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Cai W, Tao Y, Cheng X, Wan M, Gan J, Yang S, Okita TW, He S, Tian L. CaIAA2-CaARF9 module mediates the trade-off between pepper growth and immunity. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2054-2074. [PMID: 38450864 PMCID: PMC11182598 DOI: 10.1111/pbi.14325] [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: 11/27/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024]
Abstract
To challenge the invasion of various pathogens, plants re-direct their resources from plant growth to an innate immune defence system. However, the underlying mechanism that coordinates the induction of the host immune response and the suppression of plant growth remains unclear. Here we demonstrate that an auxin response factor, CaARF9, has dual roles in enhancing the immune resistance to Ralstonia solanacearum infection and in retarding plant growth by repressing the expression of its target genes as exemplified by Casmc4, CaLBD37, CaAPK1b and CaRROP1. The expression of these target genes not only stimulates plant growth but also negatively impacts pepper resistance to R. solanacearum. Under normal conditions, the expression of Casmc4, CaLBD37, CaAPK1b and CaRROP1 is active when promoter-bound CaARF9 is complexed with CaIAA2. Under R. solanacearum infection, however, degradation of CaIAA2 is triggered by SA and JA-mediated signalling defence by the ubiquitin-proteasome system, which enables CaARF9 in the absence of CaIAA2 to repress the expression of Casmc4, CaLBD37, CaAPK1b and CaRROP1 and, in turn, impeding plant growth while facilitating plant defence to R. solanacearum infection. Our findings uncover an exquisite mechanism underlying the trade-off between plant growth and immunity mediated by the transcriptional repressor CaARF9 and its deactivation when complexed with CaIAA2.
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Affiliation(s)
- Weiwei Cai
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture ScienceZhejiang A&F UniversityHangzhouZhejiangChina
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural AffairsZhejiang A&F UniversityHangzhouZhejiangChina
| | - Yilin Tao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture ScienceZhejiang A&F UniversityHangzhouZhejiangChina
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural AffairsZhejiang A&F UniversityHangzhouZhejiangChina
| | - Xingge Cheng
- Agricultural CollegeFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Meiyun Wan
- Agricultural CollegeFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Jianghuang Gan
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture ScienceZhejiang A&F UniversityHangzhouZhejiangChina
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural AffairsZhejiang A&F UniversityHangzhouZhejiangChina
| | - Sheng Yang
- Agricultural CollegeFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Thomas W. Okita
- Institute of Biological ChemistryWashington State UniversityPullmanWashingtonUSA
| | - Shuilin He
- Agricultural CollegeFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Li Tian
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture ScienceZhejiang A&F UniversityHangzhouZhejiangChina
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural AffairsZhejiang A&F UniversityHangzhouZhejiangChina
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2
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Yang Y, Furzer OJ, Fensterle EP, Lin S, Zheng Z, Kim NH, Wan L, Dangl JL. Paired plant immune CHS3-CSA1 receptor alleles form distinct hetero-oligomeric complexes. Science 2024; 383:eadk3468. [PMID: 38359131 PMCID: PMC11298796 DOI: 10.1126/science.adk3468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024]
Abstract
Plant intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) analyzed to date oligomerize and form resistosomes upon activation to initiate immune responses. Some NLRs are encoded in tightly linked co-regulated head-to-head genes whose products function together as pairs. We uncover the oligomerization requirements for different Arabidopsis paired CHS3-CSA1 alleles. These pairs form resting-state heterodimers that oligomerize into complexes distinct from NLRs analyzed previously. Oligomerization requires both conserved and allele-specific features of the respective CHS3 and CSA1 Toll-like interleukin-1 receptor (TIR) domains. The receptor kinases BAK1 and BIRs inhibit CHS3-CSA1 pair oligomerization to maintain the CHS3-CSA1 heterodimer in an inactive state. Our study reveals that paired NLRs hetero-oligomerize and likely form a distinctive "dimer of heterodimers" and that structural heterogeneity is expected even among alleles of closely related paired NLRs.
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Affiliation(s)
- Yu Yang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Oliver J. Furzer
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eleanor P. Fensterle
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shu Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Zhiyu Zheng
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nak Hyun Kim
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Li Wan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Wei W, Wu X, Garcia A, McCoppin N, Viana JPG, Murad PS, Walker DR, Hartman GL, Domier LL, Hudson ME, Clough SJ. An NBS-LRR protein in the Rpp1 locus negates the dominance of Rpp1-mediated resistance against Phakopsora pachyrhizi in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:915-933. [PMID: 36424366 DOI: 10.1111/tpj.16038] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/01/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The soybean Rpp1 locus confers resistance to Phakopsora pachyrhizi, causal agent of rust, and resistance is usually dominant over susceptibility. However, dominance of Rpp1-mediated resistance is lost when a resistant genotype (Rpp1 or Rpp1b) is crossed with susceptible line TMG06_0011, and the mechanism of this dominant susceptibility (DS) is unknown. Sequencing the Rpp1 region reveals that the TMG06_0011 Rpp1 locus has a single nucleotide-binding site leucine-rich repeat (NBS-LRR) gene (DS-R), whereas resistant PI 594760B (Rpp1b) is similar to PI 200492 (Rpp1) and has three NBS-LRR resistance gene candidates. Evidence that DS-R is the cause of DS was reflected in virus-induced gene silencing of DS-R in Rpp1b/DS-R or Rpp1/DS-R heterozygous plants with resistance partially restored. In heterozygous Rpp1b/DS-R plants, expression of Rpp1b candidate genes was not significantly altered, indicating no effect of DS-R on transcription. Physical interaction of the DS-R protein with candidate Rpp1b resistance proteins was supported by yeast two-hybrid studies and in silico modeling. Thus, we conclude that suppression of resistance most likely does not occur at the transcript level, but instead probably at the protein level, possibly with Rpp1 function inhibited by binding to the DS-R protein. The DS-R gene was found in other soybean lines, with an estimated allele frequency of 6% in a diverse population, and also found in wild soybean (Glycine soja). The identification of a dominant susceptible NBS-LRR gene provides insight into the behavior of NBS-LRR proteins and serves as a reminder to breeders that the dominance of an R gene can be influenced by a susceptibility allele.
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Affiliation(s)
- Wei Wei
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Xing Wu
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Ave # 266, New Haven, CT, 06511, USA
| | - Alexandre Garcia
- Tropical Melhoramento e Genética, LTDA, Rodovia Celso Garcia Cid, Km 87, Cambé, PR, CEP: 86183-600, Brazil
| | - Nancy McCoppin
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - João Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Praerona S Murad
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - David R Walker
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - Glen L Hartman
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Steven J Clough
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
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Allelic variation in the Arabidopsis TNL CHS3/CSA1 immune receptor pair reveals two functional cell-death regulatory modes. Cell Host Microbe 2022; 30:1701-1716.e5. [PMID: 36257318 DOI: 10.1016/j.chom.2022.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/19/2022] [Accepted: 09/20/2022] [Indexed: 01/26/2023]
Abstract
Some plant NLR immune receptors are encoded in head-to-head "sensor-executor" pairs that function together. Alleles of the NLR pair CHS3/CSA1 form three clades. The clade 1 sensor CHS3 contains an integrated domain (ID) with homology to regulatory domains, which is lacking in clades 2 and 3. In this study, we defined two cell-death regulatory modes for CHS3/CSA1 pairs. One is mediated by ID domain on clade 1 CHS3, and the other relies on CHS3/CSA1 pairs from all clades detecting perturbation of an associated pattern-recognition receptor (PRR) co-receptor. Our data support the hypothesis that an ancestral Arabidopsis CHS3/CSA1 pair gained a second recognition specificity and regulatory mechanism through ID acquisition while retaining its original specificity as a "guard" against PRR co-receptor perturbation. This likely comes with a cost, since both ID and non-ID alleles of the pair persist in diverse Arabidopsis populations through balancing selection.
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Marchal C, Michalopoulou VA, Zou Z, Cevik V, Sarris PF. Show me your ID: NLR immune receptors with integrated domains in plants. Essays Biochem 2022; 66:527-539. [PMID: 35635051 PMCID: PMC9528084 DOI: 10.1042/ebc20210084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 02/07/2023]
Abstract
Nucleotide-binding and leucine-rich repeat receptors (NLRs) are intracellular plant immune receptors that recognize pathogen effectors secreted into the plant cell. Canonical NLRs typically contain three conserved domains including a central nucleotide binding (NB-ARC) domain, C-terminal leucine-rich repeats (LRRs) and an N-terminal domain. A subfamily of plant NLRs contain additional noncanonical domain(s) that have potentially evolved from the integration of the effector targets in the canonical NLR structure. These NLRs with extra domains are thus referred to as NLRs with integrated domains (NLR-IDs). Here, we first summarize our current understanding of NLR-ID activation upon effector binding, focusing on the NLR pairs Pik-1/Pik-2, RGA4/RGA5, and RRS1/RPS4. We speculate on their potential oligomerization into resistosomes as it was recently shown for certain canonical plant NLRs. Furthermore, we discuss how our growing understanding of the mode of action of NLR-ID continuously informs engineering approaches to design new resistance specificities in the context of rapidly evolving pathogens.
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Affiliation(s)
- Clemence Marchal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
| | - Vassiliki A Michalopoulou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Crete, Greece
| | - Zhou Zou
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath BA2 7AY, United Kingdom
| | - Volkan Cevik
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath BA2 7AY, United Kingdom
| | - Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Crete, Greece
- Department of Biology, University of Crete, 714 09 Heraklion, Crete, Greece
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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Zhang B, Liu M, Wang Y, Yuan W, Zhang H. Plant NLRs: Evolving with pathogen effectors and engineerable to improve resistance. Front Microbiol 2022; 13:1018504. [PMID: 36246279 PMCID: PMC9554439 DOI: 10.3389/fmicb.2022.1018504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Pathogens are important threats to many plants throughout their lifetimes. Plants have developed different strategies to overcome them. In the plant immunity system, nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) are the most common components. And recent studies have greatly expanded our understanding of how NLRs function in plants. In this review, we summarize the studies on the mechanism of NLRs in the processes of effector recognition, resistosome formation, and defense activation. Typical NLRs are divided into three groups according to the different domains at their N termini and function in interrelated ways in immunity. Atypical NLRs contain additional integrated domains (IDs), some of which directly interact with pathogen effectors. Plant NLRs evolve with pathogen effectors and exhibit specific recognition. Meanwhile, some NLRs have been successfully engineered to confer resistance to new pathogens based on accumulated studies. In summary, some pioneering processes have been obtained in NLR researches, though more questions arise as a result of the huge number of NLRs. However, with a broadened understanding of the mechanism, NLRs will be important components for engineering in plant resistance improvement.
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