1
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Sutherland CA, Stevens DM, Seong K, Wei W, Krasileva KV. The resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops. THE PLANT CELL 2025; 37:koaf109. [PMID: 40344182 PMCID: PMC12118082 DOI: 10.1093/plcell/koaf109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 04/17/2025] [Accepted: 04/21/2025] [Indexed: 05/11/2025]
Abstract
Plants rely on germline-encoded, innate immune receptors to sense pathogens and initiate the defense response. The exponential increase in quality and quantity of genomes, RNA-seq datasets, and protein structures has underscored the incredible biodiversity of plant immunity. Arabidopsis continues to serve as a valuable model and theoretical foundation of our understanding of wild plant diversity of immune receptors, while expansion of study into agricultural crops has also revealed distinct evolutionary trajectories and challenges. Here, we provide the classical context for study of both intracellular nucleotide-binding, leucine-rich repeat receptors and surface-localized pattern recognition receptors at the levels of DNA sequences, transcriptional regulation, and protein structures. We then examine how recent technology has shaped our understanding of immune receptor evolution and informed our ability to efficiently engineer resistance. We summarize current literature and provide an outlook on how researchers take inspiration from natural diversity in bioengineering efforts for disease resistance from Arabidopsis and other model systems to crops.
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Affiliation(s)
- Chandler A Sutherland
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Danielle M Stevens
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Wei Wei
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
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2
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Robinson K, Buric L, Grenz K, Chia KS, Hulin MT, Ma W, Carella P. Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants. Curr Biol 2025; 35:1861-1869.e3. [PMID: 40174585 DOI: 10.1016/j.cub.2025.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 02/09/2025] [Accepted: 03/11/2025] [Indexed: 04/04/2025]
Abstract
Plant pathogenic Pseudomonas species naturally antagonize a diverse range of flowering plants. While emerging research demonstrates that isolates belonging to the P. syringae species complex colonize diverse hosts, the extent to which these bacteria naturally infect non-flowering plants like the model liverwort Marchantia polymorpha remains unclear. Here, we identify natural associations between Pseudomonas viridiflava and the liverwort Marchantia polymorpha. Pseudomonas bacteria isolated from diseased liverworts in the wild successfully re-infected M. polymorpha under pure culture conditions, producing high in planta bacterial densities and causing prominent tissue maceration. Comparative genomic analysis of Marchantia-associated P. viridiflava identified core virulence machinery like the type III secretion system (T3SS) and conserved effectors (AvrE and HopM1) that were essential for liverwort infection. Disease assays performed in Nicotiana benthamiana further confirmed that liverwort-associated P. viridiflava infect flowering plants in an effector-dependent manner. Our work highlights P. viridiflava as an effective broad host pathogen that relies on conserved virulence factors to manipulate evolutionarily divergent host plants.
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Affiliation(s)
- Kayla Robinson
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Lucia Buric
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Kristina Grenz
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Khong-Sam Chia
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Michelle T Hulin
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
| | - Wenbo Ma
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
| | - Philip Carella
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK.
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3
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Guo S, Zhang F, Du X, Zhang X, Huang X, Li Z, Zhang Y, Gan P, Li H, Li M, Wang X, Tang C, Wang X, Kang Z, Zhang X. TaANK-TPR1 enhances wheat resistance against stripe rust via controlling gene expression and protein activity of NLR protein TaRPP13L1. Dev Cell 2025:S1534-5807(25)00037-1. [PMID: 39954677 DOI: 10.1016/j.devcel.2025.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Revised: 11/22/2024] [Accepted: 01/27/2025] [Indexed: 02/17/2025]
Abstract
Nucleotide-binding site, leucine-rich repeat (NLR) proteins activate a robust immune response on recognition of pathogen invasion. However, the function and regulatory mechanisms of NLRs during Puccinia striiformis f. sp. tritici (Pst) infection in wheat remain elusive. Here, we identify an ankyrin (ANK) repeat and tetratricopeptide repeat (TPR)-containing protein, TaANK-TPR1, which plays a positive role in the regulation of wheat resistance against Pst and the immune response of NLR. TaANK-TPR1 targets the NLR protein TaRPP13L1 (Recognition of PeronosporaParasitica 13-like 1) to facilitate its homodimerization and cell death to enhance the resistance of wheat against Pst. Meanwhile, TaANK-TPR1 binds to the TGACGT motif (methyl jasmonate-responsive element) of the TaRPP13L1 promoter and activates TaRPP13L1 transcription. Both TaANK-TPR1 and TaRPP13L1 respond to jasmonic acid (JA) signaling via the TGACGT element. Importantly, overexpressing TaRPP13L1 confers robust rust resistance without impacting important agronomic traits in the field. These findings identify a regulatory mechanism of NLR protein and provide targets for improving crop disease resistance.
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Affiliation(s)
- Shuangyuan Guo
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Feng Zhang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoya Du
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmei Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China; College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xueling Huang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zelong Li
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanqin Zhang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengfei Gan
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huankun Li
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Li
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinyue Wang
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojie Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xinmei Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China; College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China.
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4
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Huang S, Li E, Jia F, Han Z, Chai J. Assembly and functional mechanisms of plant NLR resistosomes. Curr Opin Struct Biol 2025; 90:102977. [PMID: 39808854 DOI: 10.1016/j.sbi.2024.102977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Revised: 12/10/2024] [Accepted: 12/11/2024] [Indexed: 01/16/2025]
Abstract
Nucleotide-binding and leucine-rich repeat (NLR) proteins are essential intracellular immune receptors in both animal and plant kingdoms. Sensing of pathogen-derived signals induces oligomerization of NLR proteins, culminating in the formation of higher-order protein complexes known as resistosomes in plants. The NLR resistosomes play a pivotal role in mediating the plant immune response against invading pathogens. Over the past few years, our understanding of NLR biology has significantly advanced, particularly in the structural and biochemical aspects of the NLR resistosomes. Here, we highlight the recent advancements in the structural knowledge of how NLR resistosomes are activated and assembled, and how the structural knowledge provides insights into the biochemical functions of these NLR resistosomes, which converge on Ca2+ signals. Signaling mechanisms of the resistosomes that underpin plant immunity are also briefly discussed.
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Affiliation(s)
- Shijia Huang
- School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China
| | - Ertong Li
- School of Pharmaceutical Sciences, Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Zhengzhou University, Zhengzhou 450000, China.
| | - Fangshuai Jia
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Zhifu Han
- School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China
| | - Jijie Chai
- School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China.
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5
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Grenz K, Chia KS, Turley EK, Tyszka AS, Atkinson RE, Reeves J, Vickers M, Rejzek M, Walker JF, Carella P. A necrotizing toxin enables Pseudomonas syringae infection across evolutionarily divergent plants. Cell Host Microbe 2025; 33:20-29.e5. [PMID: 39706183 DOI: 10.1016/j.chom.2024.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 11/01/2024] [Accepted: 11/25/2024] [Indexed: 12/23/2024]
Abstract
The Pseudomonas syringae species complex harbors a diverse range of pathogenic bacteria that can infect hosts across the plant kingdom. However, much of our current understanding of P. syringae is centered on its infection of flowering plants. We took a comparative approach to understand how P. syringae infects evolutionarily divergent plants. We identified P. syringae isolates causing disease in the liverwort Marchantia polymorpha, the fern Ceratopteris richardii, and the flowering plant Nicotiana benthamiana, which last shared a common ancestor >500 million years ago. Phytotoxin-enriched phylogroup (PG) 2 isolates of P. syringae are virulent in non-flowering plants, relying on type-3 effectors and the lipopeptide phytotoxin syringomycin. Ectopic syringomycin promotes tissue necrosis, activates conserved stress-related genes, and enhances in planta bacterial growth of toxin-deficient PGs in Marchantia. Collectively, our research reveals a key role for syringomycin in promoting Pseudomonas colonization, which works alongside effectors to antagonize an exceptionally wide spectrum of land plants.
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Affiliation(s)
- Kristina Grenz
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Khong-Sam Chia
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Emma K Turley
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Alexa S Tyszka
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | - Jacob Reeves
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Martin Vickers
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Martin Rejzek
- Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK
| | - Joseph F Walker
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Philip Carella
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK.
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6
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Qin H, Cheng J, Han GZ, Gong Z. Phylogenomic insights into the diversity and evolution of RPW8-NLRs and their partners in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:1032-1046. [PMID: 39312623 DOI: 10.1111/tpj.17034] [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: 06/20/2024] [Revised: 09/05/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024]
Abstract
Plants use nucleotide-binding leucine-rich repeat receptors (NLRs) to sense pathogen effectors, initiating effector-triggered immunity (ETI). NLRs containing RESISTANCE TO POWDERY MILDEW 8 domain (RNLs) function as "helper" NLRs in flowering plants and support the immune responses mediated by "sensor" NLRs in cooperation with lipase-EP domain fused proteins (EP proteins). Despite their crucial roles in ETI, much remains unclear about the evolutionary trajectories of RNLs and their functional partners EP proteins. Here, we perform phylogenomic analyses of RNLs in 90 plants, covering the major diversity of plants, and identify the presence of RNLs in land plants and green algae, expanding the distribution of RNLs. We uncover a neglected major RNL group in gymnosperms, besides the canonical major group with NRG1s and ADR1s, and observe a drastic increase in RNL repertoire size in conifers. Phylogenetic analyses indicate that RNLs originated multiple times through domain shuffling, and the evolution of RNLs underwent a birth-and-death process. Moreover, we trace the origin of EP proteins back to the last common ancestor of vascular plants. We find that both RNLs and EP proteins evolve mainly under negative selection, revealing strong constraints on their function. Concerted losses and positive correlation in copy number are observed between RNL and EP sublineages, suggesting their cooperation in function. Together, our findings provide insights into the origin and evolution of plant helper NLRs, with implications for predicting novel innate immune signaling modules.
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Affiliation(s)
- Huiyu Qin
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Junyuan Cheng
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Zhen Gong
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
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7
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Sunil S, Beeh S, Stöbbe E, Fischer K, Wilhelm F, Meral A, Paris C, Teasdale L, Jiang Z, Zhang L, Urban M, Aguilar Parras E, Nürnberger T, Weigel D, Lozano-Duran R, El Kasmi F. Activation of an atypical plant NLR with an N-terminal deletion initiates cell death at the vacuole. EMBO Rep 2024; 25:4358-4386. [PMID: 39242777 PMCID: PMC11467418 DOI: 10.1038/s44319-024-00240-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 07/26/2024] [Accepted: 08/12/2024] [Indexed: 09/09/2024] Open
Abstract
Plants evolve nucleotide-binding leucine-rich repeat receptors (NLRs) to induce immunity. Activated coiled-coil (CC) domain containing NLRs (CNLs) oligomerize and form apparent cation channels promoting calcium influx and cell death, with the alpha-1 helix of the individual CC domains penetrating the plasma membranes. Some CNLs are characterized by putative N-myristoylation and S-acylation sites in their CC domain, potentially mediating permanent membrane association. Whether activated Potentially Membrane Localized NLRs (PMLs) mediate cell death and calcium influx in a similar way is unknown. We uncovered the cell-death function at the vacuole of an atypical but conserved Arabidopsis PML, PML5, which has a significant deletion in its CCG10/GA domain. Active PML5 oligomers localize in Golgi membranes and the tonoplast, alter vacuolar morphology, and induce cell death, with the short N-terminus being sufficient. Mutant analysis supports a potential role of PMLs in plant immunity. PML5-like deletions are found in several Brassicales paralogs, pointing to the evolutionary importance of this innovation. PML5, with its minimal CC domain, represents the first identified CNL utilizing vacuolar-stored calcium for cell death induction.
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Affiliation(s)
- Sruthi Sunil
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Simon Beeh
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Eva Stöbbe
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Kathrin Fischer
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Franziska Wilhelm
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Aron Meral
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Celia Paris
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Luisa Teasdale
- Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Zhihao Jiang
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Lisha Zhang
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Moritz Urban
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Emmanuel Aguilar Parras
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Depto. Biología Celular, Genética y Fisiología, 29010, Málaga, Spain
| | - Thorsten Nürnberger
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany
| | - Rosa Lozano-Duran
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Farid El Kasmi
- Centre for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany.
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8
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Ros-Moner E, Jiménez-Góngora T, Villar-Martín L, Vogrinec L, González-Miguel VM, Kutnjak D, Rubio-Somoza I. Conservation of molecular responses upon viral infection in the non-vascular plant Marchantia polymorpha. Nat Commun 2024; 15:8326. [PMID: 39333479 PMCID: PMC11436993 DOI: 10.1038/s41467-024-52610-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 09/12/2024] [Indexed: 09/29/2024] Open
Abstract
After plants transitioned from water to land around 450 million years ago, they faced novel pathogenic microbes. Their colonization of diverse habitats was driven by anatomical innovations like roots, stomata, and vascular tissue, which became central to plant-microbe interactions. However, the impact of these innovations on plant immunity and pathogen infection strategies remains poorly understood. Here, we explore plant-virus interactions in the bryophyte Marchantia polymorpha to gain insights into the evolution of these relationships. Virome analysis reveals that Marchantia is predominantly associated with RNA viruses. Comparative studies with tobacco mosaic virus (TMV) show that Marchantia shares core defense responses with vascular plants but also exhibits unique features, such as a sustained wound response preventing viral spread. Additionally, general defense responses in Marchantia are equivalent to those restricted to vascular tissues in Nicotiana, suggesting that evolutionary acquisition of developmental innovations results in re-routing of defense responses in vascular plants.
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Affiliation(s)
- Eric Ros-Moner
- Molecular Reprogramming and Evolution (MoRE) Laboratory, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB-Edifci CRAG, Cerdanyola del Vallés, Spain
| | - Tamara Jiménez-Góngora
- Molecular Reprogramming and Evolution (MoRE) Laboratory, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB-Edifci CRAG, Cerdanyola del Vallés, Spain
| | - Luis Villar-Martín
- Molecular Reprogramming and Evolution (MoRE) Laboratory, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB-Edifci CRAG, Cerdanyola del Vallés, Spain
| | - Lana Vogrinec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Víctor M González-Miguel
- Data Analysis area, Bioinformatics Core Unit, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB-Edifci CRAG, Cerdanyola del Vallés, Spain
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution (MoRE) Laboratory, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB-Edifci CRAG, Cerdanyola del Vallés, Spain.
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
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9
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Goh FJ, Huang CY, Derevnina L, Wu CH. NRC Immune receptor networks show diversified hierarchical genetic architecture across plant lineages. THE PLANT CELL 2024; 36:3399-3418. [PMID: 38922300 PMCID: PMC11371147 DOI: 10.1093/plcell/koae179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/28/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024]
Abstract
Plants' complex immune systems include nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins, which help recognize invading pathogens. In solanaceous plants, the NRC (NLR required for cell death) family includes helper NLRs that form a complex genetic network with multiple sensor NLRs to provide resistance against pathogens. However, the evolution and function of NRC networks outside solanaceous plants are currently unclear. Here, we conducted phylogenomic and macroevolutionary analyses comparing NLRs identified from different asterid lineages and found that NRC networks expanded significantly in most lamiids but not in Ericales and campanulids. Using transient expression assays in Nicotiana benthamiana, we showed that NRC networks are simple in Ericales and campanulids, but have high complexity in lamiids. Phylogenetic analyses grouped the NRC helper NLRs into three NRC0 subclades that are conserved, and several family-specific NRC subclades of lamiids that show signatures of diversifying selection. Functional analyses revealed that members of the NRC0 subclades are partially interchangeable, whereas family-specific NRC members in lamiids lack interchangeability. Our findings highlight the distinctive evolutionary patterns of the NRC networks in asterids and provide potential insights into transferring disease resistance across plant lineages.
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Affiliation(s)
- Foong-Jing Goh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei 115201, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 402202, Taiwan
| | - Ching-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Lida Derevnina
- Crop Science Centre, Department of Plant Science, University of Cambridge, Cambridge CB3 0LE, UK
| | - Chih-Hang Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei 115201, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 402202, Taiwan
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10
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Feng XY, Li Q, Liu Y, Zhang YM, Shao ZQ. Evolutionary and immune-activating character analyses of NLR genes in algae suggest the ancient origin of plant intracellular immune receptors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2316-2330. [PMID: 38972042 DOI: 10.1111/tpj.16919] [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: 01/15/2024] [Revised: 04/24/2024] [Accepted: 06/18/2024] [Indexed: 07/09/2024]
Abstract
Nucleotide-binding leucine-rich repeat (NLR) proteins are crucial intracellular immune receptors in plants, responsible for detecting invading pathogens and initiating defense responses. While previous studies on the evolution and function of NLR genes were mainly limited to land plants, the evolutionary trajectory and immune-activating character of NLR genes in algae remain less explored. In this study, genome-wide NLR gene analysis was conducted on 44 chlorophyte species across seven classes and seven charophyte species across five classes. A few but variable number of NLR genes, ranging from one to 20, were identified in five chlorophytes and three charophytes, whereas no NLR gene was identified from the remaining algal genomes. Compared with land plants, algal genomes possess fewer or usually no NLR genes, implying that the expansion of NLR genes in land plants can be attributed to their adaptation to the more complex terrestrial pathogen environments. Through phylogenetic analysis, domain composition analysis, and conserved motifs profiling of the NBS domain, we detected shared and lineage-specific features between NLR genes in algae and land plants, supporting the common origin and continuous evolution of green plant NLR genes. Immune-activation assays revealed that both TNL and RNL proteins from green algae can elicit hypersensitive responses in Nicotiana benthamiana, indicating the molecular basis for immune activation has emerged in the early evolutionary stage of different types of NLR proteins. In summary, the results from this study suggest that NLR proteins may have taken a role as intracellular immune receptors in the common ancestor of green plants.
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Affiliation(s)
- Xing-Yu Feng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Qian Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yan-Mei Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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Busche M, Laflamme B. From algae to apples: The structural and functional conservation of NLRs. THE PLANT CELL 2024; 36:2453-2454. [PMID: 38683733 PMCID: PMC11218760 DOI: 10.1093/plcell/koae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Michael Busche
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Bradley Laflamme
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
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