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Yan H, Liu F, Zhang G, Liu S, Ma W, Yang T, Li Y, Yang J, Cui H. PlantCHRs: A comprehensive database of plant chromatin remodeling factors. Comput Struct Biotechnol J 2023; 21:4974-4987. [PMID: 37867975 PMCID: PMC10589754 DOI: 10.1016/j.csbj.2023.10.005] [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: 06/08/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
The Snf2 protein family is a group of ATP-dependent chromatin remodeling factors (CHRs) that play an essential role in gene expression regulation. In plants, Snf2 is involved in growth, development, as well as stress resistance. However, only a very limited number of experimentally validated Snf2 have been identified and reported, while the majority remaining undiscovered in most species . In this study, we predicted 3135 Snf2 proteins and 8398 chromatin remodeling complex (CRC) subunits in diverse plant species, and constructed the Plant Chromatin Remodeling Factors Database (PlantCHRs, http://www.functionalgenomics.cn/PlantCHRs/), which provide a comprehensive resource for researchers to access information about plant CHRs. We also developed an online tool capable of predicting CHRs and CRC subunits. Moreover, we investigated the distribution of Snf2 proteins in different species and observed a significant increase in the number of Snf2 proteins and the diversity of the Snf2 subfamily during the evolution, highlighting their evolutionary importance. By analyzing the expression patterns of the Snf2 genes in different tissues of maize and Arabidopsis, we found that the Snf2 proteins may show some conservation across different species in regulating plant growth and development. Over the all, we established a comprehensive database for plant CHRs, which will facilitate the researches on plant chromatin remodeling.
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Affiliation(s)
- Hengyu Yan
- College of Agronomy, Qingdao Agricultural University, China
| | - Fangyuan Liu
- College of Agronomy, Qingdao Agricultural University, China
| | - Guowei Zhang
- College of Agronomy, Qingdao Agricultural University, China
| | - Shuai Liu
- College of Agronomy, Qingdao Agricultural University, China
| | - Weiwei Ma
- College of Agronomy, Qingdao Agricultural University, China
| | - Ting Yang
- College of Agronomy, Qingdao Agricultural University, China
| | - Yubin Li
- College of Agronomy, Qingdao Agricultural University, China
| | - Jiaotong Yang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hailong Cui
- College of Economics and Management (Cooperative College), Qingdao Agricultural University, China
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2
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Harris CJ, Amtmann A, Ton J. Epigenetic processes in plant stress priming: Open questions and new approaches. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102432. [PMID: 37523900 DOI: 10.1016/j.pbi.2023.102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 08/02/2023]
Abstract
Priming reflects the capacity of plants to memorise environmental stress experience and improve their response to recurring stress. Epigenetic modifications in DNA and associated histone proteins may carry short-term and long-term memory in the same plant or mediate transgenerational effects, but the evidence is still largely circumstantial. New experimental tools now enable scientists to perform targeted manipulations that either prevent or generate a particular epigenetic modification in a particular location of the genome. Such 'reverse epigenetics' approaches allow for the interrogation of causality between individual priming-induced modifications and their role for altering gene expression and plant performance under recurring stress. Furthermore, combining site-directed epigenetic manipulation with conditional and cell-type specific promoters creates novel opportunities to test and engineer spatiotemporal patterns of priming.
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Affiliation(s)
- C Jake Harris
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Anna Amtmann
- School of Molecular Biosciences, University of Glasgow, Glasgow, G128QQ, UK.
| | - Jurriaan Ton
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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Liu H, Li J, Wang S, Hua J, Zou B. CHROMATIN REMODELING 11-dependent nucleosome occupancy affects disease resistance in rice. PLANT PHYSIOLOGY 2023; 193:1635-1651. [PMID: 37403194 DOI: 10.1093/plphys/kiad381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023]
Abstract
Plant immune responses involve transcriptional reprograming of defense response genes, and chromatin remodeling is important for transcriptional regulation. However, nucleosome dynamics induced by pathogen infection and its association with gene transcription are largely unexplored in plants. Here, we investigated the role of the rice (Oryza sativa) gene CHROMATIN REMODELING 11 (OsCHR11) in nucleosome dynamics and disease resistance. Nucleosome profiling revealed that OsCHR11 is required for the maintaining of genome-wide nucleosome occupancy in rice. Nucleosome occupancy of 14% of the genome was regulated by OsCHR11. Infection of bacterial leaf blight Xoo (Xanthomonas oryzae pv. oryzae) repressed genome-wide nucleosome occupancy, and this process depended on OsCHR11 function. Furthermore, OsCHR11/Xoo-dependent chromatin accessibility correlated with gene transcript induction by Xoo. In addition, accompanied by increased resistance to Xoo, several defense response genes were differentially expressed in oschr11 after Xoo infection. Overall, this study reports the genome-wide effects of pathogen infection on nucleosome occupancy, its regulation, and its contribution to disease resistance in rice.
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Affiliation(s)
- He Liu
- The State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Li
- The State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Wang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Baohong Zou
- The State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
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Sheikh AH, Zacharia I, Pardal AJ, Dominguez-Ferreras A, Sueldo DJ, Kim JG, Balmuth A, Gutierrez JR, Conlan BF, Ullah N, Nippe OM, Girija AM, Wu CH, Sessa G, Jones AME, Grant MR, Gifford ML, Mudgett MB, Rathjen JP, Ntoukakis V. Dynamic changes of the Prf/Pto tomato resistance complex following effector recognition. Nat Commun 2023; 14:2568. [PMID: 37142566 PMCID: PMC10160066 DOI: 10.1038/s41467-023-38103-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 04/16/2023] [Indexed: 05/06/2023] Open
Abstract
In both plants and animals, nucleotide-binding leucine-rich repeat (NLR) immune receptors play critical roles in pathogen recognition and activation of innate immunity. In plants, NLRs recognise pathogen-derived effector proteins and initiate effector-triggered immunity (ETI). However, the molecular mechanisms that link NLR-mediated effector recognition and downstream signalling are not fully understood. By exploiting the well-characterised tomato Prf/Pto NLR resistance complex, we identified the 14-3-3 proteins TFT1 and TFT3 as interacting partners of both the NLR complex and the protein kinase MAPKKKα. Moreover, we identified the helper NRC proteins (NLR-required for cell death) as integral components of the Prf /Pto NLR recognition complex. Notably our studies revealed that TFTs and NRCs interact with distinct modules of the NLR complex and, following effector recognition, dissociate facilitating downstream signalling. Thus, our data provide a mechanistic link between activation of immune receptors and initiation of downstream signalling cascades.
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Affiliation(s)
- Arsheed H Sheikh
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Center for Desert Agriculture, BESE Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Iosif Zacharia
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Alonso J Pardal
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Daniela J Sueldo
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Department of Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Jung-Gun Kim
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Alexi Balmuth
- J.R. Simplot Company, Boise, ID, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jose R Gutierrez
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Brendon F Conlan
- Research School of Biology, The Australian National University, Acton, 2601, ACT, Australia
| | - Najeeb Ullah
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Olivia M Nippe
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Anil M Girija
- School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - Chih-Hang Wu
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Guido Sessa
- School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | | | - Murray R Grant
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Miriam L Gifford
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, UK
| | - Mary Beth Mudgett
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - John P Rathjen
- Research School of Biology, The Australian National University, Acton, 2601, ACT, Australia
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, UK.
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Yu R, Ye X, Zhang C, Hu H, Kang Y, Li Z. Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana. Curr Issues Mol Biol 2022; 45:212-222. [PMID: 36661502 PMCID: PMC9858106 DOI: 10.3390/cimb45010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/13/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Virus infestation can seriously harm the host plant's growth and development. Turnip yellows virus (TuYV) infestation of host plants can cause symptoms, such as yellowing and curling of leaves and root chlorosis. However, the regulatory mechanisms by which TuYV affects host growth and development are unclear. Hence, it is essential to mine small RNA (sRNA) and explore the regulation of sRNAs on plant hosts for disease control. In this study, we analyzed high-throughput data before and after TuYV infestation in Arabidopsis using combined genetics, statistics, and machine learning to identify 108 specifically expressed and critical functional sRNAs after TuYV infection. First, comparing the expression levels of sRNAs before and after infestation, 508 specific sRNAs were significantly up-regulated in Arabidopsis after infestation. In addition, the results show that AI models, including SVM, RF, XGBoost, and CNN using two-dimensional convolution, have robust classification features at the sequence level, with a prediction accuracy of about 96.8%. A comparison of specific sRNAs with genome sequences revealed that 247 matched precisely with the TuYV genome sequence but not with the Arabidopsis genome, suggesting that TuYV viruses may be their source. The 247 sRNAs predicted target genes and enrichment analysis, which identified 206 Arabidopsis genes involved in nine biological processes and three KEGG pathways associated with plant growth and viral stress tolerance, corresponding to 108 sRNAs. These findings provide a reference for studying sRNA-mediated interactions in pathogen infection and are essential for establishing a vital resource of regulation network for the virus infecting plants and deepening the understanding of TuYV virus infection patterns. However, further validation of these sRNAs is needed to gain a new understanding.
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Transcriptional regulation of plant innate immunity. Essays Biochem 2022; 66:607-620. [PMID: 35726519 PMCID: PMC9528082 DOI: 10.1042/ebc20210100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022]
Abstract
Transcriptional reprogramming is an integral part of plant immunity. Tight regulation of the immune transcriptome is essential for a proper response of plants to different types of pathogens. Consequently, transcriptional regulators are proven targets of pathogens to enhance their virulence. The plant immune transcriptome is regulated by many different, interconnected mechanisms that can determine the rate at which genes are transcribed. These include intracellular calcium signaling, modulation of the redox state, post-translational modifications of transcriptional regulators, histone modifications, DNA methylation, modulation of RNA polymerases, alternative transcription inititation, the Mediator complex and regulation by non-coding RNAs. In addition, on their journey from transcription to translation, mRNAs are further modulated through mechanisms such as nuclear RNA retention, storage of mRNA in stress granules and P-bodies, and post-transcriptional gene silencing. In this review, we highlight the latest insights into these mechanisms. Furthermore, we discuss some emerging technologies that promise to greatly enhance our understanding of the regulation of the plant immune transcriptome in the future.
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He YH, Zhang ZR, Xu YP, Chen SY, Cai XZ. Genome-Wide Identification of Rapid Alkalinization Factor Family in Brassica napus and Functional Analysis of BnRALF10 in Immunity to Sclerotinia sclerotiorum. FRONTIERS IN PLANT SCIENCE 2022; 13:877404. [PMID: 35592581 PMCID: PMC9113046 DOI: 10.3389/fpls.2022.877404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Rapid alkalinization factors (RALFs) were recently reported to be important players in plant immunity. Nevertheless, the signaling underlying RALF-triggered immunity in crop species against necrotrophic pathogens remains largely unknown. In this study, RALF family in the important oil crop oilseed rape (Brassica napus) was identified and functions of BnRALF10 in immunity against the devastating necrotrophic pathogen Sclerotinia sclerotiorum as well as the signaling underlying this immunity were revealed. The oilseed rape genome carried 61 RALFs, half of them were atypical, containing a less conserved YISY motif and lacking a RRXL motif or a pair of cysteines. Family-wide gene expression analyses demonstrated that patterns of expression in response to S. sclerotiorum infection and DAMP and PAMP treatments were generally RALF- and stimulus-specific. Most significantly responsive BnRALF genes were expressionally up-regulated by S. sclerotiorum, while in contrast, more BnRALF genes were down-regulated by BnPep5 and SsNLP1. These results indicate that members of BnRALF family are likely differentially involved in plant immunity. Functional analyses revealed that BnRALF10 provoked diverse immune responses in oilseed rape and stimulated resistance to S. sclerotiorum. These data support BnRALF10 to function as a DAMP to play a positive role in plant immunity. BnRALF10 interacted with BnFER. Silencing of BnFER decreased BnRALF10-induced reactive oxygen species (ROS) production and compromised rape resistance to S. sclerotiorum. These results back BnFER to be a receptor of BnRALF10. Furthermore, quantitative proteomic analysis identified dozens of BnRALF10-elicited defense (RED) proteins, which respond to BnRALF10 in protein abundance and play a role in defense. Our results revealed that BnRALF10 modulated the abundance of RED proteins to fine tune plant immunity. Collectively, our results provided some insights into the functions of oilseed rape RALFs and the signaling underlying BnRALF-triggered immunity.
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Affiliation(s)
- Yu-Han He
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhuo-Ran Zhang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - You-Ping Xu
- Centre of Analysis and Measurement, Zhejiang University, Hangzhou, China
| | - Song-Yu Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xin-Zhong Cai
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
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Sertedakis M, Kotsaridis K, Tsakiri D, Mermigka G, Dominguez‐Ferreras A, Ntoukakis V, Sarris P. Expression of putative effectors of different Xylella fastidiosa strains triggers cell death-like responses in various Nicotiana model plants. MOLECULAR PLANT PATHOLOGY 2022; 23:148-156. [PMID: 34628713 PMCID: PMC8659589 DOI: 10.1111/mpp.13147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 06/12/2023]
Abstract
The wide host range of Xylella fastidiosa (Xf) indicates the existence of yet uncharacterized virulence mechanisms that help pathogens to overcome host defences. Various bioinformatics tools combined with prediction of the functions of putative virulence proteins are valuable approaches to study microbial pathogenicity. We collected a number of putative effectors from three Xf strains belonging to different subspecies: Temecula-1 (subsp. fastidiosa), CoDiRO (subsp. pauca), and Ann-1 (subsp. sandyi). We designed an in planta Agrobacterium-based expression system that drives the expressed proteins to the cell apoplast, in order to investigate their ability to activate defence in Nicotiana model plants. Multiple Xf proteins differentially elicited cell death-like phenotypes in different Nicotiana species. These proteins are members of different enzymatic groups: (a) hydrolases/hydrolase inhibitors, (b) serine proteases, and (c) metal transferases. We also classified the Xf proteins according to their sequential and structural similarities via the I-TASSER online tool. Interestingly, we identified similar proteins that were able to differentially elicit cell death in different cultivars of the same species. Our findings provide a basis for further studies on the mechanisms that underlie both defence activation in Xf resistant hosts and pathogen adaptation in susceptible hosts.
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Affiliation(s)
| | - Konstantinos Kotsaridis
- Department of BiologyUniversity of CreteHeraklionGreece
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | - Dimitra Tsakiri
- Department of BiologyUniversity of CreteHeraklionGreece
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | - Glykeria Mermigka
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | | | | | - Panagiotis F. Sarris
- Department of BiologyUniversity of CreteHeraklionGreece
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- BiosciencesUniversity of ExeterExeterUK
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