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Kumar R, Tripathi G, Goyal I, Sharma J, Tiwari R, Shimphrui R, Sarkar NK, Grover A. Insights into genomic variations in rice Hsp100 genes across diverse rice accessions. PLANTA 2023; 257:91. [PMID: 36995438 DOI: 10.1007/s00425-023-04123-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
The Hsp101 gene is present across all sequenced rice genomes. However, as against Japonica rice, Hsp101 protein of most indica and aus rice contain insertion of glutamic acid at 907th position. The understanding of the heat stress response of rice plants is important for worldwide food security. We examined the presence/absence variations (PAVs) of heat shock proteins (Hsps)/heat shock transcription factor (Hsf) genes in cultivated rice accessions. While 53 Hsps/Hsfs genes showed variable extent of PAVs, 194 genes were the core genes present in all the rice accessions. ClpB1/Hsp101 gene, which is critically important for thermotolerance in plants, showed 100% distribution across the rice types. Within the ClpB1 gene sequence, 40 variation sites consisting of nucleotide polymorphisms (SNPs) and short insertion/deletions (InDels) were discerned. An InDel in ClpB1 leading to an in-frame insertion of 3 nucleotides (TCC) thereby an additional amino acid (glutamic acid) at 907th amino acid position was noted in most of the indica and aus as against japonica rice types. Three rice types namely Moroberekan (japonica), IR64 (indica) and N22 (aus) were further analyzed to address the question of ClpB1 genomic variations and its protein levels with the heat tolerance phenotype. The growth profiling analysis in the post heat stress (HS) period showed that N22 seedlings were most tolerant, IR64 moderately tolerant and Moroberekan highly sensitive. Importantly, the ClpB1 protein sequences of these three rice types showed distinct differences in terms of SNPs. As the ClpB1 protein levels accumulated post HS were generally higher in Moroberekan than N22 seedlings in our study, it is proposed that some additional gene loci in conjunction with ClpB1 regulate the overall rice heat stress response.
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Affiliation(s)
- Ritesh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Gayatri Tripathi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Isha Goyal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Jaydeep Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Ruchi Tiwari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Rinchuila Shimphrui
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Neelam K Sarkar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Zhang H, Zhou JF, Kan Y, Shan JX, Ye WW, Dong NQ, Guo T, Xiang YH, Yang YB, Li YC, Zhao HY, Yu HX, Lu ZQ, Guo SQ, Lei JJ, Liao B, Mu XR, Cao YJ, Yu JJ, Lin Y, Lin HX. A genetic module at one locus in rice protects chloroplasts to enhance thermotolerance. Science 2022; 376:1293-1300. [PMID: 35709289 DOI: 10.1126/science.abo5721] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
How the plasma membrane senses external heat-stress signals to communicate with chloroplasts to orchestrate thermotolerance remains elusive. We identified a quantitative trait locus, Thermo-tolerance 3 (TT3), consisting of two genes, TT3.1 and TT3.2, that interact together to enhance rice thermotolerance and reduce grain-yield losses caused by heat stress. Upon heat stress, plasma membrane-localized E3 ligase TT3.1 translocates to the endosomes, on which TT3.1 ubiquitinates chloroplast precursor protein TT3.2 for vacuolar degradation, implying that TT3.1 might serve as a potential thermosensor. Lesser accumulated, mature TT3.2 proteins in chloroplasts are essential for protecting thylakoids from heat stress. Our findings not only reveal a TT3.1-TT3.2 genetic module at one locus that transduces heat signals from plasma membrane to chloroplasts but also provide the strategy for breeding highly thermotolerant crops.
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Affiliation(s)
- Hai Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ji-Fu Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - You-Huang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Chao Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Huai-Yu Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Xiao Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shuang-Qin Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jie-Jie Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ben Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiao-Rui Mu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Jie Cao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Jun Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Youshun Lin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Xu Y, Zhang L, Ou S, Wang R, Wang Y, Chu C, Yao S. Natural variations of SLG1 confer high-temperature tolerance in indica rice. Nat Commun 2020; 11:5441. [PMID: 33116138 PMCID: PMC7595236 DOI: 10.1038/s41467-020-19320-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 10/06/2020] [Indexed: 01/28/2023] Open
Abstract
With global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living organisms. Here, we report the identification of SLG1 (Slender Guy 1), which encodes the cytosolic tRNA 2-thiolation protein 2 (RCTU2) in rice. SLG1 plays a key role in the response of rice plants to high-temperature stress at both seedling and reproductive stages. Dysfunction of SLG1 results in plants with thermosensitive phenotype, while overexpression of SLG1 enhances the tolerance of plants to high temperature. SLG1 is differentiated between the two Asian cultivated rice subspecies, indica and japonica, and the variations at both promoter and coding regions lead to an increased level of thiolated tRNA and enhanced thermotolerance of indica rice varieties. Our results demonstrate that the allelic differentiation of SLG1 confers indica rice to high-temperature tolerance, and tRNA thiolation pathway might be a potential target in the next generation rice breeding for the warming globe. Understanding the mechanism of high-temperature tolerance will help to breed crops adaptive to warming climate. Here, the authors show SLG1, a cytosolic tRNA 2-thiolation protein 2 encoding gene, is differentiated between the two Asian cultivated rice subspecies and confers high temperature tolerance of indica rice.
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Affiliation(s)
- Yufang Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Li Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ruci Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yueming Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Shanguo Yao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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