT-qPCR) analysis, we identified the expression patterns of the TaSUCL1 genes under various tissues and different heavy metal stress conditions. The functions of selected TaSUCL1-1 gene were investigated by RNA interference (RNAi). This study provided a comprehensive analysis of the TaSUCL1 gene family. Within the TaSUCL1 genes, the exon-intron structure and motif composition exhibited significant similarity among members of the same evolutionary branch. Homology analysis and phylogenetic comparison of the SUCL1 genes in different plants offered valuable insights for studying the evolutionary characteristics of the SUCL1 genes. The expression levels of the TaSUCL1 genes in different tissues and under various metal stress conditions reveal its important role in plant growth and development. Gene function analysis demonstrated that TaSUCL1-1 silenced wheat plants exhibited a decrease in the total cadmium (Cd) concentrations and gene expression levels compared to the wild type (WT). Additionally, TaSUCL1-1 belonging to class c physically interacts with the β-amylase protein TaBMY1 as verified by yeast two-hybridization. This research provides a useful resource for further study of the function and molecular genetic mechanism of the SUCL1 gene family members.
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Affiliation(s)
- Liuliu Wu
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China; Sumy National Agrarian University, Sumy 40021, Ukraine; Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Lifan Cao
- Henan Academy of Sciences, Zhengzhou 450000, China
| | - Ye Tao
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China; Sumy National Agrarian University, Sumy 40021, Ukraine; Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China
| | | | - Haiyan Hu
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Chengwei Li
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Agricultural University, Zhengzhou 450000, China; Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Henan Institute of Science and Technology, Xinxiang 453003, China; Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China.
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Subramani M, Urrea CA, Tamatamu SR, Sripathi VR, Williams K, Chintapenta LK, Todd A, Ozbay G. Comprehensive Proteomic Analysis of Common Bean ( Phaseolus vulgaris L.) Seeds Reveal Shared and Unique Proteins Involved in Terminal Drought Stress Response in Tolerant and Sensitive Genotypes. Biomolecules 2024; 14:109. [PMID: 38254709 PMCID: PMC10813106 DOI: 10.3390/biom14010109] [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: 11/27/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
This study identified proteomic changes in the seeds of two tolerant (SB-DT3 and SB-DT2) and two sensitive (Merlot and Stampede) common bean genotypes in response to terminal drought stress. Differentially expressed proteins (DEPs) were abundant in the susceptible genotype compared to the tolerant line. DEPs associated with starch biosynthesis, protein-chromophore linkage, and photosynthesis were identified in both genotypes, while a few DEPs and enriched biological pathways exhibited genotype-specific differences. The tolerant genotypes uniquely showed DEPs related to sugar metabolism and plant signaling, while the sensitive genotypes displayed more DEPs involved in plant-pathogen interaction, proteasome function, and carbohydrate metabolism. DEPs linked with chaperone and signal transduction were significantly altered between both genotypes. In summary, our proteomic analysis revealed both conserved and genotype-specific DEPs that could be used as targets in selective breeding and developing drought-tolerant common bean genotypes.
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Affiliation(s)
- Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA; (K.W.); (A.T.)
| | - Carlos A. Urrea
- Panhandle Research Extension and Education Center, University of Nebraska, 4502 Avenue I, Scottsbluff, NE 69361, USA;
| | - Sowjanya R. Tamatamu
- Center for Molecular Biology, Alabama A&M University, Normal, AL 35762, USA; (S.R.T.); (V.R.S.)
| | | | - Krystal Williams
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA; (K.W.); (A.T.)
| | - Lathadevi K. Chintapenta
- Biology Department, College of Arts and Sciences (CAS), University of Wisconsin-River Falls, River Falls, WI 54022, USA;
| | - Antonette Todd
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA; (K.W.); (A.T.)
| | - Gulnihal Ozbay
- Department of Agriculture and Natural Resources, Delaware State University, 1200 North DuPont Highway, Dover, DE 19901, USA
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Dwivedi AK, Singh V, Anwar K, Pareek A, Jain M. Integrated transcriptome, proteome and metabolome analyses revealed secondary metabolites and auxiliary carbohydrate metabolism augmenting drought tolerance in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107849. [PMID: 37393858 DOI: 10.1016/j.plaphy.2023.107849] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/01/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023]
Abstract
Drought is one of the major consequences of climate change and a serious threat to rice production. Drought stress activates interactions among genes, proteins and metabolites at the molecular level. A comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars can decipher the molecular mechanisms involved in drought tolerance/response. Here, we characterized the global-level transcriptome, proteome, and metabolome profiles, and performed integrated analyses thereof in a drought-sensitive (IR64) and a drought-tolerant (Nagina 22) rice cultivar under control and drought-stress conditions. The transcriptional dynamics and its integration with proteome analysis revealed the role of transporters in regulation of drought stress. The proteome response illustrated the contribution of translational machinery to drought tolerance in N22. The metabolite profiling revealed that aromatic amino acids and soluble sugars contribute majorly to drought tolerance in rice. The integrated transcriptome, proteome and metabolome analysis performed using statistical and knowledge-based methods revealed the preference for auxiliary carbohydrate metabolism through glycolysis and pentose phosphate pathway contributed to drought tolerance in N22. In addition, L-phenylalanine and the genes/proteins responsible for its biosynthesis were also found to contribute to drought tolerance in N22. In conclusion, our study provided mechanistic insights into the drought response/adaptation mechanism and is expected to facilitate engineering of drought tolerance in rice.
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Affiliation(s)
- Anuj Kumar Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Vikram Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Khalid Anwar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ashwani Pareek
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Javornik T, Carović-Stanko K, Gunjača J, Vidak M, Lazarević B. Monitoring Drought Stress in Common Bean Using Chlorophyll Fluorescence and Multispectral Imaging. PLANTS (BASEL, SWITZERLAND) 2023; 12:1386. [PMID: 36987074 PMCID: PMC10059887 DOI: 10.3390/plants12061386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
Drought is a significant constraint in bean production. In this study, we used high-throughput phenotyping methods (chlorophyll fluorescence imaging, multispectral imaging, 3D multispectral scanning) to monitor the development of drought-induced morphological and physiological symptoms at an early stage of development of the common bean. This study aimed to select the plant phenotypic traits which were most sensitive to drought. Plants were grown in an irrigated control (C) and under three drought treatments: D70, D50, and D30 (irrigated with 70, 50, and 30 mL distilled water, respectively). Measurements were performed on five consecutive days, starting on the first day after the onset of treatments (1 DAT-5 DAT), with an additional measurement taken on the eighth day (8 DAT) after the onset of treatments. Earliest detected changes were found at 3 DAT when compared to the control. D30 caused a decrease in leaf area index (of 40%), total leaf area (28%), reflectance in specific green (13%), saturation (9%), and green leaf index (9%), and an increase in the anthocyanin index (23%) and reflectance in blue (7%). The selected phenotypic traits could be used to monitor drought stress and to screen for tolerant genotypes in breeding programs.
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Affiliation(s)
- Tomislav Javornik
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
| | - Klaudija Carović-Stanko
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
| | - Jerko Gunjača
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
| | - Monika Vidak
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
| | - Boris Lazarević
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
- Department of Plant Nutrition, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia
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