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Pastor-Cantizano N, Angelos ER, Ruberti C, Jiang T, Weng X, Reagan BC, Haque T, Juenger TE, Brandizzi F. Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis. Nat Commun 2024; 15:5804. [PMID: 38987268 PMCID: PMC11237027 DOI: 10.1038/s41467-024-50105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/29/2024] [Indexed: 07/12/2024] Open
Abstract
Environmental and physiological situations can challenge the balance between protein synthesis and folding capacity of the endoplasmic reticulum (ER) and cause ER stress, a potentially lethal condition. The unfolded protein response (UPR) restores ER homeostasis or actuates programmed cell death (PCD) when ER stress is unresolved. The cell fate determination mechanisms of the UPR are not well understood, especially in plants. Here, we integrate genetics and ER stress profiling with natural variation and quantitative trait locus analysis of 350 natural accessions of the model species Arabidopsis thaliana. Our analyses implicate a single nucleotide polymorphism to the loss of function of the general PCD regulator BON-ASSOCIATED PROTEIN2 (BAP2) in UPR outcomes. We establish that ER stress-induced BAP2 expression is antagonistically regulated by the UPR master regulator, inositol-requiring enzyme 1 (IRE1), and that BAP2 controls adaptive UPR amplitude in ER stress and ignites pro-death mechanisms in conditions of UPR insufficiency.
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Affiliation(s)
- Noelia Pastor-Cantizano
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Burjassot, Spain
| | - Evan R Angelos
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Botany & Plant Sciences Department, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Cristina Ruberti
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Department of Biosciences, University of Milan, Milano, Italy
| | - Tao Jiang
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Mid-Florida Research and Education Center, University of Florida, Apopka, FL, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Brandon C Reagan
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
| | - Taslima Haque
- Department of Integrative Biology, University of Texas, Austin, TX, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Plant Biology Department, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
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Shu L, Li L, Jiang YQ, Yan J. Advances in membrane-tethered NAC transcription factors in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112034. [PMID: 38365003 DOI: 10.1016/j.plantsci.2024.112034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/08/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
Transcription factors are central components in cell signal transduction networks and are critical regulators for gene expression. It is estimated that approximately 10% of all transcription factors are membrane-tethered. MTFs (membrane-bound transcription factors) are latent transcription factors that are inherently anchored in the cellular membrane in a dormant form. When plants encounter environmental stimuli, they will be released from the membrane by intramembrane proteases or by the ubiquitin proteasome pathway and then were translocated to the nucleus. The capacity to instantly activate dormant transcription factors is a critical strategy for modulating diverse cellular functions in response to external or internal signals, which provides an important transcriptional regulatory network in response to sudden stimulus and improves plant survival. NTLs (NTM1-like) are a small subset of NAC (NAM, ATAF1/2, CUC2) transcription factors, which contain a conserved NAC domain at the N-terminus and a transmembrane domain at the C-terminus. In the past two decades, several NTLs have been identified from several species, and most of them are involved in both development and stress response. In this review, we review the reports and findings on NTLs in plants and highlight the mechanism of their nuclear import as well as their functions in regulating plant growth and stress response.
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Affiliation(s)
- Lin Shu
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan province 450002, China
| | - Longhui Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan province 450002, China
| | - Yuan-Qing Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi province 712100, China
| | - Jingli Yan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan province 450002, China.
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Wang D, Chen L, Liu C, Wang H, Liu Z, Ji X, He N, Xin Y. Mno-miR164a and MnNAC100 regulate the resistance of mulberry to Botrytis cinerea. PHYSIOLOGIA PLANTARUM 2024; 176:e14309. [PMID: 38659152 DOI: 10.1111/ppl.14309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/01/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
Although microRNAs (miRNAs) regulate the defense response of a variety of plant species against a variety of pathogenic fungi, the involvement of miRNAs in mulberry's defense against Botrytis cinerea has not yet been documented. In this study, we identified responsive B. cinerea miRNA mno-miR164a in mulberry trees. After infection with B. cinerea, the expression of mno-miR164a was reduced, which was fully correlated with the upregulation of its target gene, MnNAC100, responsible for encoding a transcription factor. By using transient infiltration/VIGS mulberry that overexpressed mno-miR164a or knocked-down MnNAC100, our study revealed a substantial enhancement in mulberry's resistance to B. cinerea when mno-miR164a was overexpressed or MnNAC100 expression was suppressed. This enhancement was accompanied by increased catalase (CAT) activity and reduced malondialdehyde (MDA) content. In addition, mno-miR164a-mediated inhibition of MnNAC100 enhanced the expression of a cluster of defense-related genes in transgenic plants upon exposure to B. cinerea. Meanwhile, MnNAC100 acts as a transcriptional repressor, directly suppressing the expression of MnPDF1.2. Our study indicated that the mno-miR164a-MnNAC100 regulatory module manipulates the defense response of mulberry to B. cinerea infection. This discovery has great potential in breeding of resistant varieties and disease control.
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Affiliation(s)
- Donghao Wang
- College of Forestry, Shandong Agricultural University, Tai'an, China
| | - Lin Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Chaorui Liu
- College of Forestry, Shandong Agricultural University, Tai'an, China
| | - Hairui Wang
- College of Forestry, Shandong Agricultural University, Tai'an, China
| | - Zixuan Liu
- College of Forestry, Shandong Agricultural University, Tai'an, China
| | - Xianling Ji
- College of Forestry, Shandong Agricultural University, Tai'an, China
| | - Ningjia He
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Youchao Xin
- College of Forestry, Shandong Agricultural University, Tai'an, China
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Zhang H, Chen G, Xu H, Jing S, Jiang Y, Liu Z, Zhang H, Wang F, Hu X, Zhu Y. Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination. Int J Mol Sci 2023; 24:ijms24108710. [PMID: 37240056 DOI: 10.3390/ijms24108710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dry seeds and the germinating seeds. Of these DEGs, 7109 were identified in both the embryo and endosperm, 3953 were embryo specific, and 3329 were endosperm specific. The embryo-specific DEGs were enriched in the plant-hormone signal-transduction pathway, while the endosperm-specific DEGs were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis. We categorized these DEGs into early-, intermediate-, and late-stage genes, as well as consistently responsive genes, which can be enriched in various pathways related to seed germination. Transcription-factor (TF) analysis showed that 643 TFs from 48 families were differentially expressed during seed germination. Moreover, 12 unfolded protein response (UPR) pathway genes were induced by seed germination, and the knockout of OsBiP2 resulted in reduced germination rates compared to the wild type. This study enhances our understanding of gene responses in the embryo and endosperm during seed germination and provides insight into the effects of UPR on seed germination in rice.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Heng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sasa Jing
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yingying Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ziwen Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hua Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fulin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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5
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Lacrampe N, Colombié S, Dumont D, Nicot P, Lecompte F, Lugan R. Nitrogen-mediated metabolic patterns of susceptibility to Botrytis cinerea infection in tomato (Solanum lycopersicum) stems. PLANTA 2023; 257:41. [PMID: 36680621 PMCID: PMC9867679 DOI: 10.1007/s00425-022-04065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Severe N stress allows an accumulation of C-based compounds but impedes that of N-based compounds required to lower the susceptibility of tomato stem to Botrytis cinerea. Botrytis cinerea, a necrotrophic filamentous fungus, forms potentially lethal lesions on the stems of infected plants. Contrasted levels of susceptibility to B. cinerea were obtained in a tomato cultivar grown on a range of nitrate concentration: low N supply resulted in high susceptibility while high N supply conferred a strong resistance. Metabolic deviations and physiological traits resulting from both infection and nitrogen limitation were investigated in the symptomless stem tissue surrounding the necrotic lesion. Prior to infection, nitrogen-deficient plants showed reduced levels of nitrogen-based compounds such as amino acids, proteins, and glutathione and elevated levels of carbon-based and defence compounds such as α-tomatine and chlorogenic acid. After B. cinerea inoculation, all plants displayed a few common responses, mainly alanine accumulation and galactinol depletion. The metabolome of resistant plants grown under high N supply showed no significant change after inoculation. On the contrary, the metabolome of susceptible plants grown under low N supply showed massive metabolic adjustments, including changes in central metabolism around glutamate and respiratory pathways, suggesting active resource mobilization and production of energy and reducing power. Redox and defence metabolisms were also stimulated by the infection in plants grown under low N supply; glutathione and chlorogenic acid accumulated, as well as metabolites with more controversial defensive roles, such as polyamines, GABA, branched-chain amino acids and phytosterols. Taken together, the results showed that nitrogen deficiency, although leading to an increase in secondary metabolites even before the pathogen attack, must have compromised the constitutive levels of defence proteins and delayed or attenuated the induced responses. The involvement of galactinol, alanine, cycloartenol and citramalate in the tomato stem response to B. cinerea is reported here for the first time.
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Affiliation(s)
- Nathalie Lacrampe
- PSH Unit, INRAE, 84914 Avignon, France
- UMR Qualisud, Avignon Université, 84916 Avignon, France
| | - Sophie Colombié
- UMR 1332 BFP, INRAE, Univ Bordeaux, 33883 Villenave d’Ornon, France
| | | | | | | | - Raphaël Lugan
- UMR Qualisud, Avignon Université, 84916 Avignon, France
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Zhang M, Cao B, Zhang H, Fan Z, Zhou X, Li F. Geminivirus satellite-encoded βC1 activates UPR, induces bZIP60 nuclear export, and manipulates the expression of bZIP60 downstream genes to benefit virus infection. SCIENCE CHINA LIFE SCIENCES 2022:10.1007/s11427-022-2196-y. [DOI: 10.1007/s11427-022-2196-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
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7
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Bai S, Niu Q, Wu Y, Xu K, Miao M, Mei J. Genome-Wide Identification of the NAC Transcription Factors in Gossypium hirsutum and Analysis of Their Responses to Verticillium wilt. PLANTS (BASEL, SWITZERLAND) 2022; 11:2661. [PMID: 36235527 PMCID: PMC9571985 DOI: 10.3390/plants11192661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
The NAC transcription factors (NACs) are among the largest plant-specific gene regulators and play essential roles in the transcriptional regulation of both biotic and abiotic stress responses. Verticillium wilt of cotton caused by Verticillium dahliae (V. dahliae) is a destructive soil-borne disease that severely decreases cotton yield and quality. Although NACs constitute a large family in upland cotton (G. hirsutum L.), there is little systematic investigation of the NACs’ responsive to V. dahliae that has been reported. To further explore the key NACs in response to V. dahliae resistance and obtain a better comprehension of the molecular basis of the V. dahliae stress response in cotton, a genome-wide survey was performed in this study. To investigate the roles of GhNACs under V. dahliae induction in upland cotton, mRNA libraries were constructed from mocked and infected roots of upland cotton cultivars with the V. dahliae-sensitive cultivar “Jimian 11” (J11) and V. dahliae-tolerant cultivar “Zhongzhimian 2” (Z2). A total of 271 GhNACs were identified. Genome analysis showed GhNACs phylogenetically classified into 12 subfamilies and distributed across 26 chromosomes and 20 scaffolds. A comparative transcriptome analysis revealed 54 GhNACs were differentially expressed under V. dahliae stress, suggesting a potential role of these GhNACs in disease response. Additionally, one NAC090 homolog, GhNAC204, could be a positive regulator of cotton resistance to V. dahliae infection. These results give insight into the GhNAC gene family, identify GhNACs’ responsiveness to V. dahliae infection, and provide potential molecular targets for future studies for improving V. dahliae resistance in cotton.
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Affiliation(s)
| | | | | | | | | | - Jun Mei
- Correspondence: (M.M.); (J.M.)
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8
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Medina-Puche L, Lozano-Durán R. Plasma membrane-to-organelle communication in plant stress signaling. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102269. [PMID: 35939892 DOI: 10.1016/j.pbi.2022.102269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/19/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Intracellular compartments engage in extensive communication with one another, an essential ability for cells to respond and adapt to changing environmental and developmental conditions. The plasma membrane (PM), as the interface between the cellular and the outside media, plays a central role in the perception and relay of information about external stimuli, which needs to be ultimately addressed to the relevant subcellular organelles. Interest in PM-organelle communication has increased dramatically in recent years, as examples arise that illustrate different strategies through which information from the PM can be transmitted. In this review, we will discuss mechanisms enabling PM-to-organelle communication in plants, specifically in biotic and abiotic stress signaling.
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Affiliation(s)
- Laura Medina-Puche
- Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, D-72076 Tübingen, Germany
| | - Rosa Lozano-Durán
- Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, D-72076 Tübingen, Germany.
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Meng F, Zhao Q, Zhao X, Yang C, Liu R, Pang J, Zhao W, Wang Q, Liu M, Zhang Z, Kong Z, Liu J. A rice protein modulates endoplasmic reticulum homeostasis and coordinates with a transcription factor to initiate blast disease resistance. Cell Rep 2022; 39:110941. [PMID: 35705042 DOI: 10.1016/j.celrep.2022.110941] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 02/26/2022] [Accepted: 05/19/2022] [Indexed: 11/03/2022] Open
Abstract
Endoplasmic reticulum (ER) homeostasis is essential for plants to manage responses under environmental stress. Plant immune activation requires the ER, but how ER homeostasis is associated with plant immune activation is largely unexplored. Here we find that transcription of an HVA22 family gene, OsHLP1 (HVA22-like protein 1), is induced by Magnaporthe oryzae infection. Overexpression of OsHLP1 significantly enhances blast disease resistance but impairs ER morphology in rice (Oryza sativa), resulting in enhanced sensitivity to ER stress. OsHLP1 interacts with the NAC (NAM, ATAF, and CUC) transcription factor OsNTL6 at the ER. OsNTL6 localizes to the ER and is relocated to the nucleus after cleavage of the transmembrane domain. OsHLP1 suppresses OsNTL6 protein accumulation, whereas OsNTL6 counteracts OsHLP1 by alleviating sensitivity to ER stress and decreasing disease resistance in OsHLP1 overexpression plants. These findings unravel a mechanism whereby OsHLP1 promotes disease resistance by compromising ER homeostasis when plants are infected by pathogens.
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Affiliation(s)
- Fanwei Meng
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qiqi Zhao
- School of Life Sciences, University of Inner Mongolia, Hohhot 010021, China
| | - Xia Zhao
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chao Yang
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Rui Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinhuan Pang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wensheng Zhao
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qi Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Muxing Liu
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengguang Zhang
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Liu
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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An J, Liu Y, Han J, He C, Chen M, Zhu X, Hu W, Song W, Hu J, Guan Y. Transcriptional multiomics reveals the mechanism of seed deterioration in Nicotiana tabacum L. and Oryza sativa L. J Adv Res 2022; 42:163-176. [PMID: 36513411 PMCID: PMC9788960 DOI: 10.1016/j.jare.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Mature seeds deteriorate gradually and die eventually during long-term storage. Controlled deterioration is often used to accelerate the seed deterioration rate to assess the seed vigor and physiological quality of seed lots. OBJECTIVES Although it is well known that the process of seed deterioration produced by controlled deterioration is distinct from that caused by long-term storage, the differences in transcriptional levels have not been reported. Clarifying the mechanism of seed deterioration is critical for identifying, conserving and utilizing germplasm resources. METHODS Tobacco (Nicotiana tabacum L.) seeds were studied thoroughly using transcriptome, small RNA, and degradome sequencing after long-term storage (LS) and controlled deterioration (CD). Co-expression trend analysis identified transcripts involved in tobacco seed deterioration, while phylogenetic analysis helped to uncover comparable targets in rice (Oryza sativa L.) for further verification and utilization. RESULTS In LS and CD, a total of 2,112 genes and 164 miRNAs were differentially expressed, including 20 interaction miRNA-mRNA pairs with contrasting expression. Transcriptional multiomics found that the main causes of LS were plant hormone signal transduction and protein processing in the endoplasmic reticulum, whereas the primary cause of CD was nucleotide excision repair dysfunction. The homeostatic balance of RNA degradation and the spliceosome occurred in both modes of seed deterioration. Additionally, co-expression trend analysis identified two coherent pairs, nta-miR160b-NtARF18 and nta-miR396c-NtMBD10, as being significant in LS and CD, respectively. For utilization, rice homologous targets OsARF18 and OsMBD707 were verified to play similar roles in LS and CD, respectively. CONCLUSION This study demonstrated the transcriptional mechanism of tobacco and key genes in seed deterioration. And the application of key genes in rice also verified the feasibility of the multiomics method, guiding the identification of candidate genes to precisely delay seed deterioration in other species of seed research.
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Affiliation(s)
- Jianyu An
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Yihan Liu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Jiajun Han
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Can He
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Min Chen
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Xiaobo Zhu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Weimin Hu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Wenjian Song
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Jin Hu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Yajing Guan
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China,Corresponding author.
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11
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Simoni EB, Oliveira CC, Fraga OT, Reis PAB, Fontes EPB. Cell Death Signaling From Endoplasmic Reticulum Stress: Plant-Specific and Conserved Features. FRONTIERS IN PLANT SCIENCE 2022; 13:835738. [PMID: 35185996 PMCID: PMC8850647 DOI: 10.3389/fpls.2022.835738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/10/2022] [Indexed: 05/06/2023]
Abstract
The endoplasmic reticulum (ER) stress response is triggered by any condition that disrupts protein folding and promotes the accumulation of unfolded proteins in the lumen of the organelle. In eukaryotic cells, the evolutionarily conserved unfolded protein response is activated to clear unfolded proteins and restore ER homeostasis. The recovery from ER stress is accomplished by decreasing protein translation and loading into the organelle, increasing the ER protein processing capacity and ER-associated protein degradation activity. However, if the ER stress persists and cannot be reversed, the chronically prolonged stress leads to cellular dysfunction that activates cell death signaling as an ultimate attempt to survive. Accumulating evidence implicates ER stress-induced cell death signaling pathways as significant contributors for stress adaptation in plants, making modulators of ER stress pathways potentially attractive targets for stress tolerance engineering. Here, we summarize recent advances in understanding plant-specific molecular mechanisms that elicit cell death signaling from ER stress. We also highlight the conserved features of ER stress-induced cell death signaling in plants shared by eukaryotic cells.
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