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Yu X, Niu H, Liu C, Wang H, Yin W, Xia X. PTI-ETI synergistic signal mechanisms in plant immunity. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2113-2128. [PMID: 38470397 PMCID: PMC11258992 DOI: 10.1111/pbi.14332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 02/16/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024]
Abstract
Plants face a relentless onslaught from a diverse array of pathogens in their natural environment, to which they have evolved a myriad of strategies that unfold across various temporal scales. Cell surface pattern recognition receptors (PRRs) detect conserved elicitors from pathogens or endogenous molecules released during pathogen invasion, initiating the first line of defence in plants, known as pattern-triggered immunity (PTI), which imparts a baseline level of disease resistance. Inside host cells, pathogen effectors are sensed by the nucleotide-binding/leucine-rich repeat (NLR) receptors, which then activate the second line of defence: effector-triggered immunity (ETI), offering a more potent and enduring defence mechanism. Moreover, PTI and ETI collaborate synergistically to bolster disease resistance and collectively trigger a cascade of downstream defence responses. This article provides a comprehensive review of plant defence responses, offering an overview of the stepwise activation of plant immunity and the interactions between PTI-ETI synergistic signal transduction.
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Affiliation(s)
- Xiao‐Qian Yu
- State Key Laboratory of Tree Genetics and BreedingCollege of Biological Sciences and Technology, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Hao‐Qiang Niu
- State Key Laboratory of Tree Genetics and BreedingCollege of Biological Sciences and Technology, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Chao Liu
- State Key Laboratory of Tree Genetics and BreedingCollege of Biological Sciences and Technology, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Hou‐Ling Wang
- State Key Laboratory of Tree Genetics and BreedingCollege of Biological Sciences and Technology, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Weilun Yin
- State Key Laboratory of Tree Genetics and BreedingCollege of Biological Sciences and Technology, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Xinli Xia
- State Key Laboratory of Tree Genetics and BreedingCollege of Biological Sciences and Technology, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
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Li S, Zhao Y, Wu P, Grierson D, Gao L. Ripening and rot: How ripening processes influence disease susceptibility in fleshy fruits. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39016673 DOI: 10.1111/jipb.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024]
Abstract
Fleshy fruits become more susceptible to pathogen infection when they ripen; for example, changes in cell wall properties related to softening make it easier for pathogens to infect fruits. The need for high-quality fruit has driven extensive research on improving pathogen resistance in important fruit crops such as tomato (Solanum lycopersicum). In this review, we summarize current progress in understanding how changes in fruit properties during ripening affect infection by pathogens. These changes affect physical barriers that limit pathogen entry, such as the fruit epidermis and its cuticle, along with other defenses that limit pathogen growth, such as preformed and induced defense compounds. The plant immune system also protects ripening fruit by recognizing pathogens and initiating defense responses involving reactive oxygen species production, mitogen-activated protein kinase signaling cascades, and jasmonic acid, salicylic acid, ethylene, and abscisic acid signaling. These phytohormones regulate an intricate web of transcription factors (TFs) that activate resistance mechanisms, including the expression of pathogenesis-related genes. In tomato, ripening regulators, such as RIPENING INHIBITOR and NON_RIPENING, not only regulate ripening but also influence fruit defenses against pathogens. Moreover, members of the ETHYLENE RESPONSE FACTOR (ERF) family play pivotal and distinct roles in ripening and defense, with different members being regulated by different phytohormones. We also discuss the interaction of ripening-related and defense-related TFs with the Mediator transcription complex. As the ripening processes in climacteric and non-climacteric fruits share many similarities, these processes have broad applications across fruiting crops. Further research on the individual contributions of ERFs and other TFs will inform efforts to diminish disease susceptibility in ripe fruit, satisfy the growing demand for high-quality fruit and decrease food waste and related economic losses.
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Affiliation(s)
- Shan Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yu Zhao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pan Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Donald Grierson
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Lei Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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Zhang N, Gan J, Carneal L, González-Tobón J, Filiatrault M, Martin GB. Helper NLRs Nrc2 and Nrc3 act codependently with Prf/Pto and activate MAPK signaling to induce immunity in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:7-22. [PMID: 37844152 DOI: 10.1111/tpj.16502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023]
Abstract
Plant intracellular immune receptors, primarily nucleotide-binding, leucine-rich repeat proteins (NLRs), detect pathogen effector proteins and activate NLR-triggered immunity (NTI). Recently, 'sensor' NLRs have been reported to function with 'helper' NLRs to activate immunity. We investigated the role of two helper NLRs, Nrc2 and Nrc3, on immunity in tomato to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) mediated by the sensor NLR Prf and the Pto kinase. An nrc2/nrc3 mutant no longer activated Prf/Pto-mediated NTI to Pst containing the effectors AvrPto and AvrPtoB. An nrc3 mutant showed intermediate susceptibility between wild-type plants and a Prf mutant, while an nrc2 mutant developed only mild disease. These observations indicate that Nrc2 and Nrc3 act additively in Prf-/Pto-mediated immunity. We examined at what point Nrc2 and Nrc3 act in the Prf/Pto-mediated immune response. In the nrc2/3 mutant, programmed cell death (PCD) normally induced by constitutively active variants of AvrPtoB, Pto, or Prf was abolished, but that induced by M3Kα or Mkk2 was not. PCD induced by a constitutively active Nrc3 was also abolished in a Nicotiana benthamiana line with reduced expression of Prf. MAPK activation triggered by expression of AvrPto in the wild-type tomato plants was completely abolished in the nrc2/3 mutant. These results indicate that Nrc2 and Nrc3 act with Prf/Pto and upstream of MAPK signaling. Nrc2 and Nrc3 were not required for PCD triggered by Ptr1, another sensor NLR-mediating Pst resistance, although these helper NLRs do appear to be involved in resistance to certain Pst race 1 strains.
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Affiliation(s)
- Ning Zhang
- Boyce Thompson Institute for Plant Research, Ithaca, New York, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA
| | - Joyce Gan
- Boyce Thompson Institute for Plant Research, Ithaca, New York, 14853, USA
| | - Lauren Carneal
- Boyce Thompson Institute for Plant Research, Ithaca, New York, 14853, USA
| | - Juliana González-Tobón
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA
| | - Melanie Filiatrault
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, 14853, USA
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, Ithaca, New York, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA
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Oh Y, Ingram T, Shekasteband R, Adhikari T, Louws FJ, Dean RA. Tissues and mechanisms associated with Verticillium wilt resistance in tomato using bi-grafted near-isogenic lines. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4685-4706. [PMID: 37184211 PMCID: PMC10433936 DOI: 10.1093/jxb/erad182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/12/2023] [Indexed: 05/16/2023]
Abstract
Host resistance is the primary means to control Verticillium dahliae, a soil-borne pathogen causing major losses on a broad range of plants, including tomato. The tissues and mechanisms responsible for resistance remain obscure. In the field, resistant tomato used as rootstocks does not confer resistance. Here, we created bi-grafted plants with near-isogenic lines (NILs) exhibiting (Ve1) or lacking (ve1) resistance to V. dahliae race 1. Ten days after inoculation, scion and rootstock tissues were subjected to differential gene expression and co-expression network analyses. Symptoms only developed in susceptible scions regardless of the rootstock. Infection caused more dramatic alteration of tomato gene expression in susceptible compared with resistant tissues, including pathogen receptor, signaling pathway, pathogenesis-related protein, and cell wall modification genes. Differences were observed between scions and rootstocks, primarily related to physiological processes in these tissues. Gene expression in scions was influenced by the rootstock genotype. A few genes were associated with the Ve1 genotype, which was independent of infection or tissue type. Several were physically clustered, some near the Ve1 locus on chromosome 9. Transcripts mapped to V. dahliae were dominated by secreted candidate effector proteins. These findings advance knowledge of molecular mechanisms underlying the tomato-V. dahliae interaction.
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Affiliation(s)
- Yeonyee Oh
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Thomas Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Reza Shekasteband
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Tika Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Ralph A Dean
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
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Andolfo G, Di Donato A, Ercolano MR. NB-LRR Lineage-Specific Equipment Is Sorted Out by Sequence Pattern Adaptation and Domain Segment Shuffling. Int J Mol Sci 2022; 23:ijms232214269. [PMID: 36430746 PMCID: PMC9696612 DOI: 10.3390/ijms232214269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
The nucleotide-binding and leucine-rich repeat (NB-LRR) genes, also known as resistance (R)-genes, play an important role in the activation of immune responses. In recent years, large-scale studies have been performed to highlight the diversification of plant NB-LRR repertories. It is well known that, to provide new functionalities, NB-LRR sequences are subject to duplication, domain fusions and acquisition and other kinds of mutations. Although some mechanisms that govern NB-LRR protein domain adaptations have been uncovered, to retrace the plant-lineage-specific evolution routes of R protein structure, a multi-genome comparative analysis was performed. This study allowed us to define groups of genes sharing homology relationships across different species. It is worth noting that the most populated groups contained well-characterized R proteins. The arsenal profile of such groups was investigated in five botanical families, including important crop species, to underline specific adaptation signatures. In addition, the dissection of 70 NB domains of well-characterized R-genes revealed the NB core motifs from which the three main R protein classes have been diversified. The structural remodeling of domain segments shaped the specific NB-LRR repertoires observed in each plant species. This analysis provided new evolutionary and functional insights on NB protein domain shuffling. Taken together, such findings improved our understanding of the molecular adaptive selection mechanisms occurring at plant R loci.
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Martin EC, Ion CF, Ifrimescu F, Spiridon L, Bakker J, Goverse A, Petrescu AJ. NLRscape: an atlas of plant NLR proteins. Nucleic Acids Res 2022; 51:D1470-D1482. [PMID: 36350627 PMCID: PMC9825502 DOI: 10.1093/nar/gkac1014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
NLRscape is a webserver that curates a collection of over 80 000 plant protein sequences identified in UniProtKB to contain NOD-like receptor signatures, and hosts in addition a number of tools aimed at the exploration of the complex sequence landscape of this class of plant proteins. Each entry gathers sequence information, domain and motif annotations from multiple third-party sources but also in-house advanced annotations aimed at addressing caveats of the existing broad-based annotations. NLRscape provides a top-down perspective of the NLR sequence landscape but also services for assisting a bottom-up approach starting from a given input sequence. Sequences are clustered by their domain organization layout, global homology and taxonomic spread-in order to allow analysis of how particular traits of an NLR family are scattered within the plant kingdom. Tools are provided for users to locate their own protein of interest in the overall NLR landscape, generate custom clusters centered around it and perform a large number of sequence and structural analyses using included interactive online instruments. Amongst these, we mention: taxonomy distribution plots, homology cluster graphs, identity matrices and interactive MSA synchronizing secondary structure and motif predictions. NLRscape can be found at: https://nlrscape.biochim.ro/.
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Affiliation(s)
- Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Catalin F Ion
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Florin Ifrimescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Laurentiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Jaap Bakker
- Laboratory of Nematology, Wageningen University and Research, Wageningen 6700ES, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University and Research, Wageningen 6700ES, The Netherlands
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Zhang L, Liu Y, Wang Q, Wang C, Lv S, Wang Y, Wang J, Wang Y, Yuan J, Zhang H, Kang Z, Ji W. An alternative splicing isoform of wheat TaYRG1 resistance protein activates immunity by interacting with dynamin-related proteins. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5474-5489. [PMID: 35652375 DOI: 10.1093/jxb/erac245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Wheat (Triticum aestivum) is a commercially important crop and its production is seriously threatened by the fungal pathogen Puccinia striiformis f. sp. tritici West (Pst). Resistance (R) genes are critical factors that facilitate plant immune responses. Here, we report a wheat R gene NB-ARC-LRR ortholog, TaYRG1, that is associated with distinct alternative splicing events in wheat infected by Pst. The native splice variant, TaYRG1.6, encodes internal-motif-deleted polypeptides with the same N- and C-termini as TaYRG1.1, resulting in gain of function. Transient expression of protein variants in Nicotiana benthamiana showed that the NB and ARC domains, and TaYRG1.6 (half LRR domain), stimulate robust elicitor-independent cell death based on a signal peptide, although the activity was negatively modulated by the CC and complete LRR domains. Furthermore, molecular genetic analyses indicated that TaYRG1.6 enhanced resistance to Pst in wheat. Moreover, we provide multiple lines of evidence that TaYRG1.6 interacts with a dynamin-related protein, TaDrp1. Proteome profiling suggested that the TaYRG1.6-TaDrp1-DNM complex in the membrane trafficking systems may trigger cell death by mobilizing lipid and kinase signaling in the endocytosis pathway. Our findings reveal a unique mechanism by which TaYRG1 activates cell death and enhances disease resistance by reconfiguring protein structure through alternative splicing.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuanming Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiaohui Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Chao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Shikai Lv
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
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Mondal S, Mohamed Shafi K, Raizada A, Song H, Badigannavar AM, Sowdhamini R. Development of candidate gene-based markers and map-based cloning of a dominant rust resistance gene in cultivated groundnut (Arachis hypogaea L.). Gene 2022; 827:146474. [PMID: 35390447 DOI: 10.1016/j.gene.2022.146474] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/22/2022] [Accepted: 03/31/2022] [Indexed: 11/18/2022]
Abstract
A dominant rust resistance gene, VG 9514-Rgene was isolated through map-based cloning. Sequence analysis revealed non-synonymous mutations in the TIR, NBS and LRR region of the R-protein. Candidate gene-based markers from these SNPs revealed complete co-segregation of the isolated VG 9514-Rgene with rust resistance in a RIL population and confirmed their map position in between FRS 72 and SSR_GO340445 markers in arahy03 chromosome. Blastp search of VG 9514-Rprotein detected Arahy.T6DCA5 with >80.0% identity that localized at 142,544,745.0.142,549,184 in arahy03 chromosome. Ka/Ks calculation revealed that VG 9514-Rgene had undergone positive selection compared to four homologous genes in the groundnut genome. Homology based structure modelling of this R-protein revealed a typical consensus three-dimensional folding of TIR-NBS-LRR protein. Non-synonymous mutations in susceptible version of R-protein were mapped and found E268Q mutation in hhGRExE motif, Y309F in RNBS-A motif and I579T in MHD motif of NB-ARC domain are probable candidates for loss of function.
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Affiliation(s)
- Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, Maharashtra, India.
| | - K Mohamed Shafi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, Karnataka, India.
| | - Avi Raizada
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, Maharashtra, India
| | - Hui Song
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Anand M Badigannavar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, Maharashtra, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, Karnataka, India.
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Förderer A, Yu D, Li E, Chai J. Resistosomes at the interface of pathogens and plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102212. [PMID: 35462196 DOI: 10.1016/j.pbi.2022.102212] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Nucleotide-binding and leucine-rich repeat (NLR) proteins are a large family of intracellular immune receptors that detect specific pathogen effector proteins secreted into plant cells. Upon direct or indirect recognition of effector proteins, NLRs form higher-order oligomeric complexes termed resistosomes that trigger defence responses typically associated with a regulated cell death. Here, we review recent advances in our understanding of signalling mediated by plant NLR resistosomes. Emphasis is placed on discussing the activation mechanisms and biochemical functions of resistosomes. We also summarize the most recent research in structure-based rational engineering of NLRs. At the end, we outline challenging questions concerning the elucidation of resistosome signalling.
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Affiliation(s)
- Alexander Förderer
- Institute of Biochemistry, University of Cologne, Cologne, Germany; Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dongli Yu
- Institute of Biochemistry, University of Cologne, Cologne, Germany; Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ertong Li
- Institute of Biochemistry, University of Cologne, Cologne, Germany; Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jijie Chai
- Institute of Biochemistry, University of Cologne, Cologne, Germany; Max Planck Institute for Plant Breeding Research, Cologne, Germany; Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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10
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Xu X, Chen Y, Li B, Zhang Z, Qin G, Chen T, Tian S. Molecular mechanisms underlying multi-level defense responses of horticultural crops to fungal pathogens. HORTICULTURE RESEARCH 2022; 9:uhac066. [PMID: 35591926 PMCID: PMC9113409 DOI: 10.1093/hr/uhac066] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/07/2022] [Indexed: 05/21/2023]
Abstract
The horticultural industry helps to enrich and improve the human diet while contributing to growth of the agricultural economy. However, fungal diseases of horticultural crops frequently occur during pre- and postharvest periods, reducing yields and crop quality and causing huge economic losses and wasted food. Outcomes of fungal diseases depend on both horticultural plant defense responses and fungal pathogenicity. Plant defense responses are highly sophisticated and are generally divided into preformed and induced defense responses. Preformed defense responses include both physical barriers and phytochemicals, which are the first line of protection. Induced defense responses, which include innate immunity (pattern-triggered immunity and effector-triggered immunity), local defense responses, and systemic defense signaling, are triggered to counterstrike fungal pathogens. Therefore, to develop regulatory strategies for horticultural plant resistance, a comprehensive understanding of defense responses and their underlying mechanisms is critical. Recently, integrated multi-omics analyses, CRISPR-Cas9-based gene editing, high-throughput sequencing, and data mining have greatly contributed to identification and functional determination of novel phytochemicals, regulatory factors, and signaling molecules and their signaling pathways in plant resistance. In this review, research progress on defense responses of horticultural crops to fungal pathogens and novel regulatory strategies to regulate induction of plant resistance are summarized, and then the problems, challenges, and future research directions are examined.
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Affiliation(s)
- Xiaodi Xu
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Abebe AM, Oh CS, Kim HT, Choi G, Seo E, Yeam I, Lee JM. QTL-Seq Analysis for Identification of Resistance Loci to Bacterial Canker in Tomato. FRONTIERS IN PLANT SCIENCE 2022; 12:809959. [PMID: 35154207 PMCID: PMC8826648 DOI: 10.3389/fpls.2021.809959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Bacterial canker caused by Clavibacter michiganensis (Cm) is one of the most economically important vascular diseases causing unilateral leaf wilting, stem canker, a bird's-eye lesion on fruit, and whole plant wilting in tomato. There is no commercially available cultivar with bacterial canker resistance, and genomics-assisted breeding can accelerate the development of cultivars with enhanced resistance. Solanum lycopersicum "Hawaii 7998" was found to show bacterial canker resistance. A Quantitative trait loci (QTL)-seq was performed to identify the resistance loci using 909 F2 individuals derived from a cross between S. lycopersicum "E6203" (susceptible) and "Hawaii 7998," and a genomic region (37.24-41.15 Mb) associated with bacterial canker resistance on chromosome 6 (Rcm6) was found. To dissect the Rcm6 region, 12 markers were developed and several markers were associated with the resistance phenotypes. Among the markers, the Rcm6-9 genotype completely matched with the phenotype in the 47 cultivars. To further validate the Rcm6 as a resistance locus and the Rcm6-9 efficiency, subsequent analysis using F2 and F3 progenies was conducted. The progeny individuals with homozygous resistance allele at the Rcm6-9 showed significantly lower disease severity than those possessing homozygous susceptibility alleles. Genomes of five susceptible and two resistant cultivars were analyzed and previously known R-genes were selected to find candidate genes for Rcm6. Nucleotide-binding leucine-rich repeat, receptor-like kinase, and receptor-like protein were identified to have putative functional mutations and show differential expression upon the Cm infection. The DNA markers and candidate genes will facilitate marker-assisted breeding and provide genetic insight of bacterial canker resistance in tomato.
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Affiliation(s)
- Alebel Mekuriaw Abebe
- Department of Horticultural Science, Kyungpook National University, Daegu, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Hyoung Tae Kim
- Department of Horticultural Science, Kyungpook National University, Daegu, South Korea
| | - Giwon Choi
- Department of Horticultural Science, Kyungpook National University, Daegu, South Korea
| | - Eunyoung Seo
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Inhwa Yeam
- Department of Horticulture and Breeding, Andong National University, Andong, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu, South Korea
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12
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Martin EC, Spiridon L, Goverse A, Petrescu AJ. NLRexpress-A bundle of machine learning motif predictors-Reveals motif stability underlying plant Nod-like receptors diversity. FRONTIERS IN PLANT SCIENCE 2022; 13:975888. [PMID: 36186050 PMCID: PMC9519389 DOI: 10.3389/fpls.2022.975888] [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: 06/22/2022] [Accepted: 08/19/2022] [Indexed: 05/13/2023]
Abstract
Examination of a collection of over 80,000 Plant Nod-like receptors (NLRs) revealed an overwhelming sequence diversity underlying functional specificity of pathogen detection, signaling and cooperativity. The NLR canonical building blocks-CC/TIR/RPW8, NBS and LRR-contain, however, a number of conserved sequence motifs showing a significant degree of invariance amongst different NLR groups. To identify these motifs we developed NLRexpress-a bundle of 17 machine learning (ML)-based predictors, able to swiftly and precisely detect CC, TIR, NBS, and LRR motifs while minimizing computing time without accuracy losses-aimed as an instrument scalable for screening overall proteomes, transcriptomes or genomes for identifying integral NLRs and discriminating them against incomplete sequences lacking key motifs. These predictors were further used to screen a subset of ∼34,000 regular plant NLR sequences. Motifs were analyzed using unsupervised ML techniques to assess the structural correlations hidden underneath pattern variabilities. Both the NB-ARC switch domain which admittedly is the most conserved region of NLRs and the highly diverse LRR domain with its vastly variable lengths and repeat irregularities-show well-defined relations between motif subclasses, highlighting the importance of structural invariance in shaping NLR sequence diversity. The online NLRexpress webserver can be accessed at https://nlrexpress.biochim.ro.
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Affiliation(s)
- Eliza C. Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Laurentiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Andrei-José Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- *Correspondence: Andrei-José Petrescu,
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13
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Lu M, Feau N, Vidakovic DO, Ukrainetz N, Wong B, Aitken SN, Hamelin RC, Yeaman S. Comparative Gene Expression Analysis Reveals Mechanism of Pinus contorta Response to the Fungal Pathogen Dothistroma septosporum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:397-409. [PMID: 33258711 DOI: 10.1094/mpmi-10-20-0282-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study, we investigated the gene expression response of lodgepole pine (Pinus contorta) to attack by the fungal pathogen Dothistroma septosporum, which causes Dothistroma needle blight, a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two D. septosporum isolates and analyzed the differentially expressed genes (DEGs), differential exon usage, and coexpressed gene modules using RNA-sequencing data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one D. septosporum isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene module-identified genes to the reference plant-pathogen interaction pathway deposited in the Kyoto Encyclopedia of Genes and Genomes database. These genes are present in PAMP-triggered and effector-triggered immunity pathways. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to D. septosporum effectors. Taken together, our results show that gene expression response to D. septosporum infection in lodgepole pine varies both among tree genotypes and pathogen strains and involves both known candidate genes and a number of genes with previously unknown functions.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, Canada
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, Canada
| | - Dragana Obreht Vidakovic
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, Canada
| | - Nicholas Ukrainetz
- Forest Improvement and Research Management Branch, Ministry of Forests, Lands and Natural Resource Operations & Rural Development, 18793-32nd Ave., Surrey, Canada
| | - Barbara Wong
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand 1030, avenue de la Médecine, Québec, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, Canada
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand 1030, avenue de la Médecine, Québec, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, Canada
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14
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Barragan AC, Collenberg M, Wang J, Lee RRQ, Cher WY, Rabanal FA, Ashkenazy H, Weigel D, Chae E. A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana. Mol Biol Evol 2021; 38:557-574. [PMID: 32966577 PMCID: PMC7826191 DOI: 10.1093/molbev/msaa245] [Citation(s) in RCA: 24] [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] [Indexed: 12/11/2022] Open
Abstract
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies 3 weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR (nucleotide-binding site leucine-rich repeat) disease-resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR-PL (leucine-rich repeat [LRR]-post-LRR) region, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the nonrisk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain-a region from which the DM10 risk haplotype is absent-indicating that the ranges of DM10 and DM11 risk alleles may be nonoverlapping.
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Affiliation(s)
- Ana Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jinge Wang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rachelle R Q Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Wei Yuan Cher
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Haim Ashkenazy
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biological Sciences, National University of Singapore, Singapore
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15
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Marchal C, Haberer G, Spannagl M, Uauy C. Comparative Genomics and Functional Studies of Wheat BED-NLR Loci. Genes (Basel) 2020; 11:E1406. [PMID: 33256067 PMCID: PMC7761493 DOI: 10.3390/genes11121406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/30/2020] [Accepted: 05/10/2020] [Indexed: 12/01/2022] Open
Abstract
Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genomic regions and show that, unlike known NLR-ID loci, there is no evidence for a NLR-partner in their vicinity. Using neighbor-network analyses, we observed that BED domains from BED-NLRs share more similarities with BED domains from single-BED proteins and from BED-containing proteins harboring domains that are conserved in transposases. We identified a nuclear localization signal (NLS) in Yr7, Yr5, and the other characterized BED-NLRs. We thus propose that this is a feature of BED-NLRs that confer resistance to plant pathogens. We show that the NLS was functional in truncated versions of the Yr7 protein when expressed in N. benthamiana. We did not observe cell-death upon the overexpression of Yr7 full-length, truncated, and 'MHD' variants in N. benthamiana. This suggests that either this system is not suitable to study BED-NLR signaling or that BED-NLRs require additional components to trigger cell death. These results define novel future directions to further understand the role of BED domains in BED-NLR mediated resistance.
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Affiliation(s)
| | | | - Georg Haberer
- Plant Genome and Systems Biology, Helmholtz Center Munich, D-85764 Neuherberg, Germany; (G.H.); (M.S.)
| | - Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Center Munich, D-85764 Neuherberg, Germany; (G.H.); (M.S.)
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK;
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16
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Xie Z, Yan B, Shou J, Tang J, Wang X, Zhai K, Liu J, Li Q, Luo M, Deng Y, He Z. A nucleotide-binding site-leucine-rich repeat receptor pair confers broad-spectrum disease resistance through physical association in rice. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180308. [PMID: 30967012 DOI: 10.1098/rstb.2018.0308] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rice blast caused by Magnaporthe oryzae is the most destructive fungal disease in crops, greatly threatening rice production and food security worldwide. The identification and utilization of broad-spectrum resistance genes are considered to be the most economic and effective method to control the disease. In the past decade, many blast resistance ( R) genes have been identified, which mainly encode nucleotide-binding leucine-rich repeat (NLR) receptor family and confer limited race-specific resistance to the fungal pathogen. Resistance genes conferring broad-spectrum blast resistance are still largely lacking. In this study, we carried out a map-based cloning of the new blast R locus Pizh in variety ZH11. A bacterial artificial chromosome (BAC) clone of 165 kb spanning the Pizh locus was sequenced and identified 9 NLR genes, among which only Pizh-1 and Pizh-2 were expressed. Genetic complementation experiments indicated that Pizh-1 but not Pizh-2 alone could confer blast resistance. Intriguingly, both mutations on Pizh-1 and Pizh-2 by CRISPR-Cas9 abolished the Pizh-mediated resistance. We also observed that Pizh-1-mediated resistance was partially dependent on Pizh-2. Pizh-1 and Pizh-2 form a complex of NLRs through direct interaction. This suggests that Pizh-1 may function as the executor NLR and Pizh-2 as a 'helper' NLR that shares functional redundancy with other NLRs. Our current study provides not only a good tool for rice disease resistance breeding but also deep insight into NLR association and function in plant immunity. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.
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Affiliation(s)
- Zhen Xie
- 1 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032 , People's Republic of China.,2 College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058 , People's Republic of China
| | - Bingxiao Yan
- 1 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032 , People's Republic of China.,3 University of the Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Jianyao Shou
- 4 Zhuji Agricultural Technology Promotion Center , Zhejiang 311800 , People's Republic of China
| | - Jun Tang
- 1 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032 , People's Republic of China
| | - Xin Wang
- 1 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032 , People's Republic of China
| | - Keran Zhai
- 1 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032 , People's Republic of China
| | - Jiyun Liu
- 1 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032 , People's Republic of China
| | - Qun Li
- 1 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032 , People's Republic of China
| | - Meizhong Luo
- 5 College of Life Science and Technology, Huazhong Agricultural University , Wuhan 430070 , People's Republic of China
| | - Yiwen Deng
- 1 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032 , People's Republic of China
| | - Zuhua He
- 1 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai 200032 , People's Republic of China.,2 College of Agriculture and Biotechnology, Zhejiang University , Hangzhou 310058 , People's Republic of China
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17
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Baudin M, Schreiber KJ, Martin EC, Petrescu AJ, Lewis JD. Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:352-370. [PMID: 31557357 DOI: 10.1111/tpj.14547] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 05/26/2023]
Abstract
NLR (nucleotide-binding [NB] leucine-rich repeat [LRR] receptor) proteins are critical for inducing immune responses in response to pathogen proteins, and must be tightly modulated to prevent spurious activation in the absence of a pathogen. The ZAR1 NLR recognizes diverse effector proteins from Pseudomonas syringae, including HopZ1a, and Xanthomonas species. Receptor-like cytoplasmic kinases (RLCKs) such as ZED1, interact with ZAR1 and provide specificity for different effector proteins, such as HopZ1a. We previously developed a transient expression system in Nicotiana benthamiana that allowed us to demonstrate that ZAR1 function is conserved from the Brassicaceae to the Solanaceae. Here, we combined structural modelling of ZAR1, with molecular and functional assays in our transient system, to show that multiple intramolecular and intermolecular interactions modulate ZAR1 activity. We identified determinants required for the formation of the ZARCC oligomer and its activity. Lastly, we characterized intramolecular interactions between ZAR1 subdomains that participate in keeping ZAR1 immune complexes inactive. This work identifies molecular constraints on immune receptor function and activation.
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Affiliation(s)
- Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
| | - Karl J Schreiber
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
| | - Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Andrei J Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, USA
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18
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Zhang H, Mao R, Wang Y, Zhang L, Wang C, Lv S, Liu X, Wang Y, Ji W. Transcriptome-wide alternative splicing modulation during plant-pathogen interactions in wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110160. [PMID: 31521219 DOI: 10.1016/j.plantsci.2019.05.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/11/2019] [Accepted: 05/29/2019] [Indexed: 05/07/2023]
Abstract
Alternative splicing (AS) enhances the diversities of both transcripts and proteins in eukaryotes, which contribute to stress adaptation. To catalog wheat (Triticum aestivum L.) AS genes, we characterized 45 RNA-seq libraries from wheat seedlings infected by powdery mildew, Blumeria graminis f. sp. tritici (Bgt) or stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst). We discovered that 11.2% and 10.4% of the multiexon genes had AS transcripts during Bgt and Pst infections, respectively. In response to fungal infection, wheat modulated AS not only in disease resistance proteins, but also in splicing related factors. Apart from the stress induced or activated splicing variants by pathogen, the differential expression profiles were fold increased through changing the ratio of full spliced transcripts versus intron retention (IR) transcripts. Comparing AS transcripts produced by the same gene in Bgt with Pst stress, the spliced terminal exons and the stranded introns are independent and different. This demonstrated that differential induction of specific splice variants were activated against two fungal pathogens. The specific induced AS genes in the Pst-resistant plants were enriched in improving the membrane permeability and protein modification ability, whereas gene expression involved in protein translation and transport were strengthened in Pst-susceptible plants.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Rui Mao
- College of Information Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Shikai Lv
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
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19
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Stam R, Silva-Arias GA, Tellier A. Subsets of NLR genes show differential signatures of adaptation during colonization of new habitats. THE NEW PHYTOLOGIST 2019; 224:367-379. [PMID: 31230368 DOI: 10.1111/nph.16017] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
Nucleotide binding site, leucine-rich repeat receptors (NLRs) are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonization of novel habitats in a model tomato species, Solanum chilense. We used R-gene enrichment sequencing to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonization by resequencing whole genomes from three S. chilense plants from three key populations and performing approximate Bayesian computation using data from the 14 populations. Using these parameters, we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution and identified small subsets of outlier NLRs exhibiting signatures of selection across populations. NLRs under selection between habitats are more often helper genes, whereas those showing signatures of adaptation in single populations are more often sensor-NLRs. Thus, centrality in the NLR network does not constrain NLR evolvability, and new mutations in central genes in the network are key for R-gene adaptation during colonization of different habitats.
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Affiliation(s)
- Remco Stam
- Phytopathology, Technical University Munich, 85354, Freising, Germany
- Population Genetics, Technical University Munich, 85354, Freising, Germany
| | | | - Aurelien Tellier
- Population Genetics, Technical University Munich, 85354, Freising, Germany
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20
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Steele JFC, Hughes RK, Banfield MJ. Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor. PLoS One 2019; 14:e0221226. [PMID: 31461469 PMCID: PMC6713354 DOI: 10.1371/journal.pone.0221226] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022] Open
Abstract
Plant NLRs are modular immune receptors that trigger rapid cell death in response to attempted infection by pathogens. A highly conserved nucleotide-binding domain shared with APAF-1, various R-proteins and CED-4 (NB-ARC domain) is proposed to act as a molecular switch, cycling between ADP (repressed) and ATP (active) bound forms. Studies of plant NLR NB-ARC domains have revealed functional similarities to mammalian homologues, and provided insight into potential mechanisms of regulation. However, further advances have been limited by difficulties in obtaining sufficient yields of protein suitable for structural and biochemical techniques. From protein expression screens in Escherichia coli and Sf9 insect cells, we defined suitable conditions to produce the NB-ARC domain from the tomato NLR NRC1. Biophysical analyses of this domain showed it is a folded, soluble protein. Structural studies revealed the NRC1 NB-ARC domain had co-purified with ADP, and confirmed predicted structural similarities between plant NLR NB-ARC domains and their mammalian homologues.
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Affiliation(s)
- John F. C. Steele
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, England, United Kingdom
| | - Richard K. Hughes
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, England, United Kingdom
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, England, United Kingdom
- * E-mail:
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21
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Animal NLRs continue to inform plant NLR structure and function. Arch Biochem Biophys 2019; 670:58-68. [PMID: 31071301 DOI: 10.1016/j.abb.2019.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/10/2019] [Accepted: 05/01/2019] [Indexed: 12/22/2022]
Abstract
Plant NLRs share many of the structural hallmarks of their animal counterparts. At a functional level, the central nucleotide-binding pocket appears to have binding and hydrolysis activities, similar to that of animal NLRs. The TIR domains of plant NLRs have been shown to self-associate, and there is emerging evidence that full-length plant NLRs may do so as well. It is therefore tempting to speculate that plant NLRs may form higher-order complexes similar to those of the mammalian inflammasome. Here we review the available knowledge on structure-function relationships in plant NLRs, focusing on how the information available on animal NLRs informs the mechanism of plant NLR function, and highlight the evidence that innate immunity signalling pathways in multicellular organisms often require the formation of higher-order protein complexes.
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22
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Araújo ACD, Fonseca FCDA, Cotta MG, Alves GSC, Miller RNG. Plant NLR receptor proteins and their potential in the development of durable genetic resistance to biotic stresses. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biori.2020.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Abstract
The first plant disease resistance (R) genes were identified and cloned more than two decades ago. Since then, many more R genes have been identified and characterized in numerous plant pathosystems. Most of these encode members of the large family of intracellular NLRs (NOD-like receptors), which also includes animal immune receptors. New discoveries in this expanding field of research provide new elements for our understanding of plant NLR function. But what do we know about plant NLR function today? Genetic, structural, and functional analyses have uncovered a number of commonalities and differences in pathogen recognition strategies as well as how NLRs are regulated and activate defense signaling, but many unknowns remain. This review gives an update on the latest discoveries and breakthroughs in this field, with an emphasis on structural findings and some comparison to animal NLRs, which can provide additional insights and paradigms in plant NLR function.
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Affiliation(s)
- Xiaoxiao Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
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Bentham A, Burdett H, Anderson PA, Williams SJ, Kobe B. Animal NLRs provide structural insights into plant NLR function. ANNALS OF BOTANY 2017; 119:827-702. [PMID: 27562749 PMCID: PMC5378188 DOI: 10.1093/aob/mcw171] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 05/26/2016] [Accepted: 06/07/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND The plant immune system employs intracellular NLRs (nucleotide binding [NB], leucine-rich repeat [LRR]/nucleotide-binding oligomerization domain [NOD]-like receptors) to detect effector proteins secreted into the plant cell by potential pathogens. Activated plant NLRs trigger a range of immune responses, collectively known as the hypersensitive response (HR), which culminates in death of the infected cell. Plant NLRs show structural and functional resemblance to animal NLRs involved in inflammatory and innate immune responses. Therefore, knowledge of the activation and regulation of animal NLRs can help us understand the mechanism of action of plant NLRs, and vice versa. SCOPE This review provides an overview of the innate immune pathways in plants and animals, focusing on the available structural and biochemical information available for both plant and animal NLRs. We highlight the gap in knowledge between the animal and plant systems, in particular the lack of structural information for plant NLRs, with crystal structures only available for the N-terminal domains of plant NLRs and an integrated decoy domain, in contrast to the more complete structures available for animal NLRs. We assess the similarities and differences between plant and animal NLRs, and use the structural information on the animal NLR pair NAIP/NLRC4 to derive a plausible model for plant NLR activation. CONCLUSIONS Signalling by cooperative assembly formation (SCAF) appears to operate in most innate immunity pathways, including plant and animal NLRs. Our proposed model of plant NLR activation includes three key steps: (1) initially, the NLR exists in an inactive auto-inhibited state; (2) a combination of binding by activating elicitor and ATP leads to a structural rearrangement of the NLR; and (3) signalling occurs through cooperative assembly of the resistosome. Further studies, structural and biochemical in particular, will be required to provide additional evidence for the different features of this model and shed light on the many existing variations, e.g. helper NLRs and NLRs containing integrated decoys.
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Affiliation(s)
- Adam Bentham
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hayden Burdett
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Peter A. Anderson
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Simon J. Williams
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- For correspondence. E-mail
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de Wit PJGM. Cladosporium fulvum Effectors: Weapons in the Arms Race with Tomato. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:1-23. [PMID: 27215970 DOI: 10.1146/annurev-phyto-011516-040249] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In this review, I recount my personal history. My drive to study host-pathogen interactions was to find alternatives for agrochemicals, which was triggered after reading the book "Silent Spring" by Rachel Carson. I reflect on my research at the Laboratory of Phytopathology at Wageningen University, where I have worked for my entire career on the interaction between Cladosporium fulvum and tomato, and related gene-for-gene pathosystems. I describe different methods used to identify and sequence avirulence (Avr) genes from the pathogen and resistance (R) genes from the host. The major genes involved in classical gene-for-gene interactions have now been identified, and breeders can produce plants with multiple R genes providing durable and environmentally safe protection against pathogens. In some cases, this might require the use of genetically modified plants when R genes cannot be introduced by classical breeding.
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Affiliation(s)
- Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University, 6700 AA, Wageningen, The Netherlands; ,
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Sukarta OCA, Slootweg EJ, Goverse A. Structure-informed insights for NLR functioning in plant immunity. Semin Cell Dev Biol 2016; 56:134-149. [PMID: 27208725 DOI: 10.1016/j.semcdb.2016.05.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 01/07/2023]
Abstract
To respond to foreign invaders, plants have evolved a cell autonomous multilayered immune system consisting of extra- and intracellular immune receptors. Nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs) mediate recognition of pathogen effectors inside the cell and trigger a host specific defense response, often involving controlled cell death. NLRs consist of a central nucleotide-binding domain, which is flanked by an N-terminal CC or TIR domain and a C-terminal leucine-rich repeat domain (LRR). These multidomain proteins function as a molecular switch and their activity is tightly controlled by intra and inter-molecular interactions. In contrast to metazoan NLRs, the structural basis underlying NLR functioning as a pathogen sensor and activator of immune responses in plants is largely unknown. However, the first crystal structures of a number of plant NLR domains were recently obtained. In addition, biochemical and structure-informed analyses revealed novel insights in the cooperation between NLR domains and the formation of pre- and post activation complexes, including the coordinated activity of NLR pairs as pathogen sensor and executor of immune responses. Moreover, the discovery of novel integrated domains underscores the structural diversity of NLRs and provides alternative models for how these immune receptors function in plants. In this review, we will highlight these recent advances to provide novel insights in the structural, biochemical and molecular aspects involved in plant NLR functioning.
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Affiliation(s)
- Octavina C A Sukarta
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Erik J Slootweg
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Aska Goverse
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Wu CH, Belhaj K, Bozkurt TO, Birk MS, Kamoun S. Helper NLR proteins NRC2a/b and NRC3 but not NRC1 are required for Pto-mediated cell death and resistance in Nicotiana benthamiana. THE NEW PHYTOLOGIST 2016; 209:1344-52. [PMID: 26592988 DOI: 10.1111/nph.13764] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Affiliation(s)
- Chih-Hang Wu
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Khaoula Belhaj
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Tolga O Bozkurt
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Marlène S Birk
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
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