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Butt H, Bazin J, Alshareef S, Eid A, Benhamed M, Reddy ASN, Crespi M, Mahfouz MM. Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation. Commun Biol 2021; 4:529. [PMID: 33953336 PMCID: PMC8100303 DOI: 10.1038/s42003-021-02051-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/26/2021] [Indexed: 01/02/2023] Open
Abstract
The SF3B complex, a multiprotein component of the U2 snRNP of the spliceosome, plays a crucial role in recognizing branch point sequence and facilitates spliceosome assembly and activation. Several chemicals that bind SF3B1 and PHF5A subunits of the SF3B complex inhibit splicing. We recently generated a splicing inhibitor-resistant SF3B1 mutant named SF3B1GEX1ARESISTANT 4 (SGR4) using CRISPR-mediated directed evolution, whereas splicing inhibitor-resistant mutant of PHF5A (Overexpression-PHF5A GEX1A Resistance, OGR) was generated by expressing an engineered version PHF5A-Y36C. Global analysis of splicing in wild type and these two mutants revealed the role of SF3B1 and PHF5A in splicing regulation. This analysis uncovered a set of genes whose intron retention is regulated by both proteins. Further analysis of these retained introns revealed that they are shorter, have a higher GC content, and contain shorter and weaker polypyrimidine tracts. Furthermore, splicing inhibition increased seedlings sensitivity to salt stress, consistent with emerging roles of splicing regulation in stress responses. In summary, we uncovered the functions of two members of the plant branch point recognition complex. The novel strategies described here should be broadly applicable in elucidating functions of splicing regulators, especially in studying the functions of redundant paralogs in plants. Butt et al. used CRISPR-mediated directed evolution to generate rice mutants for the spliceosome components SF3B1 and PHF5A. They demonstrate that these mutants have different levels of sensitivity to salt treatments and suggest that the strategies they employed can be used in the future to study functions of redundant paralogs in plants.
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Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Sahar Alshareef
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Moussa Benhamed
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Li Y, Guo Q, Liu P, Huang J, Zhang S, Yang G, Wu C, Zheng C, Yan K. Dual roles of the serine/arginine-rich splicing factor SR45a in promoting and interacting with nuclear cap-binding complex to modulate the salt-stress response in Arabidopsis. THE NEW PHYTOLOGIST 2021; 230:641-655. [PMID: 33421141 DOI: 10.1111/nph.17175] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/23/2020] [Indexed: 05/23/2023]
Abstract
Alternative splicing (AS) is emerging as a critical co-transcriptional regulation for plants in response to environmental stresses. Although multiple splicing factors have been linked to the salt-sensitive signaling network, the molecular mechanism remains unclear. We discovered that a conserved serine/arginine-rich (SR)-like protein, SR45a, as a component of the spliceosome, was involved in post-transcriptional regulation of salinity tolerance in Arabidopsis thaliana. Furthermore, SR45a was required for the AS and messenger RNA (mRNA) maturation of several salt-tolerance genes. Two alternatively spliced variants of SR45a were induced by salt stress, full-length SR45a-1a and the truncated isoform SR45a-1b, respectively. Lines with overexpression of SR45a-1a and SR45a-1b exhibited hypersensitive to salt stress. Our data indicated that SR45a directly interacted with the cap-binding complex (CBC) subunit cap-binding protein 20 (CBP20) which mediated salt-stress responses. Instead of binding to other spliceosome components, SR45a-1b promoted the association of SR45a-1a with CBP20, therefore mediating salt-stress signal transduction pathways. Additionally, the mutations in SR45a and CBP20 led to different salt-stress phenotypes. Together, these results provide the evidence that SR45a-CBP20 acts as a regulatory complex to regulate the plant response to salt stress, through a regulatory mechanism to fine-tune the splicing factors, especially in stressful conditions.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Qianhuan Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Peng Liu
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
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Weng X, Zhou X, Xie S, Gu J, Wang ZY. Identification of cassava alternative splicing-related genes and functional characterization of MeSCL30 involvement in drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:130-142. [PMID: 33486203 DOI: 10.1016/j.plaphy.2021.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/12/2021] [Indexed: 05/24/2023]
Abstract
Alternative splicing (AS) is an important post-transcriptional regulation strategy that can increase the proteome diversity and regulate mRNA level in eukaryote. Multi-exon genes can be alternative spliced to generate two or more transcripts, thereby increasing the adaptation to the external stress conditions in planta. However, AS-related proteins were less explored in cassava which is an important staple crop in the tropical area. A total of 365 genes encoding AS-related proteins were identified and renamed in the cassava genome, and the transcriptional and splicing changes of 15 randomly selected genes were systematically investigated in the tissues under diverse abiotic stress conditions. 13 out of 15 genes undergo AS in the tissues and under diverse environmental stress condition. Importantly, the greatest changes of splicing patterns were found in the leaf or in response to temperature stress, indicating that AS-related proteins had their tissue-specific regulation patterns and might be participated in the plant adaptation to temperature stress. We then found that overexpression of MeSCL30 in Arabidopsis enhanced the tolerance to drought stress through maintaining reactive oxygen species (ROS) homeostasis and increasing the expression of drought-responsive genes. Therefore, these findings refined the AS-related protein-coding genes and provided novel insights for manipulation of AS-related genes in order to enhance the resistance to environmental stress in plant.
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Affiliation(s)
- Xun Weng
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangdong, 510316, China; Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Xiaoxia Zhou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Shangqian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Natural Rubber Cooperative Innovation Centre of Hainan Province & Ministry of Education of China, Hainan University, Haikou, China
| | - Jinbao Gu
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangdong, 510316, China.
| | - Zhen-Yu Wang
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangdong, 510316, China; Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China.
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Liu B, Zhao S, Li P, Yin Y, Niu Q, Yan J, Huang D. Plant buffering against the high-light stress-induced accumulation of CsGA2ox8 transcripts via alternative splicing to finely tune gibberellin levels and maintain hypocotyl elongation. HORTICULTURE RESEARCH 2021; 8:2. [PMID: 33384414 PMCID: PMC7775442 DOI: 10.1038/s41438-020-00430-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/13/2020] [Accepted: 10/17/2020] [Indexed: 05/09/2023]
Abstract
In plants, alternative splicing (AS) is markedly induced in response to environmental stresses, but it is unclear why plants generate multiple transcripts under stress conditions. In this study, RNA-seq was performed to identify AS events in cucumber seedlings grown under different light intensities. We identified a novel transcript of the gibberellin (GA)-deactivating enzyme Gibberellin 2-beta-dioxygenase 8 (CsGA2ox8). Compared with canonical CsGA2ox8.1, the CsGA2ox8.2 isoform presented intron retention between the second and third exons. Functional analysis proved that the transcript of CsGA2ox8.1 but not CsGA2ox8.2 played a role in the deactivation of bioactive GAs. Moreover, expression analysis demonstrated that both transcripts were upregulated by increased light intensity, but the expression level of CsGA2ox8.1 increased slowly when the light intensity was >400 µmol·m-2·s-1 PPFD (photosynthetic photon flux density), while the CsGA2ox8.2 transcript levels increased rapidly when the light intensity was >200 µmol·m-2·s-1 PPFD. Our findings provide evidence that plants might finely tune their GA levels by buffering against the normal transcripts of CsGA2ox8 through AS.
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Affiliation(s)
- Bin Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Dongchuan Road, Shanghai, 200240, China
- Department of Plant Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, 08193, Spain
| | - Shuo Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Dongchuan Road, Shanghai, 200240, China
| | - Pengli Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Dongchuan Road, Shanghai, 200240, China
| | - Yilu Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Dongchuan Road, Shanghai, 200240, China
| | - Qingliang Niu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Dongchuan Road, Shanghai, 200240, China
| | - Jinqiang Yan
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China.
| | - Danfeng Huang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Dongchuan Road, Shanghai, 200240, China.
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Song L, Pan Z, Chen L, Dai Y, Wan J, Ye H, Nguyen HT, Zhang G, Chen H. Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions. Genes (Basel) 2020; 11:E1520. [PMID: 33352659 PMCID: PMC7765832 DOI: 10.3390/genes11121520] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/10/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) is a common post-transcriptional regulatory mechanism that modulates gene expression to increase proteome diversity. Increasing evidence indicates that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate drought responses in soybean remains poorly understood. In this study, we performed a genome-wide analysis of AS events in soybean (Glycine max) roots grown under various drought conditions using the high-throughput RNA-sequencing method, identifying 385, 989, 1429, and 465 AS events that were significantly differentially spliced under very mild drought stress, mild drought stress, severe drought stress, and recovery after severe drought conditions, respectively. Among them, alternative 3' splice sites and skipped exons were the major types of AS. Overall, 2120 genes that experienced significant AS regulation were identified from these drought-treated root samples. Gene Ontology term analysis indicated that the AS regulation of binding activity has vital roles in the drought response of soybean root. Notably, the genes encoding splicing regulatory factors in the spliceosome pathway and mRNA surveillance pathway were enriched according to the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Splicing regulatory factor-related genes in soybean root also responded to drought stress and were alternatively spliced under drought conditions. Taken together, our data suggest that drought-responsive AS acts as a direct or indirect mode to regulate drought response of soybean roots. With further in-depth research of the function and mechanism of AS in the process of abiotic stress, these results will provide a new strategy for enhancing stress tolerance of plants.
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Affiliation(s)
- Li Song
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (Z.P.); (L.C.); (Y.D.)
| | - Zhenzhi Pan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (Z.P.); (L.C.); (Y.D.)
| | - Lin Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (Z.P.); (L.C.); (Y.D.)
| | - Yi Dai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (Z.P.); (L.C.); (Y.D.)
| | - Jinrong Wan
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (J.W.); (H.Y.); (H.T.N.)
| | - Heng Ye
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (J.W.); (H.Y.); (H.T.N.)
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (J.W.); (H.Y.); (H.T.N.)
| | - Guozheng Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China;
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Zhang H, Yin L, Song F, Jiang M. SKIP Silencing Decreased Disease Resistance Against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 in Tomato. FRONTIERS IN PLANT SCIENCE 2020; 11:593267. [PMID: 33381133 PMCID: PMC7767821 DOI: 10.3389/fpls.2020.593267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/19/2020] [Indexed: 05/29/2023]
Abstract
SKIP, a component of the spliceosome, is involved in numerous signaling pathways. However, there is no direct genetic evidence supporting the function of SKIP in defense responses. In this paper, two SKIPs, namely, SlSKIP1a and SlSKIP1b, were analyzed in tomato. qRT-PCR analysis showed that the SlSKIP1b expression was triggered via Pseudomonas syringae pv. tomato (Pst) DC3000 and Botrytis cinerea (B. cinerea), together with the defense-associated signals. In addition, the functions of SlSKIP1a and SlSKIP1b in disease resistance were analyzed in tomato through the virus-induced gene silencing (VIGS) technique. VIGS-mediated SlSKIP1b silencing led to increased accumulation of reactive oxygen species (ROS), along with the decreased expression of defense-related genes (DRGs) after pathogen infection, suggesting that it reduced B. cinerea and Pst DC3000 resistance. There was no significant difference in B. cinerea and Pst DC3000 resistance in TRV-SlSKIP1a-infiltrated plants compared with the TRV-GUS-silencing counterparts. As suggested by the above findings, SlSKIP1b plays a vital role in disease resistance against pathogens possibly by regulating the accumulation of ROS as well as the expression of DRGs.
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Affiliation(s)
- Huijuan Zhang
- Life Science Collegue, Taizhou University, Taizhou, China
| | - Longfei Yin
- Life Science Collegue, Taizhou University, Taizhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ming Jiang
- Life Science Collegue, Taizhou University, Taizhou, China
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57
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Banikamali M, Soltanloo H, Ramezanpour SS, Yamchi A, Sorahinobar M. Identification of salinity responsive genes in lavender through cDNA-AFLP. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00520. [PMID: 32963973 PMCID: PMC7490537 DOI: 10.1016/j.btre.2020.e00520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/13/2020] [Accepted: 08/10/2020] [Indexed: 01/01/2023]
Abstract
Currently, a global demand exists forlavender as a significant medicinal plant and source of essential oils. Freshwater and arable lands are two major factors that inhibit extensive farming of medicinal plants in Iran. Saline water from seas and salty soil may be new resources for agricultural use, especially for medicinal plants. We sought to extend our knowledge of the Lavandula angustifolia genome and molecular basis of its salinity tolerance by using cDNA amplified fragment length polymorphism (cDNA-AFLP) to investigate the changes in plant transcriptomes in response to NaCl. All identified transcript derived fragments (TDF) were assigned as novel L. angustifolia genes related to signal transduction, regulation of gene expression, alternative splicing, autophagy, and secondary metabolite biosynthesis. qRT-PCR analysis of the TDFs in response to different concentrations of NaCl revealed various levels of mRNA of the identified genes in this plant. Our findings provided primary insights into the molecular response of L. angustifolia to salinity.
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Affiliation(s)
- Mania Banikamali
- Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Science and Natural Resources, Gorgan, Golestan, Iran
| | - Hassan Soltanloo
- Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Science and Natural Resources, Gorgan, Golestan, Iran
| | - S Sanaz Ramezanpour
- Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Science and Natural Resources, Gorgan, Golestan, Iran
| | - Ahad Yamchi
- Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Science and Natural Resources, Gorgan, Golestan, Iran
| | - Mona Sorahinobar
- Department of Plant Biology, Faculty of Biological Science, Alzahra University, Tehran, Iran
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58
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Chen MX, Zhang KL, Zhang M, Das D, Fang YM, Dai L, Zhang J, Zhu FY. Alternative splicing and its regulatory role in woody plants. TREE PHYSIOLOGY 2020; 40:1475-1486. [PMID: 32589747 DOI: 10.1093/treephys/tpaa076] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 05/22/2023]
Abstract
Alternative splicing (AS) is an important post-transcriptional process to enhance proteome diversity in eukaryotic organisms. In plants, numerous reports have primarily focused on AS analysis in model plant species or herbaceous plants, leading to a notable lack of research on AS in woody plants. More importantly, emerging evidence indicates that many important traits, including wood formation and stress resistance, in woody plants are controlled by AS. In this review article, we summarize the current progress of all kinds of AS studies in different tree species at various stages of development and in response to various stresses, revealing the significant role played by AS in woody plants, as well as the similar properties and differential regulation within their herbaceous counterparts. Furthermore, we propose several potential strategies to facilitate the functional characterization of splicing factors in woody plants and evaluate a general pipeline for the systematic characterization of splicing isoforms in a complex AS regulatory network. The utilization of genetic studies and high-throughput omics integration approaches to analyze AS genes and splicing factors is likely to further advance our understanding of AS modulation in woody plants.
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Affiliation(s)
- Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128, China
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Debatosh Das
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Yan-Ming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Lei Dai
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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Zhang Q, Zhang WJ, Yin ZG, Li WJ, Zhao HH, Zhang S, Zhuang L, Wang YX, Zhang WH, Du JD. Genome- and Transcriptome-Wide Identification of C3Hs in Common Bean ( Phaseolus vulgaris L.) and Structural and Expression-Based Analyses of Their Functions During the Sprout Stage Under Salt-Stress Conditions. Front Genet 2020; 11:564607. [PMID: 33101386 PMCID: PMC7522512 DOI: 10.3389/fgene.2020.564607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022] Open
Abstract
CCCH (C3H) zinc-finger proteins are involved in plant biotic and abiotic stress responses, growth and development, and disease resistance. However, studies on C3H genes in Phaseolus vulgaris L. (common bean) are limited. Here, 29 protein-encoding C3H genes, located on 11 different chromosomes, were identified in P. vulgaris. A phylogenetic analysis categorized the PvC3Hs into seven subfamilies on the basis of distinct features, such as exon–intron structure, cis-regulatory elements, and MEME motifs. A collinearity analysis revealed connections among the PvC3Hs in the same and different species. The PvC3H genes showed tissue-specific expression patterns during the sprout stage, as assessed by real-time quantitative PCR (RT-qPCR). Using RNA-sequencing and RT-qPCR data, PvC3Hs were identified as being enriched through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses in binding, channel activity, and the spliceosome pathway. These results provide useful information and a rich resource that can be exploited to functionally characterize and understand PvC3Hs. These PvC3Hs, especially those enriched in binding, channel activity, and the spliceosome pathway will further facilitate the molecular breeding of common bean and provide insights into the correlations between PvC3Hs and salt-stress responses during the sprout stage.
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Affiliation(s)
- Qi Zhang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wen-Jing Zhang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhen-Gong Yin
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang, China
| | - Wei-Jia Li
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hao-Hao Zhao
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shuo Zhang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Lin Zhuang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yu-Xin Wang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wen-Hui Zhang
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Ji-Dao Du
- Laboratory Crop Genetics and Breeding, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China.,Laboratory Crop Genetics and Breeding, National Coarse Cereals Engineering Research Center, Daqing, China
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60
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Tognacca RS, Kubaczka MG, Servi L, Rodríguez FS, Godoy Herz MA, Petrillo E. Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout Arabidopsis thaliana's life cycle. Transcription 2020; 11:117-133. [PMID: 32748694 DOI: 10.1080/21541264.2020.1796473] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of A. thaliana's life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.
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Affiliation(s)
- Rocío S Tognacca
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - M Guillermina Kubaczka
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Lucas Servi
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Florencia S Rodríguez
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina.,Departamento De Biodiversidad Y Biología Experimental, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Micaela A Godoy Herz
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Ezequiel Petrillo
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
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61
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Feng G, Yoo M, Davenport R, Boatwright JL, Koh J, Chen S, Barbazuk WB. Jasmonate induced alternative splicing responses in Arabidopsis. PLANT DIRECT 2020; 4:e00245. [PMID: 32875268 PMCID: PMC7450174 DOI: 10.1002/pld3.245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 06/04/2020] [Accepted: 06/24/2020] [Indexed: 05/14/2023]
Abstract
Jasmonate is an essential phytohormone regulating plant growth, development, and defense. Alternative splicing (AS) in jasmonate ZIM-domain (JAZ) repressors is well-characterized and plays an important role in jasmonate signaling regulation. However, it is unknown whether other genes in the jasmonate signaling pathway are regulated by AS. We explore the potential for AS regulation in three Arabidopsis genotypes (WT, jaz2, jaz7) in response to methyl jasmonate (MeJA) treatment with respect to: (a) differential AS, (b) differential miRNA targeted AS, and (c) AS isoforms with novel functions. AS events identified from transcriptomic data were validated with proteomic data. Protein interaction networks identified two genes, SKIP and ALY4 whose products have both DNA- and RNA-binding affinities, as potential key regulators mediating jasmonate signaling and AS regulation. We observed cases where AS alone, or AS and transcriptional regulation together, can influence gene expression in response to MeJA. Twenty-one genes contain predicted miRNA target sites subjected to AS, which implies that AS is coupled to miRNA regulation. We identified 30 cases where alternatively spliced isoforms may have novel functions. For example, AS of bHLH160 generates an isoform without a basic domain, which may convert it from an activator to a repressor. Our study identified potential key regulators in AS regulation of jasmonate signaling pathway. These findings highlight the importance of AS regulation in the jasmonate signaling pathway, both alone and in collaboration with other regulators. SIGNIFICANCE STATEMENT By exploring alternative splicing, we demonstrate its regulation in the jasmonate signaling pathway alone or in collaboration with other posttranscriptional regulations such as nonsense and microRNA-mediated decay. A signal transduction network model for alternative splicing in jasmonate signaling pathway was generated, contributing to our understanding for this important, prevalent, but relatively unexplored regulatory mechanism in plants.
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Affiliation(s)
- Guanqiao Feng
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
| | - Mi‐Jeong Yoo
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Ruth Davenport
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | | | - Jin Koh
- The Interdisciplinary Center for Biotechnology Research (ICBR)University of FloridaGainesvilleFLUSA
| | - Sixue Chen
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- The Interdisciplinary Center for Biotechnology Research (ICBR)University of FloridaGainesvilleFLUSA
- The Genetics InstituteUniversity of FloridaGainesvilleFLUSA
| | - W. Brad Barbazuk
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- The Interdisciplinary Center for Biotechnology Research (ICBR)University of FloridaGainesvilleFLUSA
- The Genetics InstituteUniversity of FloridaGainesvilleFLUSA
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62
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First Come, First Served: Sui Generis Features of the First Intron. PLANTS 2020; 9:plants9070911. [PMID: 32707681 PMCID: PMC7411622 DOI: 10.3390/plants9070911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes undergo alternative splicing (AS), which ostensibly is considered to increase protein diversity as one of the intrinsic mechanisms for fitness to the varying environment or the internal developmental program. In addition, recent findings have prevailed in terms of overlooked intron functions. Here, we review recent progress in the underlying mechanisms of intron function, in particular by focusing on unique features of the first intron that is located in close proximity to the transcription start site. The distinct deposition of epigenetic marks and nucleosome density on the first intronic DNA sequence, the impact of the first intron on determining the transcription start site and elongation of its own expression (called intron-mediated enhancement, IME), translation control in 5′-UTR, and the new mechanism of the trans-acting function of the first intron in regulating gene expression at the post-transcriptional level are summarized.
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63
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Alternative splicing of flowering time gene FT is associated with halving of time to flowering in coconut. Sci Rep 2020; 10:11640. [PMID: 32669611 PMCID: PMC7363896 DOI: 10.1038/s41598-020-68431-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/24/2020] [Indexed: 11/08/2022] Open
Abstract
Coconut palm has two distinct types-"tall" and "dwarf"-which differ morphologically. Tall coconut varieties need 8-10 years to start flowering, while dwarf coconut varieties only require 3-5 years. We compared seedling and reproductive stage transcriptomes for both coconut types to determine potential molecular mechanisms underlying control of flowering time in coconut. Several key genes in the photoperiod pathway were differentially expressed between seedling and reproductive leaf samples in both tall and dwarf coconut. These genes included suppressor of overexpression of constans (SOC1), flowering locus T (FT), and Apetala 1 (AP1). Alternative splicing analysis of genes in the photoperiod pathway further revealed that the FT gene produces different transcripts in tall compared to dwarf coconut. The shorter alternative splice variant of FT [which included a 6 bp deletion, alternative 3' splicing sites (A3SS)] was found to be exclusively present in dwarf coconut varieties but absent in most tall coconut varieties. Our results provide a valuable information resource as well as suggesting a probable mechanism for differentiation of flowering time onset in coconut, providing a target for future breeding work in accelerating time to flowering in this crop species.
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64
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Zhang H, Li G, Fu C, Duan S, Hu D, Guo X. Genome-wide identification, transcriptome analysis and alternative splicing events of Hsf family genes in maize. Sci Rep 2020; 10:8073. [PMID: 32415117 PMCID: PMC7229205 DOI: 10.1038/s41598-020-65068-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/26/2020] [Indexed: 12/13/2022] Open
Abstract
Heat shock transcription factor (Hsf) plays a transcriptional regulatory role in plants during heat stress and other abiotic stresses. 31 non-redundant ZmHsf genes from maize were identified and clustered in the reference genome sequenced by Single Molecule Real Time (SMRT). The amino acid length, chromosome location, and presence of functional domains and motifs of all ZmHsfs sequences were analyzed and determined. Phylogenetics and collinearity analyses reveal gene duplication events in Hsf family and collinearity blocks shared by maize, rice and sorghum. The results of RNA-Seq analysis of anthesis and post-anthesis periods in maize show different expression patterns of ZmHsf family members. Specially, ZmHsf26 of A2 subclass and ZmHsf23 of A6 subclass were distinctly up-regulated after heat shock (HS) at post-anthesis stage. Nanopore transcriptome sequencing of maize seedlings showed that alternative splicing (AS) events occur in ZmHsf04 and ZmHsf17 which belong to subclass A2 after heat shock. Through sequence alignment, semi-quantitative and quantitative RT-PCR, we found that intron retention events occur in response to heat shock, and newly splice isoforms, ZmHsf04-II and ZmHsf17-II, were transcribed. Both new isoforms contain several premature termination codons in their introns which may lead to early termination of translation. The ZmHsf04 expression was highly increased than that of ZmHsf17, and the up-regulation of ZmHsf04-I transcription level were significantly higher than that of ZmHsf04-II after HS.
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Affiliation(s)
- Huaning Zhang
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China
| | - Guoliang Li
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China
| | - Cai Fu
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China
| | - Shuonan Duan
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China
| | - Dong Hu
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China.
| | - Xiulin Guo
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China.
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65
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Ye W, Wang T, Wei W, Lou S, Lan F, Zhu S, Li Q, Ji G, Lin C, Wu X, Ma L. The Full-Length Transcriptome of Spartina alterniflora Reveals the Complexity of High Salt Tolerance in Monocotyledonous Halophyte. PLANT & CELL PHYSIOLOGY 2020; 61:882-896. [PMID: 32044993 DOI: 10.1093/pcp/pcaa013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 01/31/2020] [Indexed: 05/09/2023]
Abstract
Spartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used Pacific Biosciences (PacBio) full-length single-molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt gradient experiments. High-quality unigenes, transcription factors, non-coding RNA and Spartina-specific transcripts were identified. Co-expression network analysis found that protein kinase-encoding genes (SaOST1, SaCIPK10 and SaLRRs) are hub genes in the salt tolerance regulatory network. High salt stress induced the expression of transcription factors but repressed the expression of long non-coding RNAs. The Spartina transcriptome is closer to rice than Arabidopsis, and a higher proportion of transporter and transcription factor-encoding transcripts have been found in Spartina. Transcriptome analysis showed that high salt stress induced the expression of carbohydrate metabolism, especially cell-wall biosynthesis-related genes in Spartina, and repressed its expression in rice. Compared with rice, high salt stress highly induced the expression of stress response, protein modification and redox-related gene expression and greatly inhibited translation in Spartina. High salt stress also induced alternative splicing in Spartina, while differentially expressed alternative splicing events associated with photosynthesis were overrepresented in Spartina but not in rice. Finally, we built the SAPacBio website for visualizing full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes and alternative splicing events in Spartina. Overall, this study suggests that the salt tolerance mechanism in Spartina is different from rice in many aspects and is far more complex than expected.
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Affiliation(s)
- Wenbin Ye
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Taotao Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Wei
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuaitong Lou
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Faxiu Lan
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sheng Zhu
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Qinzhen Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Chentao Lin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Liuyin Ma
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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66
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Time Series RNA-seq in Pigeonpea Revealed the Core Genes in Metabolic Pathways under Aluminum Stress. Genes (Basel) 2020; 11:genes11040380. [PMID: 32244575 PMCID: PMC7230159 DOI: 10.3390/genes11040380] [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: 02/02/2020] [Revised: 02/18/2020] [Accepted: 03/12/2020] [Indexed: 11/17/2022] Open
Abstract
Pigeonpea is an important economic crop in the world and is mainly distributed in tropical and subtropical regions. In order to further expand the scope of planting, one of the problems that must be solved is the impact of soil acidity on plants in these areas. Based on our previous work, we constructed a time series RNA sequencing (RNA-seq) analysis under aluminum (Al) stress in pigeonpea. Through a comparison analysis, 11,425 genes were found to be differentially expressed among all the time points. After clustering these genes by their expression patterns, 12 clusters were generated. Many important functional pathways were identified by gene ontology (GO) analysis, such as biological regulation, localization, response to stimulus, metabolic process, detoxification, and so on. Further analysis showed that metabolic pathways played an important role in the response of Al stress. Thirteen out of the 23 selected genes related to flavonoids and phenols were downregulated in response to Al stress. In addition, we verified these key genes of flavonoid- and phenol-related metabolism pathways by qRT-PCR. Collectively, our findings not only revealed the regulation mechanism of pigeonpea under Al stress but also provided methodological support for further exploration of plant stress regulation mechanisms.
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67
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Tack DC, Su Z, Yu Y, Bevilacqua PC, Assmann SM. Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis. RNA (NEW YORK, N.Y.) 2020; 26:492-511. [PMID: 31937672 PMCID: PMC7075263 DOI: 10.1261/rna.072850.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/13/2020] [Indexed: 05/22/2023]
Abstract
Little is known concerning the effects of abiotic factors on in vivo RNA structures. We applied Structure-seq to assess the in vivo mRNA structuromes of Arabidopsis thaliana under salinity stress, which negatively impacts agriculture. Structure-seq utilizes dimethyl sulfate reactivity to identify As and Cs that lack base-pairing or protection. Salt stress refolded transcripts differentially in root versus shoot, evincing tissue specificity of the structurome. Both tissues exhibited an inverse correlation between salt stress-induced changes in transcript reactivity and changes in abundance, with stress-related mRNAs showing particular structural dynamism. This inverse correlation is more pronounced in mRNAs wherein the mean reactivity of the 5'UTR, CDS, and 3'UTR concertedly change under salinity stress, suggesting increased susceptibility to abundance control mechanisms in transcripts exhibiting this phenomenon, which we name "concordancy." Concordant salinity-induced increases in reactivity were notably observed in photosynthesis genes, thereby implicating mRNA structural loss in the well-known depression of photosynthesis by salt stress. Overall, changes in secondary structure appear to impact mRNA abundance, molding the functional specificity of the transcriptome under stress.
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Affiliation(s)
- David C Tack
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Spectrum Health Office of Research, Grand Rapids, Michigan 49503, USA
| | - Zhao Su
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Yunqing Yu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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68
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Wani SH, Kumar V, Khare T, Guddimalli R, Parveda M, Solymosi K, Suprasanna P, Kavi Kishor PB. Engineering salinity tolerance in plants: progress and prospects. PLANTA 2020; 251:76. [PMID: 32152761 DOI: 10.1007/s00425-020-03366-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/24/2020] [Indexed: 05/20/2023]
Abstract
There is a need to integrate conceptual framework based on the current understanding of salt stress responses with different approaches for manipulating and improving salt tolerance in crop plants. Soil salinity exerts significant constraints on global crop production, posing a serious challenge for plant breeders and biotechnologists. The classical transgenic approach for enhancing salinity tolerance in plants revolves by boosting endogenous defence mechanisms, often via a single-gene approach, and usually involves the enhanced synthesis of compatible osmolytes, antioxidants, polyamines, maintenance of hormone homeostasis, modification of transporters and/or regulatory proteins, including transcription factors and alternative splicing events. Occasionally, genetic manipulation of regulatory proteins or phytohormone levels confers salinity tolerance, but all these may cause undesired reduction in plant growth and/or yields. In this review, we present and evaluate novel and cutting-edge approaches for engineering salt tolerance in crop plants. First, we cover recent findings regarding the importance of regulatory proteins and transporters, and how they can be used to enhance salt tolerance in crop plants. We also evaluate the importance of halobiomes as a reservoir of genes that can be used for engineering salt tolerance in glycophytic crops. Additionally, the role of microRNAs as critical post-transcriptional regulators in plant adaptive responses to salt stress is reviewed and their use for engineering salt-tolerant crop plants is critically assessed. The potentials of alternative splicing mechanisms and targeted gene-editing technologies in understanding plant salt stress responses and developing salt-tolerant crop plants are also discussed.
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Affiliation(s)
- Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Anantnag, Jammu and Kashmir, 192 101, India.
| | - Vinay Kumar
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | - Tushar Khare
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | | | | | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, ELTE-Eötvös Loránd University, Budapest, 1053, Hungary
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - P B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science Technology and Research, Vadlamudi, Guntur, 522 213, India
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69
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Jin H, Lin J, Zhu Z. PIF4 and HOOKLESS1 Impinge on Common Transcriptome and Isoform Regulation in Thermomorphogenesis. PLANT COMMUNICATIONS 2020; 1:100034. [PMID: 33367235 PMCID: PMC7748007 DOI: 10.1016/j.xplc.2020.100034] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/12/2019] [Accepted: 02/14/2020] [Indexed: 05/04/2023]
Abstract
High temperature activates the transcription factor PHYTOCHROME-INTERACTING FACTOR4 (PIF4) to stimulate auxin signaling, which causes hypocotyl elongation and leaf hyponasty (thermomorphogenesis). HOOKLESS1 (HLS1) is a recently reported positive regulator of thermomorphogenesis, but the molecular mechanisms by which HLS1 regulates thermomorphogenesis remain unknown. In this study, we initially compared PIF4- and/or HLS1-dependent differential gene expression (DEG) upon high-temperature treatment. We found that a large number of genes are coregulated by PIF4 and HLS1, especially genes involved in plant growth or defense responses. Moreover, we found that HLS1 interacts with PIF4 to form a regulatory module and that, among the HLS1-PIF4-coregulated genes, 27.7% are direct targets of PIF4. We also identified 870 differentially alternatively spliced genes (DASGs) in wild-type plants under high temperature. Interestingly, more than half of these DASG events (52.4%) are dependent on both HLS1 and PIF4, and the spliceosome-defective mutant plantsexhibit a hyposensitive response to high temperature, indicating that DASGs are required for thermomorphogenesis. Further comparative analyses showed that the HLS1/PIF4-coregulated DEGs and DASGs exhibit almost no overlap, suggesting that high temperature triggers two distinct strategies to control plant responses and thermomorphogenesis. Taken together, these results demonstrate that the HLS1-PIF4 module precisely controls both transcriptional and posttranscriptional regulation during plant thermomorphogenesis.
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Affiliation(s)
- Huanhuan Jin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jingya Lin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ziqiang Zhu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730000, China
- Corresponding author
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70
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Di F, Wang T, Ding Y, Chen X, Wang H, Li J, Liu L. Genetic Mapping Combined with a Transcriptome Analysis to Screen for Candidate Genes Responsive to Abscisic Acid Treatment in Brassica napus Embryos During Seed Germination. DNA Cell Biol 2020; 39:533-547. [PMID: 32031882 DOI: 10.1089/dna.2019.5169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Brassica napus embryos contain precursor tissues for the leaves, stem, and root, as well as the cotyledons, and these precursor tissues play key roles in seed germination, seedling survival, and subsequent seedling growth. Abscisic acid (ABA) plays a prominent role in the inhibition of seed germination. The underlying molecular mechanisms of the embryo responses to ABA stress followed by inhibited seed germination have not been reported in B. napus to date. In this study, we conducted quantitative trait locus (QTL) analysis of B. napus seed in response to ABA stress using 170 recombinant inbred lines. Furthermore, we performed transcriptome sequencing (RNA-seq) analyses by using B. napus ZS11 embryos under sterile deionized water (control) and 10 mg/L (10A), 20 mg/L (20A), and 30 mg/L (30A) ABA treatment conditions. In total, 10 QTLs were screened for explaining 2.70-6.73% of the phenotypic variation under ABA stress. In addition, 1495, 3332, and 3868 differentially expressed genes (DEGs) were identified in the "control vs 10A," "control vs 20A," and "control vs 30A" comparisons, respectively. Gene Ontology (GO) enrichment analysis indicated that DEG functions are mainly related to response to stimuli, response to oxygen-containing compounds, response to lipids, and the transport and seed dormancy processes. These DEGs mainly participated in the response to plant hormone signal transduction, starch and sucrose metabolism, cutin, suberine, and wax biosynthesis, and phenylpropanoid biosynthesis processes pathways. Our results provide a foundation for further explorations of the molecular regulatory mechanisms of B. napus embryos in response to abiotic stress during the seed germination stage.
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Affiliation(s)
- Feifei Di
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Tengyue Wang
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Yiran Ding
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Xueping Chen
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shanxi Rapeseed Branch of National Center for Oil Crops Genetic Improvement, Yangling, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
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71
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Li S, Wang Y, Zhao Y, Zhao X, Chen X, Gong Z. Global Co-transcriptional Splicing in Arabidopsis and the Correlation with Splicing Regulation in Mature RNAs. MOLECULAR PLANT 2020; 13:266-277. [PMID: 31759129 PMCID: PMC8034514 DOI: 10.1016/j.molp.2019.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 05/20/2023]
Abstract
RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription. However, co-transcriptional splicing has not yet been explored in plants. Here, we built transcriptomes of nascent chromatin RNAs in Arabidopsis thaliana and showed that nearly all introns undergo co-transcriptional splicing, which occurs with higher efficiency for introns in protein-coding genes than for those in noncoding RNAs. Total intron number and intron position are two predominant features that correlate with co-transcriptional splicing efficiency, and introns with alternative 5' or 3' splice sites are less efficiently spliced. Furthermore, we found that mutations in genes encoding trans-acting proteins lead to more introns with increased splicing defects in nascent RNAs than in mature RNAs, and that introns with increased splicing defects in mature RNAs are inefficiently spliced at the co-transcriptional level. Collectively, our results not only uncovered widespread co-transcriptional splicing in Arabidopsis but also identified features that may affect or be affected by co-transcriptional splicing efficiency.
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Affiliation(s)
- Shaofang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China.
| | - Yuan Wang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yonghui Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing 210018, China
| | - Xinjie Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
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72
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Wang L, Chen M, Zhu F, Fan T, Zhang J, Lo C. Alternative splicing is a Sorghum bicolor defense response to fungal infection. PLANTA 2019; 251:14. [PMID: 31776670 DOI: 10.1007/s00425-019-03309-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/29/2019] [Indexed: 05/24/2023]
Abstract
This study provides new insights that alternative splicing participates with transcriptional control in defense responses to Colletotrichum sublineola in sorghum In eukaryotic organisms, alternative splicing (AS) is an important post-transcriptional mechanism to generate multiple transcript isoforms from a single gene. Protein variants translated from splicing isoforms may have altered molecular characteristics in signal transduction and metabolic activities. However, which transcript isoforms will be translated into proteins and the biological functions of the resulting proteoforms are yet to be identified. Sorghum is one of the five major cereal crops, but its production is severely affected by fungal diseases. For example, sorghum anthracnose caused by Colletotrichum sublineola greatly reduces grain yield and biomass production. In this study, next-generation sequencing technology was used to analyze C. sublineola-inoculated sorghum seedlings compared with mock-inoculated control. It was identified that AS regulation may be as important as traditional transcriptional control during defense responses to fungal infection. Moreover, several genes involved in flavonoid and phenylpropanoid biosynthetic pathways were found to undergo multiple AS modifications. Further analysis demonstrated that non-conventional targets of both 5'- and 3'-splice sites were alternatively used in response to C. sublineola infection. Splicing factors were also affected at both transcriptional and post-transcriptional levels. As the first transcriptome report on C. sublineola infected sorghum, our work also suggested that AS plays crucial functions in defense responses to fungal invasion.
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Affiliation(s)
- Lanxiang Wang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Moxian Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fuyuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Tao Fan
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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Xu Q, Cheng L, Mei Y, Huang L, Zhu J, Mi X, Yu Y, Wei C. Alternative Splicing of Key Genes in LOX Pathway Involves Biosynthesis of Volatile Fatty Acid Derivatives in Tea Plant ( Camellia sinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13021-13032. [PMID: 31693357 DOI: 10.1021/acs.jafc.9b05925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Volatile fatty acid derivatives (VFADs) produced in tea plants (Camellia sinensis) not only have been shown to function as defense compounds but also impart a "fresh green" odor to green tea products; however, little is known about alternative splicing (AS) of genes in regulating the production of VFADs in plants. In this study, the contents of VFADs and corresponding transcriptome profiles were obtained in five different months (April, June, August, September, and October). Correlation analysis identified seven unique transcripts of enzyme-coding genes (CsLOX2, CsLOX4, CsADH4, CsADH8, and CsADH10), which are responsible for regulating VFAD biosynthesis; four AS transcripts of these genes (CsLOX2, CsLOX4, CsADH4, and CsADH8) were validated by RT-PCR. By employing the gene-specific antisense oligodeoxynucleotide-mediated reduction method, we found the expression levels of alternatively spliced transcripts of CsLOX4-iso1, CsLOX4-iso2, and CsADH4-iso3 were lower, and the contents of cis-3-hexenol were correspondingly reduced in the leaves of tea plant; this result suggested that the AS play important roles in regulating biosynthesis of VFADs in C. sinensis. Our results provide new insights into the important contribution of AS events in regulating the VFAD biosynthesis in tea plant.
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Affiliation(s)
- Qingshan Xu
- College of Horticulture , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Long Cheng
- College of Horticulture , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Yu Mei
- State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei , Anhui , China
| | - Linli Huang
- College of Horticulture , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei , Anhui , China
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei , Anhui , China
| | - Youben Yu
- College of Horticulture , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization , Anhui Agricultural University , Hefei , Anhui , China
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Khokhar W, Hassan MA, Reddy ASN, Chaudhary S, Jabre I, Byrne LJ, Syed NH. Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:1160. [PMID: 31632417 PMCID: PMC6785726 DOI: 10.3389/fpls.2019.01160] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/26/2019] [Indexed: 05/27/2023]
Abstract
Alternative splicing (AS) of pre-mRNAs contributes to transcriptome diversity and enables plants to generate different protein isoforms from a single gene and/or fine-tune gene expression during different development stages and environmental changes. Although AS is pervasive, the genetic basis for differential isoform usage in plants is still emerging. In this study, we performed genome-wide analysis in 666 geographically distributed diverse ecotypes of Arabidopsis thaliana to identify genomic regions [splicing quantitative trait loci (sQTLs)] that may regulate differential AS. These ecotypes belong to different microclimatic conditions and are part of the relict and non-relict populations. Although sQTLs were spread across the genome, we observed enrichment for trans-sQTL (trans-sQTLs hotspots) on chromosome one. Furthermore, we identified several sQTL (911) that co-localized with trait-linked single nucleotide polymorphisms (SNP) identified in the Arabidopsis genome-wide association studies (AraGWAS). Many sQTLs were enriched among circadian clock, flowering, and stress-responsive genes, suggesting a role for differential isoform usage in regulating these important processes in diverse ecotypes of Arabidopsis. In conclusion, the current study provides a deep insight into SNPs affecting isoform ratios/genes and facilitates a better mechanistic understanding of trait-associated SNPs in GWAS studies. To the best of our knowledge, this is the first report of sQTL analysis in a large set of Arabidopsis ecotypes and can be used as a reference to perform sQTL analysis in the Brassicaceae family. Since whole genome and transcriptome datasets are available for these diverse ecotypes, it could serve as a powerful resource for the biological interpretation of trait-associated loci, splice isoform ratios, and their phenotypic consequences to help produce more resilient and high yield crop varieties.
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Affiliation(s)
- Waqas Khokhar
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Musa A. Hassan
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Edinburgh, United Kingdom
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Saurabh Chaudhary
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Ibtissam Jabre
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Lee J. Byrne
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Naeem H. Syed
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
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Li Y, Yang J, Shang X, Lv W, Xia C, Wang C, Feng J, Cao Y, He H, Li L, Ma L. SKIP regulates environmental fitness and floral transition by forming two distinct complexes in Arabidopsis. THE NEW PHYTOLOGIST 2019; 224:321-335. [PMID: 31209881 DOI: 10.1111/nph.15990] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/07/2019] [Indexed: 05/08/2023]
Abstract
Ski-interacting protein (SKIP) is a bifunctional regulator of gene expression that works as a splicing factor as part of the spliceosome and as a transcriptional activator by interacting with EARLY FLOWERING 7 (ELF7). MOS4-Associated Complex 3A (MAC3A) and MAC3B interact physically and genetically with SKIP, mediate the alternative splicing of c. 50% of the expressed genes in the Arabidopsis genome, and are required for the splicing of a similar set of genes to that of SKIP. SKIP interacts physically and genetically with splicing factors and Polymerase-Associated Factor 1 complex (Paf1c) components. However, these splicing factors do not interact either physically or genetically with Paf1c components. The SKIP-spliceosome complex mediates circadian clock function and abiotic stress responses by controlling the alternative splicing of pre-mRNAs encoded by clock- and stress tolerance-related genes. The SKIP-Paf1c complex regulates the floral transition by activating FLOWERING LOCUS C (FLC) transcription. Our data reveal that SKIP regulates floral transition and environmental fitness via its incorporation into two distinct complexes that regulate gene expression transcriptionally and post-transcriptionally, respectively. It will be interesting to discover in future studies whether SKIP is required for integration of environmental fitness and growth by control of the incorporation of SKIP into spliceosome or Paf1c in plants.
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Affiliation(s)
- Yan Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
| | - Jing Yang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
| | - Xudong Shang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
| | - Wenzhu Lv
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
| | - Congcong Xia
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
| | - Chen Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
| | - Jinlin Feng
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
| | - Ying Cao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
| | - Hang He
- College of Life Sciences, Peking University, Beijing, 100048, China
| | - Legong Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
| | - Ligeng Ma
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
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Gu J, Xia Z, Luo Y, Jiang X, Qian B, Xie H, Zhu JK, Xiong L, Zhu J, Wang ZY. Spliceosomal protein U1A is involved in alternative splicing and salt stress tolerance in Arabidopsis thaliana. Nucleic Acids Res 2019; 46:1777-1792. [PMID: 29228330 PMCID: PMC5829640 DOI: 10.1093/nar/gkx1229] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/30/2017] [Indexed: 12/14/2022] Open
Abstract
Soil salinity is a significant threat to sustainable agricultural production worldwide. Plants must adjust their developmental and physiological processes to cope with salt stress. Although the capacity for adaptation ultimately depends on the genome, the exceptional versatility in gene regulation provided by the spliceosome-mediated alternative splicing (AS) is essential in these adaptive processes. However, the functions of the spliceosome in plant stress responses are poorly understood. Here, we report the in-depth characterization of a U1 spliceosomal protein, AtU1A, in controlling AS of pre-mRNAs under salt stress and salt stress tolerance in Arabidopsis thaliana. The atu1a mutant was hypersensitive to salt stress and accumulated more reactive oxygen species (ROS) than the wild-type under salt stress. RNA-seq analysis revealed that AtU1A regulates AS of many genes, presumably through modulating recognition of 5′ splice sites. We showed that AtU1A is associated with the pre-mRNA of the ROS detoxification-related gene ACO1 and is necessary for the regulation of ACO1 AS. ACO1 is important for salt tolerance because ectopic expression of ACO1 in the atu1a mutant can partially rescue its salt hypersensitive phenotype. Our findings highlight the critical role of AtU1A as a regulator of pre-mRNA processing and salt tolerance in plants.
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Affiliation(s)
- Jinbao Gu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Zhiqiang Xia
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yuehua Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Xingyu Jiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Bilian Qian
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - He Xie
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Liming Xiong
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Jianhua Zhu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Zhen-Yu Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
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Albaqami M, Laluk K, Reddy ASN. The Arabidopsis splicing regulator SR45 confers salt tolerance in a splice isoform-dependent manner. PLANT MOLECULAR BIOLOGY 2019; 100:379-390. [PMID: 30968308 DOI: 10.1007/s11103-019-00864-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/28/2019] [Indexed: 05/08/2023]
Abstract
Functions of most splice isoforms that are generated by alternative splicing are unknown. We show that two splice variants that encode proteins differing in only eight amino acids have distinct functions in a stress response. Serine/arginine-rich (SR) and SR-like proteins, a conserved family of RNA binding proteins across eukaryotes, play important roles in pre-mRNA splicing and other post-transcriptional processes. Pre-mRNAs of SR and SR-like proteins undergo extensive alternative splicing in response to diverse stresses and produce multiple splice isoforms. However, the functions of most splice isoforms remain elusive. Alternative splicing of pre-mRNA of Arabidopsis SR45, which encodes an SR-like splicing regulator, generates two isoforms (long-SR45.1 and short-SR45.2). The proteins encoded by these two isoforms differ in eight amino acids. Here, we investigated the role of SR45 and its splice variants in salt stress tolerance. The loss of SR45 resulted in enhanced sensitivity to salt stress and changes in expression and splicing of genes involved in regulating salt stress response. Interestingly, only the long isoform (SR45.1) rescued the salt-sensitive phenotype as well as the altered gene expression and splicing patterns in the mutant. These results suggest that SR45 positively regulates salt tolerance. Furthermore, only the long isoform is required for SR45-mediated salt tolerance.
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Affiliation(s)
- Mohammed Albaqami
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Mecca, 21955, Kingdom of Saudi Arabia
| | - K Laluk
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
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Feng J, Huang S, Guo Y, Liu D, Song J, Gao J, Li H, Chen L. Plant ISOform sequencing database (PISO): a comprehensive repertory of full-length transcripts in plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1001-1003. [PMID: 30633419 PMCID: PMC6523585 DOI: 10.1111/pbi.13076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Jia‐Wu Feng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Shanshan Huang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yi‐Xiong Guo
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Dongxu Liu
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jia‐Ming Song
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Junxiang Gao
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Huan Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Ling‐Ling Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
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79
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Chen MX, Wijethunge BDIK, Zhou SM, Yang JF, Dai L, Wang SS, Chen C, Fu LJ, Zhang J, Hao GF, Yang GF. Chemical Modulation of Alternative Splicing for Molecular-Target Identification by Potential Genetic Control in Agrochemical Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5072-5084. [PMID: 30986354 DOI: 10.1021/acs.jafc.9b02086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Alternative splicing (AS), the process of removing introns from pre-mRNA and the rearrangement of exons to produce several types of mature transcripts, is a remarkable step preceding protein synthesis. In particular, it has now been conclusively shown that up to ∼95% of genes are alternatively spliced to generate a complex and diverse proteome in eukaryotic organisms. Consequently, AS is one of the determinants of the functional repertoire of cells. Many studies have revealed that AS in plants can be regulated by cell type, developmental stage, environmental stress, and the circadian clock. Moreover, increasing amounts of evidence reveal that chemical compounds can affect various steps during splicing to induce major effects on plant physiology. Hence, the chemical modulation of AS can serve as a good strategy for molecular-target identification in attempts to potentially control plant genetics. However, the kind of mechanisms involved in the chemical modulation of AS that can be used in agrochemical research remain largely unknown. This review introduces recent studies describing the specific roles AS plays in plant adaptation to environmental stressors and in the regulation of development. We also discuss recent advances in small molecules that induce alterations of AS and the possibility of using this strategy in agrochemical-target identification, giving a new direction for potential genetic control in agrochemical research.
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Affiliation(s)
- Mo-Xian Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education; Research and Development Center for Fine Chemicals , Guizhou University , Guiyang 550025 , PR China
- Division of Gastroenterology , Shenzhen Children's Hospital , Shenzhen 518038 , PR China
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology , Chinese Academy of Sciences , Shenzhen 518055 , PR China
- School of Life Sciences and Shenzhen Research Institute , The Chinese University of Hong Kong , Shenzhen 518063 , PR China
| | - Boyagane D I K Wijethunge
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , PR China
| | - Shao-Ming Zhou
- Division of Gastroenterology , Shenzhen Children's Hospital , Shenzhen 518038 , PR China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , PR China
| | - Lei Dai
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology , Chinese Academy of Sciences , Shenzhen 518055 , PR China
| | - Shan-Shan Wang
- School of Life Sciences and Shenzhen Research Institute , The Chinese University of Hong Kong , Shenzhen 518063 , PR China
| | - Chen Chen
- Department of Infectious Disease, Nanjing Second Hospital , Nanjing University of Chinese Medicine , Nanjing 210003 , PR China
| | - Li-Jun Fu
- Fujian Provincial Key Laboratory of Ecology-Toxicological Effects & Control for Emerging Contaminants , Putian University , Putian , Fujian 351100 , PR China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University and State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong , PR China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education; Research and Development Center for Fine Chemicals , Guizhou University , Guiyang 550025 , PR China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , PR China
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80
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Carbonell C, Ulsamer A, Vivori C, Papasaikas P, Böttcher R, Joaquin M, Miñana B, Tejedor JR, de Nadal E, Valcárcel J, Posas F. Functional Network Analysis Reveals the Relevance of SKIIP in the Regulation of Alternative Splicing by p38 SAPK. Cell Rep 2019; 27:847-859.e6. [PMID: 30995481 PMCID: PMC6484779 DOI: 10.1016/j.celrep.2019.03.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023] Open
Abstract
Alternative splicing is a prevalent mechanism of gene regulation that is modulated in response to a wide range of extracellular stimuli. Stress-activated protein kinases (SAPKs) play a key role in controlling several steps of mRNA biogenesis. Here, we show that osmostress has an impact on the regulation of alternative splicing (AS), which is partly mediated through the action of p38 SAPK. Splicing network analysis revealed a functional connection between p38 and the spliceosome component SKIIP, whose depletion abolished a significant fraction of p38-mediated AS changes. Importantly, p38 interacted with and directly phosphorylated SKIIP, thereby altering its activity. SKIIP phosphorylation regulated AS of GADD45α, the upstream activator of the p38 pathway, uncovering a negative feedback loop involving AS regulation. Our data reveal mechanisms and targets of SAPK function in stress adaptation through the regulation of AS.
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Affiliation(s)
- Caterina Carbonell
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Arnau Ulsamer
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Claudia Vivori
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Panagiotis Papasaikas
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - René Böttcher
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Manel Joaquin
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Belén Miñana
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juan Ramón Tejedor
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain.
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
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Wang Z, Zhang H, Gong W. Genome-wide identification and comparative analysis of alternative splicing across four legume species. PLANTA 2019; 249:1133-1142. [PMID: 30603789 DOI: 10.1007/s00425-018-03073-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/18/2018] [Indexed: 05/07/2023]
Abstract
MAIN CONCLUSION Alternative splicing EVENTS were genome-wide identified for four legume species, and nitrogen fixation-related gene families and evolutionary analysis was also performed. Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. Investigation of the genome-wide conserved AS events across different species will help with the understanding of the evolution of the functional diversity in legumes, allowing for genetic improvement. Genome-wide identification and characterization of AS were performed using the publically available mRNA, EST, and RNA-Seq data for four important legume species. A total of 15,165 AS genes in Glycine max, 6077 in Cicer arietinum, 7240 in Medicago truncatula, and 7358 in Lotus japonicus were identified. Intron retention (IntronR) was the dominant AS type among the identified events, with IntronR occurring from 53.76% in M. truncatula to 43.91% in C. arietinum. We identified 1159 AS genes that were conserved among four species. Furthermore, nine nitrogen fixation-related gene families with 237 genes were identified, and 80 of them were AS, accounting for the 43.48% in G. max and 27.78% in C. arietinum. An evolutionary analysis showed that these AS genes tended to be located adjacent to each other in the evolutionary tree and are unbalanced in the distribution in the sub-family. This study provides a foundation for future studies on transcription complexity, evolution, and the role of AS on plant functional regulation.
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Affiliation(s)
- Zan Wang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China.
| | - Han Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Wenlong Gong
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
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82
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Li Z, Shen J, Liang J. Genome-Wide Identification, Expression Profile, and Alternative Splicing Analysis of the Brassinosteroid-Signaling Kinase (BSK) Family Genes in Arabidopsis. Int J Mol Sci 2019; 20:ijms20051138. [PMID: 30845672 PMCID: PMC6429265 DOI: 10.3390/ijms20051138] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/01/2019] [Accepted: 03/02/2019] [Indexed: 01/05/2023] Open
Abstract
Brassinosteroids (BRs) are steroid hormones essential for different biological processes, ranging from growth to environmental adaptation in plants. The plant brassinosteroid-signaling kinase (BSK) proteins belong to a family of receptor-like cytoplasmic kinases, which have been reported to play an important role in BR signal transduction. However, the knowledge of BSK genes in plants is still quite limited. In the present study, a total of 143 BSK proteins were identified by a genome-wide search in 17 plant species. A phylogenetic analysis showed that the BSK gene originated in embryophytes, with no BSK found in green algae, and these BSK genes were divided into six groups by comparison with orthologs/paralogs. A further study using comparative analyses of gene structure, expression patterns and alternative splicing of BSK genes in Arabidopsis revealed that all BSK proteins shared similar protein structure with some exception and post-translation modifications including sumolyation and ubiquitination. An expression profile analysis showed that most Arabidopsis BSK genes were constitutively expressed in different tissues; of these, several BSK genes were significantly expressed in response to some hormones or abiotic stresses. Furthermore, reverse transcription-polymerase chain reaction (RT-PCR) assays showed that BSK5, BSK7, and BSK9 underwent alternative splicing in specific stress induced and tissue-dependent patterns. Collectively, these results lay the foundation for further functional analyses of these genes in plants.
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Affiliation(s)
- Zhiyong Li
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China.
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China.
| | - Jinyu Shen
- Co-Innovation Center for Modern Production Technology of Grain Crop, Yangzhou University, Yangzhou 225000, China.
| | - Jiansheng Liang
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China.
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83
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Chen MX, Zhu FY, Wang FZ, Ye NH, Gao B, Chen X, Zhao SS, Fan T, Cao YY, Liu TY, Su ZZ, Xie LJ, Hu QJ, Wu HJ, Xiao S, Zhang J, Liu YG. Alternative splicing and translation play important roles in hypoxic germination in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:817-833. [PMID: 30535157 PMCID: PMC6363088 DOI: 10.1093/jxb/ery393] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/27/2018] [Indexed: 05/04/2023]
Abstract
Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ~1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum protein processing and export, proteasome, phagosome, oxidative phosphorylation, and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI.
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Affiliation(s)
- Mo-Xian Chen
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Feng-Zhu Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Neng-Hui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, China
| | - Bei Gao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xi Chen
- SpecAlly Life Technology Co., Ltd, Wuhan, China
| | - Shan-Shan Zhao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Fan
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Yun-Ying Cao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- College of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Tie-Yuan Liu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ze-Zhuo Su
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Li-Juan Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi-Juan Hu
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hui-Jie Wu
- College of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianhua Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Correspondence: or
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- Correspondence: or
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84
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Yu X, Meng X, Liu Y, Wang X, Wang TJ, Zhang A, Li N, Qi X, Liu B, Xu ZY. The chromatin remodeler ZmCHB101 impacts alternative splicing contexts in response to osmotic stress. PLANT CELL REPORTS 2019; 38:131-145. [PMID: 30443733 DOI: 10.1007/s00299-018-2354-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 11/07/2018] [Indexed: 05/16/2023]
Abstract
Maize SWI3-type chromatin remodeler impacts alternative splicing contexts in response to osmotic stress by altering nucleosome density and affecting transcriptional elongation rate. Alternative splicing (AS) is commonly found in higher eukaryotes and is an important posttranscriptional regulatory mechanism to generate transcript diversity. AS has been widely accepted as playing essential roles in different biological processes including growth, development, signal transduction and responses to biotic and abiotic stresses in plants. However, whether and how chromatin remodeling complex functions in AS in plant under osmotic stress remains unknown. Here, we show that a maize SWI3D protein, ZmCHB101, impacts AS contexts in response to osmotic stress. Genome-wide analysis of mRNA contexts in response to osmotic stress using ZmCHB101-RNAi lines reveals that ZmCHB101 impacts alternative splicing contexts of a subset of osmotic stress-responsive genes. Intriguingly, ZmCHB101-mediated regulation of gene expression and AS is largely uncoupled, pointing to diverse molecular functions of ZmCHB101 in transcriptional and posttranscriptional regulation. We further found ZmCHB101 impacts the alternative splicing contexts by influencing alteration of chromatin and histone modification status as well as transcriptional elongation rates mediated by RNA polymerase II. Taken together, our findings suggest a novel insight of how plant chromatin remodeling complex impacts AS under osmotic stress .
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Affiliation(s)
- Xiaoming Yu
- School of Agronomy, Jilin Agricultural Science and Technology University, Jilin, 132301, People's Republic of China
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
- Department of Agronomy, Purdue University, West Lafayette, USA
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Xin Qi
- Department of Agronomy, Jilin Agricultural University, Changchun, 130118, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China.
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China.
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85
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Cao Y, Ma L. To Splice or to Transcribe: SKIP-Mediated Environmental Fitness and Development in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1222. [PMID: 31632433 PMCID: PMC6785753 DOI: 10.3389/fpls.2019.01222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/04/2019] [Indexed: 05/04/2023]
Abstract
Gene expression in eukaryotes is controlled at multiple levels, including transcriptional and post-transcriptional levels. The transcriptional regulation of gene expression is complex and includes the regulation of the initiation and elongation phases of transcription. Meanwhile, the post-transcriptional regulation of gene expression includes precursor messenger RNA (pre-mRNA) splicing, 5' capping, and 3' polyadenylation. Among these events, pre-mRNA splicing, conducted by the spliceosome, plays a key role in the regulation of gene expression, and the efficiency and precision of pre-mRNA splicing are critical for gene function. Ski-interacting protein (SKIP) is an evolutionarily conserved protein from yeast to humans. In plants, SKIP is a bifunctional regulator that works as a splicing factor as part of the spliceosome and as a transcriptional regulator via interactions with the transcriptional regulatory complex. Here, we review how the functions of SKIP as a splicing factor and a transcriptional regulator affect environmental fitness and development in plants.
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86
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Catalá R, Carrasco-López C, Perea-Resa C, Hernández-Verdeja T, Salinas J. Emerging Roles of LSM Complexes in Posttranscriptional Regulation of Plant Response to Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:167. [PMID: 30873189 PMCID: PMC6401655 DOI: 10.3389/fpls.2019.00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/31/2019] [Indexed: 05/04/2023]
Abstract
It has long been assumed that the wide reprogramming of gene expression that modulates plant response to unfavorable environmental conditions is mainly controlled at the transcriptional level. A growing body of evidence, however, indicates that posttranscriptional regulatory mechanisms also play a relevant role in this control. Thus, the LSMs, a family of proteins involved in mRNA metabolism highly conserved in eukaryotes, have emerged as prominent regulators of plant tolerance to abiotic stress. Arabidopsis contains two main LSM ring-shaped heteroheptameric complexes, LSM1-7 and LSM2-8, with different subcellular localization and function. The LSM1-7 ring is part of the cytoplasmic decapping complex that regulates mRNA stability. On the other hand, the LSM2-8 complex accumulates in the nucleus to ensure appropriate levels of U6 snRNA and, therefore, correct pre-mRNA splicing. Recent studies reported unexpected results that led to a fundamental change in the assumed consideration that LSM complexes are mere components of the mRNA decapping and splicing cellular machineries. Indeed, these data have demonstrated that LSM1-7 and LSM2-8 rings operate in Arabidopsis by selecting specific RNA targets, depending on the environmental conditions. This specificity allows them to actively imposing particular gene expression patterns that fine-tune plant responses to abiotic stresses. In this review, we will summarize current and past knowledge on the role of LSM rings in modulating plant physiology, with special focus on their function in abiotic stress responses.
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87
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Zhu J, Wang X, Xu Q, Zhao S, Tai Y, Wei C. Global dissection of alternative splicing uncovers transcriptional diversity in tissues and associates with the flavonoid pathway in tea plant (Camellia sinensis). BMC PLANT BIOLOGY 2018; 18:266. [PMID: 30400863 PMCID: PMC6219262 DOI: 10.1186/s12870-018-1497-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/25/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Alternative splicing (AS) regulates mRNA at the post-transcriptional level to change gene function in organisms. However, little is known about the AS and its roles in tea plant (Camellia sinensis), widely cultivated for making a popular beverage tea. RESULTS In our study, the AS landscape and dynamics were characterized in eight tissues (bud, young leaf, summer mature leaf, winter old leaf, stem, root, flower, fruit) of tea plant by Illumina RNA-Seq and confirmed by Iso-Seq. The most abundant AS (~ 20%) was intron retention and involved in RNA processes. The some alternative splicings were found to be tissue specific in stem and root etc. Thirteen co-expressed modules of AS transcripts were identified, which revealed a similar pattern between the bud and young leaves as well as a distinct pattern between seasons. AS events of structural genes including anthocyanidin reductase and MYB transcription factors were involved in biosynthesis of flavonoid, especially in vegetative tissues. The AS isoforms rather than the full-length ones were the major transcripts involved in flavonoid synthesis pathway, and is positively correlated with the catechins content conferring the tea taste. We propose that the AS is an important functional mechanism in regulating flavonoid metabolites. CONCLUSION Our study provides the insight into the AS events underlying tea plant's uniquely different developmental process and highlights the important contribution and efficacy of alternative splicing regulatory function to biosynthesis of flavonoids.
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Affiliation(s)
- Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Xuewen Wang
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
- Department of Genetics, University of Georgia, 120 E Green Street, Athens, GA 30602 USA
| | - Qingshan Xu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Shiqi Zhao
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Yuling Tai
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
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88
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Zhu J, Wang X, Guo L, Xu Q, Zhao S, Li F, Yan X, Liu S, Wei C. Characterization and Alternative Splicing Profiles of the Lipoxygenase Gene Family in Tea Plant (Camellia sinensis). PLANT & CELL PHYSIOLOGY 2018; 59:1765-1781. [PMID: 29726968 PMCID: PMC6135896 DOI: 10.1093/pcp/pcy091] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/28/2018] [Indexed: 05/22/2023]
Abstract
Oxylipins, including jasmonic acid (JA) and volatiles, are important for signaling in plants, and these are formed by the lipoxygenase (LOX) enzyme family. There is a large gap in understanding of the underlying molecular basis of their roles in tea plants. Here, we identified 11 CsLOX genes from the tea plant (Camellia sinensis), and characterized their phylogeny, gene structure and protein features into three subclasses. We then examined their enzymatic activities, LOX expression and alternative splicing of transcripts during development and in response to abiotic or biotic stresses in tea plants. In vitro expressed protein assays showed that the CsLOX2, 3 and 9 enzymatically function to produce 9/13-HPOT, 13-HPOT and 9-HPOT, respectively. CsLOX2 and CsLOX9 green fluorescent protein (GFP) fusion proteins localized to chloroplasts and the cytoplasm, respectively. RNA sequencing, quantitative reverse transcription-PCR and Northern blot analysis suggested that CsLOX5, 6 and 9 were predominantly expressed in seeds, flowers and roots, respectively. CsLOX2, 3, 4, 6 and 7 were up-regulated after attack by the insect Ectropis oblique, while CsLOX1 was induced after infection with the pathogen Glomerella cingulata. CsLOX3, 7 and 10 were up-regulated by JA but not ABA or salicylic acid. Long-term cold stress down-regulated CsLOX expression while a short duration of cold induced the expression of CsLOX1, 6 and 7. Alternatively spliced transcripts of six CsLOX genes were dynamically regulated through time and varied in relative abundances under the investigated stresses; we propose a mechanism of competing or compensating regulation between isoforms. This study improves our understanding of evolution of LOXs and regulation of their diverse functions in plants.
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Affiliation(s)
- Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, PR China
| | - Xuewen Wang
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, PR China
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Lingxiao Guo
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, PR China
| | - Qingshan Xu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, PR China
| | - Shiqi Zhao
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, PR China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, PR China
| | - Xiaomei Yan
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, PR China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, PR China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, PR China
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Ashwini N, Sajeevan RS, Udayakumar M, Nataraja KN. Identification of splice variant of OsGBF1 in Oryza sativa ssp. indica genotypes under salinity stress. 3 Biotech 2018; 8:345. [PMID: 30073130 DOI: 10.1007/s13205-018-1370-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 07/24/2018] [Indexed: 11/25/2022] Open
Abstract
G-box-binding factors are plant transcription factors, involved in a wide range of biological processes including abiotic stress responses. In this study, we analyzed the expression of OsGBF1 during salt stress in two contrasting Oryza sativa spp. indica genotypes, Rasi and Tellahamsa. Two-day-old seedlings were exposed to NaCl stress under two different conditions. One set was exposed to 100 mM NaCl before transferring to 250 mM (induction stress), while another set was transferred directly to 250 mM (shock stress). During early induction stress, OsGBF1 was up-regulated in Rasi when compared to Tellahamsa. We cloned full-length OsGBF1 from these two genotypes, and analyzed the sequences. Our analysis indicated the presence of transcript variants, which are designated as OsGBF1a and 1b. OsGBF1b variant retained introns, which lead to the generation of premature termination codon. OsGBF1b transcript levels were not significantly different at 12-h of induction stress in Tellahamsa and Rasi. At 24-h of shock stress, OsGBF1b was up-regulated in both genotypes and the transcript was more in Rasi. Since, OsGBF1a and 1b are predicted to be splice variants, we examined expression pattern of OsSKIP, a splicing factor and component of the spliceosome. In induction stress, OsSKIP was up-regulated at 12- and 24-h in Rasi when compared to Tellahamsa. On the contrary, at 24-h shock stress, OsSKIP was down-regulated in Rasi when compared to Tellahamsa. It is possible that OsSKIP expression was increased in Rasi during induction stress for accurate splicing that could aid in tolerance. This is the first report on OsGBF1 splice variant and the variant could have specific functions linked to stress tolerance in rice.
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Affiliation(s)
- Narasimha Ashwini
- 1Department of Crop Physiology, University of Agricultural Sciences (UAS), GKVK, Bangalore, Karnataka 560 065 India
| | - Radha Sivarajan Sajeevan
- 1Department of Crop Physiology, University of Agricultural Sciences (UAS), GKVK, Bangalore, Karnataka 560 065 India
- 2Present Address: National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore, 560 065 India
| | - Makarala Udayakumar
- 1Department of Crop Physiology, University of Agricultural Sciences (UAS), GKVK, Bangalore, Karnataka 560 065 India
| | - Karaba N Nataraja
- 1Department of Crop Physiology, University of Agricultural Sciences (UAS), GKVK, Bangalore, Karnataka 560 065 India
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90
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The DNA Methylome and Association of Differentially Methylated Regions with Differential Gene Expression during Heat Stress in Brassica rapa. Int J Mol Sci 2018; 19:ijms19051414. [PMID: 29747401 PMCID: PMC5983725 DOI: 10.3390/ijms19051414] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/16/2018] [Accepted: 04/29/2018] [Indexed: 01/04/2023] Open
Abstract
Cytosine DNA methylation is a critical epigenetic mechanism in the silencing of transposable elements, imprinting and regulating gene expression. However, little is known about the potential role of mC in response to heat stress. To determine and explore the functions of the dynamic DNA methylome during heat stress, we characterized single-base resolution methylome maps of Brassica rapa and assessed the dynamic changes of mC under heat stress using whole genome bisulfite sequencing. On average, the DNA methylation levels of CG, CHG and CHH are 39.3%, 15.38% and 5.24% in non-heading Chinese cabbage (NHCC), respectively. We found that the patterns of methylation are similar to other eudicot plants, but with higher CHH methylation levels. Further comparative analysis revealed varying patterns for three sequence contexts (mCG, mCHG and mCHH) under heat stress indicating context- and position-dependent methylation regulation. DNA methylation near the TSS and TES may be closely associated with methylation-dependent transcriptional silencing. Association analysis of differential methylation and differential gene expression revealed a different set of methDEGs involved at early and late stages under heat stress. The systemic characterization of the dynamic DNA methylome during heat stress will improve our understanding of the mechanism of epigenetic regulation under heat stress.
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91
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Laloum T, Martín G, Duque P. Alternative Splicing Control of Abiotic Stress Responses. TRENDS IN PLANT SCIENCE 2018; 23:140-150. [PMID: 29074233 DOI: 10.1016/j.tplants.2017.09.019] [Citation(s) in RCA: 281] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 05/20/2023]
Abstract
Alternative splicing, which generates multiple transcripts from the same gene, is an important modulator of gene expression that can increase proteome diversity and regulate mRNA levels. In plants, this post-transcriptional mechanism is markedly induced in response to environmental stress, and recent studies have identified alternative splicing events that allow rapid adjustment of the abundance and function of key stress-response components. In agreement, plant mutants defective in splicing factors are severely impaired in their response to abiotic stress. Notably, mounting evidence indicates that alternative splicing regulates stress responses largely by targeting the abscisic acid (ABA) pathway. We review here current understanding of post-transcriptional control of plant stress tolerance via alternative splicing and discuss research challenges for the near future.
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Affiliation(s)
- Tom Laloum
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Guiomar Martín
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Paula Duque
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal.
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92
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Zhu G, Li W, Zhang F, Guo W. RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii. BMC Genomics 2018; 19:73. [PMID: 29361913 PMCID: PMC5782385 DOI: 10.1186/s12864-018-4449-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/14/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Numerous studies have focused on the regulation of gene expression in response to salt stress at the transcriptional level; however, little is known about this process at the post-transcriptional level. RESULTS Using a diploid D genome wild salinity-tolerant cotton species, Gossypium davidsonii, we analyzed alternative splicing (AS) of genes related to salt stress by comparing high-throughput transcriptomes from salt-treated and well-watered roots and leaves. A total of 14,172 AS events were identified involving 6798 genes, of which intron retention (35.73%) was the most frequent, being detected in 3492 genes. Under salt stress, 1287 and 1228 differential alternative splicing (DAS) events were identified in roots and leaves, respectively. These DAS genes were associated with specific functional pathways, such as "responses to stress", "metabolic process" and "RNA splicing", implying that AS represents an important pathway of gene regulation in response to salt stress. Several salt response genes, such as pyrroline-5-carboxylate synthase (P5CS), K+ channel outward (KCO1), plasma membrane intrinsic protein (PIP) and WRKY33 which were involved in osmotic balance, ion homeostasis, water transportation and transcriptional regulation, respectively, were identified with differential alternative splicing under salt stress. Moreover, we revealed that 13 genes encoding Ser/Arg-rich (SR) proteins related to AS regulation were differentially alternatively spliced under salt stress. CONCLUSION This study first provide a comprehensive view of AS in G. davidsonii, and highlight novel insights into the potential roles of AS in plant responses to salt stress.
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Affiliation(s)
- Guozhong Zhu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weixi Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.
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93
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Carrasco-López C, Hernández-Verdeja T, Perea-Resa C, Abia D, Catalá R, Salinas J. Environment-dependent regulation of spliceosome activity by the LSM2-8 complex in Arabidopsis. Nucleic Acids Res 2017; 45:7416-7431. [PMID: 28482101 PMCID: PMC5499552 DOI: 10.1093/nar/gkx375] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 04/25/2017] [Indexed: 11/20/2022] Open
Abstract
Spliceosome activity is tightly regulated to ensure adequate splicing in response to internal and external cues. It has been suggested that core components of the spliceosome, such as the snRNPs, would participate in the control of its activity. The experimental indications supporting this proposition, however, remain scarce, and the operating mechanisms poorly understood. Here, we present genetic and molecular evidence demonstrating that the LSM2–8 complex, the protein moiety of the U6 snRNP, regulates the spliceosome activity in Arabidopsis, and that this regulation is controlled by the environmental conditions. Our results show that the complex ensures the efficiency and accuracy of constitutive and alternative splicing of selected pre-mRNAs, depending on the conditions. Moreover, miss-splicing of most targeted pre-mRNAs leads to the generation of nonsense mediated decay signatures, indicating that the LSM2–8 complex also guarantees adequate levels of the corresponding functional transcripts. Interestingly, the selective role of the complex has relevant physiological implications since it is required for adequate plant adaptation to abiotic stresses. These findings unveil an unanticipated function for the LSM2–8 complex that represents a new layer of posttranscriptional regulation in response to external stimuli in eukaryotes.
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Affiliation(s)
- Cristian Carrasco-López
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Tamara Hernández-Verdeja
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Carlos Perea-Resa
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - David Abia
- Unidad de Bioinformática, Centro de Biología Molecular Severo Ochoa, CSIC, 28049 Madrid, Spain
| | - Rafael Catalá
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Julio Salinas
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
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94
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De Diego N, Fürst T, Humplík JF, Ugena L, Podlešáková K, Spíchal L. An Automated Method for High-Throughput Screening of Arabidopsis Rosette Growth in Multi-Well Plates and Its Validation in Stress Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:1702. [PMID: 29046681 PMCID: PMC5632805 DOI: 10.3389/fpls.2017.01702] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/19/2017] [Indexed: 05/02/2023]
Abstract
High-throughput plant phenotyping platforms provide new possibilities for automated, fast scoring of several plant growth and development traits, followed over time using non-invasive sensors. Using Arabidopsis as a model offers important advantages for high-throughput screening with the opportunity to extrapolate the results obtained to other crops of commercial interest. In this study we describe the development of a highly reproducible high-throughput Arabidopsis in vitro bioassay established using our OloPhen platform, suitable for analysis of rosette growth in multi-well plates. This method was successfully validated on example of multivariate analysis of Arabidopsis rosette growth in different salt concentrations and the interaction with varying nutritional composition of the growth medium. Several traits such as changes in the rosette area, relative growth rate, survival rate and homogeneity of the population are scored using fully automated RGB imaging and subsequent image analysis. The assay can be used for fast screening of the biological activity of chemical libraries, phenotypes of transgenic or recombinant inbred lines, or to search for potential quantitative trait loci. It is especially valuable for selecting genotypes or growth conditions that improve plant stress tolerance.
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Affiliation(s)
- Nuria De Diego
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Tomáš Fürst
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan F. Humplík
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czechia
| | - Lydia Ugena
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Kateřina Podlešáková
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Lukáš Spíchal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
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95
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Ranwez V, Serra A, Pot D, Chantret N. Domestication reduces alternative splicing expression variations in sorghum. PLoS One 2017; 12:e0183454. [PMID: 28886042 PMCID: PMC5590825 DOI: 10.1371/journal.pone.0183454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/06/2017] [Indexed: 01/09/2023] Open
Abstract
Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession. Noticeably, for a given gene, one isoform can either be overexpressed or underexpressed in some wild accessions, whereas in the cultivated accessions, the balance between the two isoforms of the same gene appears to be much more homogenous. Indeed, we observe in sorghum significantly more variation in isoform expression balance among wild accessions than among domesticated accessions. The possibility exists that the loss of nucleotide diversity due to domestication could affect regulatory elements, controlling transcription or degradation of these isoforms. Impact on the isoform expression balance is discussed. As far as we know, this is the first time that the impact of domestication on transcript isoform balance has been studied at the genomic scale. This could pave the way towards the identification of key domestication genes with finely tuned isoform expressions in domesticated accessions while being highly variable in their wild relatives.
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Affiliation(s)
| | - Audrey Serra
- Montpellier SupAgro, UMR AGAP, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
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96
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Evolutionarily Conserved Alternative Splicing Across Monocots. Genetics 2017; 207:465-480. [PMID: 28839042 DOI: 10.1534/genetics.117.300189] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splice-factor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.
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97
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Zhu FY, Chen MX, Ye NH, Shi L, Ma KL, Yang JF, Cao YY, Zhang Y, Yoshida T, Fernie AR, Fan GY, Wen B, Zhou R, Liu TY, Fan T, Gao B, Zhang D, Hao GF, Xiao S, Liu YG, Zhang J. Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:518-533. [PMID: 28407323 DOI: 10.1111/tpj.13571] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 05/19/2023]
Abstract
In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.
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Affiliation(s)
- Fu-Yuan Zhu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Mo-Xian Chen
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Neng-Hui Ye
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128, China
| | - Lu Shi
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Jing-Fang Yang
- College of Chemistry, Central China Normal University, Wuhan, China
| | - Yun-Ying Cao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- College of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Takuya Yoshida
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Bo Wen
- BGI-Shenzhen, Shenzhen, China
| | | | - Tie-Yuan Liu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tao Fan
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Bei Gao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Di Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ge-Fei Hao
- College of Chemistry, Central China Normal University, Wuhan, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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98
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Han N, Ji XL, Du YP, He X, Zhao XJ, Zhai H. Identification of a Novel Alternative Splicing Variant of VvPMA1 in Grape Root under Salinity. FRONTIERS IN PLANT SCIENCE 2017; 8:605. [PMID: 28484478 PMCID: PMC5399082 DOI: 10.3389/fpls.2017.00605] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
It has been well-demonstrated that the control of plasma membrane H+-ATPase (PM H+-ATPase) activity is important to plant salt tolerance. This study found a significant increase in PM H+-ATPase (PMA) activity in grape root exposed to NaCl. Furthermore, 7 Vitis vinifera PM H+-ATPase genes (VvPMAs) were identified within the grape genome and the expression response of these VvPMAs in grape root under salinity was analyzed. Two VvPMAs (VvPMA1 and VvPMA3) were expressed more strongly in roots than the other five VvPMAs. Moreover, roots exhibited diverse patterns of gene expression of VvPMA1 and VvPMA3 responses to salt stress. Interestingly, two transcripts of VvPMA1, which were created through alternative splicing (AS), were discovered and isolated from salt stressed root. Comparing the two VvPMA1 cDNA sequences (designated VvPMA1α and VvPMA1β) with the genomic sequence revealed that the second intron was retained in the VvPMA1β cDNA. This intron retention was predicted to generate a novel VvPMA1 through N-terminal truncation because of a 5'- terminal frame shift. Yeast complementation assays of the two splice variants showed that VvPMA1β could enhance the ability to complement Saccharomyces cerevisiae deficient in PM H+-ATPase activity. In addition, the expression profiles of VvPMA1α and VvPMA1β differed under salinity. Our data suggests that through AS, the N-terminal length of VvPMA1 may be regulated to accurately modulate PM H+-ATPase activity of grape root in salt stress.
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Affiliation(s)
- Ning Han
- Department of Pomology, College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
- Shandong Provincial Key Laboratory of Microbial Engineering, School of Biologic Engineering, Qi Lu University of TechnologyJinan, China
| | - Xing-Long Ji
- Department of Pomology, College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
| | - Yuan-Peng Du
- Department of Pomology, College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
| | - Xi He
- Shandong Provincial Key Laboratory of Microbial Engineering, School of Biologic Engineering, Qi Lu University of TechnologyJinan, China
| | - Xin-Jie Zhao
- Shandong Provincial Key Laboratory of Microbial Engineering, School of Biologic Engineering, Qi Lu University of TechnologyJinan, China
| | - Heng Zhai
- Department of Pomology, College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
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99
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Alternative Splicing in Plant Genes: A Means of Regulating the Environmental Fitness of Plants. Int J Mol Sci 2017; 18:ijms18020432. [PMID: 28230724 PMCID: PMC5343966 DOI: 10.3390/ijms18020432] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 02/04/2017] [Accepted: 02/10/2017] [Indexed: 01/01/2023] Open
Abstract
Gene expression can be regulated through transcriptional and post-transcriptional mechanisms. Transcription in eukaryotes produces pre-mRNA molecules, which are processed and spliced post-transcriptionally to create translatable mRNAs. More than one mRNA may be produced from a single pre-mRNA by alternative splicing (AS); thus, AS serves to diversify an organism’s transcriptome and proteome. Previous studies of gene expression in plants have focused on the role of transcriptional regulation in response to environmental changes. However, recent data suggest that post-transcriptional regulation, especially AS, is necessary for plants to adapt to a changing environment. In this review, we summarize recent advances in our understanding of AS during plant development in response to environmental changes. We suggest that alternative gene splicing is a novel means of regulating the environmental fitness of plants.
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100
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Deng X, Cao X. Roles of pre-mRNA splicing and polyadenylation in plant development. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:45-53. [PMID: 27866125 DOI: 10.1016/j.pbi.2016.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 05/20/2023]
Abstract
Plants possess amazing plasticity of growth and development, allowing them to adjust continuously and rapidly to changes in the environment. Over the past two decades, numerous molecular studies have illuminated the role of transcriptional regulation in plant development and environmental responses. However, emerging studies in Arabidopsis have uncovered an unexpectedly widespread role for post-transcriptional regulation in development and responses to environmental changes. In this review, we summarize recent discoveries detailing the contribution of two post-transcriptional mechanisms, pre-mRNA splicing and polyadenylation, to the regulation of plant development, with an emphasis on the control of flowering time. We also discuss future directions in the field and new technological approaches.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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