1
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Jones JDG, Staskawicz BJ, Dangl JL. The plant immune system: From discovery to deployment. Cell 2024; 187:2095-2116. [PMID: 38670067 DOI: 10.1016/j.cell.2024.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/08/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
Plant diseases cause famines, drive human migration, and present challenges to agricultural sustainability as pathogen ranges shift under climate change. Plant breeders discovered Mendelian genetic loci conferring disease resistance to specific pathogen isolates over 100 years ago. Subsequent breeding for disease resistance underpins modern agriculture and, along with the emergence and focus on model plants for genetics and genomics research, has provided rich resources for molecular biological exploration over the last 50 years. These studies led to the identification of extracellular and intracellular receptors that convert recognition of extracellular microbe-encoded molecular patterns or intracellular pathogen-delivered virulence effectors into defense activation. These receptor systems, and downstream responses, define plant immune systems that have evolved since the migration of plants to land ∼500 million years ago. Our current understanding of plant immune systems provides the platform for development of rational resistance enhancement to control the many diseases that continue to plague crop production.
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Affiliation(s)
- Jonathan D G Jones
- Sainsbury Lab, University of East Anglia, Colney Lane, Norwich NR4 7UH, UK.
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology and Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill and Howard Hughes Medical Institute, Chapel Hill, NC 27599, USA
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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 DOI: 10.1126/science.adk3468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [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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3
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Russ D, Fitzpatrick CR, Teixeira PJPL, Dangl JL. Deep discovery informs difficult deployment in plant microbiome science. Cell 2023; 186:4496-4513. [PMID: 37832524 DOI: 10.1016/j.cell.2023.08.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 10/15/2023]
Abstract
Plant-associated microbiota can extend plant immune system function, improve nutrient acquisition and availability, and alleviate abiotic stresses. Thus, naturally beneficial microbial therapeutics are enticing tools to improve plant productivity. The basic definition of plant microbiota across species and ecosystems, combined with the development of reductionist experimental models and the manipulation of plant phenotypes with microbes, has fueled interest in its translation to agriculture. However, the great majority of microbes exhibiting plant-productivity traits in the lab and greenhouse fail in the field. Therapeutic microbes must reach détente, the establishment of uneasy homeostasis, with the plant immune system, invade heterogeneous pre-established plant-associated communities, and persist in a new and potentially remodeled community. Environmental conditions can alter community structure and thus impact the engraftment of therapeutic microbes. We survey recent breakthroughs, challenges, and opportunities in translating beneficial microbes from the lab to the field.
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Affiliation(s)
- Dor Russ
- 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
| | - Connor R Fitzpatrick
- 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
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - 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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4
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Wang Z, Liu X, Yu J, Yin S, Cai W, Kim NH, El Kasmi F, Dangl JL, Wan L. Plasma membrane association and resistosome formation of plant helper immune receptors. Proc Natl Acad Sci U S A 2023; 120:e2222036120. [PMID: 37523563 PMCID: PMC10410763 DOI: 10.1073/pnas.2222036120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/21/2023] [Indexed: 08/02/2023] Open
Abstract
Intracellular plant immune receptors, termed NLRs (Nucleotide-binding Leucine-rich repeat Receptors), confer effector-triggered immunity. Sensor NLRs are responsible for pathogen effector recognition. Helper NLRs function downstream of sensor NLRs to transduce signaling and induce cell death and immunity. Activation of sensor NLRs that contain TIR (Toll/interleukin-1receptor) domains generates small molecules that induce an association between a downstream heterodimer signalosome of EDS1 (EnhancedDisease Susceptibility 1)/SAG101 (Senescence-AssociatedGene 101) and the helper NLR of NRG1 (NRequired Gene 1). Autoactive NRG1s oligomerize and form calcium signaling channels largely localized at the plasma membrane (PM). The molecular mechanisms of helper NLR PM association and effector-induced NRG1 oligomerization are not well characterized. We demonstrate that helper NLRs require positively charged residues in their N-terminal domains for phospholipid binding and PM association before and after activation, despite oligomerization and conformational changes that accompany activation. We demonstrate that effector activation of a TIR-containing sensor NLR induces NRG1 oligomerization at the PM and that the cytoplasmic pool of EDS1/SAG101 is critical for cell death function. EDS1/SAG101 cannot be detected in the oligomerized NRG1 resistosome, suggesting that additional unknown triggers might be required to induce the dissociation of EDS1/SAG101 from the previously described NRG1/EDS1/SAG101 heterotrimer before subsequent NRG1 oligomerization. Alternatively, the conformational changes resulting from NRG1 oligomerization abrogate the interface for EDS1/SAG101 association. Our data provide observations regarding dynamic PM association during helper NLR activation and underpin an updated model for effector-induced NRG1 resistosome formation.
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Affiliation(s)
- Zaiqing Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Xiaoxiao Liu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Jie Yu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Shuining Yin
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Wenjuan Cai
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Nak Hyun Kim
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Farid El Kasmi
- Centre for Plant Molecular Biology (ZMBP), University of Tubingen, 72076Tubingen, Germany
| | - Jeffery L. Dangl
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Li Wan
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
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5
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Jacob P, Hige J, Dangl JL. Is localized acquired resistance the mechanism for effector-triggered disease resistance in plants? Nat Plants 2023; 9:1184-1190. [PMID: 37537398 DOI: 10.1038/s41477-023-01466-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/23/2023] [Indexed: 08/05/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat receptors (NLRs) are intracellular immune receptors that are activated by their direct or indirect interactions with virulence effectors. NLR activation triggers a strong immune response and consequent disease resistance. However, the NLR-driven immune response can be targeted by virulence effectors. It is thus unclear how immune activation can occur concomitantly with virulence effector suppression of immunity. Recent observations suggest that the activation of effector-triggered immunity does not sustain defence gene expression in tissues in contact with the hemi-biotrophic pathogen Pseudomonas syringae pv. tomato. Instead, strong defence was observed on the border of the infection area. This response is reminiscent of localized acquired resistance (LAR). LAR is a strong defence response occurring in a ~2 mm area around cells in contact with the pathogen and probably serves to prevent the spread of pathogens. Here we propose that effector-triggered immunity is essentially a quarantining mechanism to prevent systemic pathogen spread and disease, and that the induction of LAR is a key component of this mechanism.
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Affiliation(s)
- Pierre Jacob
- 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
| | - Junko Hige
- 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
| | - 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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6
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Qi M, Berry JC, Veley KM, O'Connor L, Finkel OM, Salas-González I, Kuhs M, Jupe J, Holcomb E, Glavina Del Rio T, Creech C, Liu P, Tringe SG, Dangl JL, Schachtman DP, Bart RS. Correction: Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. ISME J 2023:10.1038/s41396-023-01442-9. [PMID: 37322286 DOI: 10.1038/s41396-023-01442-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Mingsheng Qi
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Kira M Veley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Lily O'Connor
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Washington University, St. Louis, MO, USA
| | - Omri M Finkel
- 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
- Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- 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
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Molly Kuhs
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Emily Holcomb
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Cody Creech
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - 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
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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7
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Salvato F, Vintila S, Finkel OM, Dangl JL, Kleiner M. Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes. Mol Plant Microbe Interact 2022; 35:977-988. [PMID: 35876747 DOI: 10.1094/mpmi-05-22-0116-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry-based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Fernanda Salvato
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Omri M Finkel
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
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8
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Conway JM, Walton WG, Salas-González I, Law TF, Lindberg CA, Crook LE, Kosina SM, Fitzpatrick CR, Lietzan AD, Northen TR, Jones CD, Finkel OM, Redinbo MR, Dangl JL. Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome. Nat Microbiol 2022; 7:1817-1833. [PMID: 36266335 PMCID: PMC9613470 DOI: 10.1038/s41564-022-01244-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 09/02/2022] [Indexed: 11/13/2022]
Abstract
Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon's MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac-like and iad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad-like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
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Affiliation(s)
- Jonathan M Conway
- 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
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Isai Salas-González
- 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
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Theresa F Law
- 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
| | - Chloe A Lindberg
- 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
| | - Laura E Crook
- 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
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connor R Fitzpatrick
- 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
| | - Adam D Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Omri M Finkel
- 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
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - 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.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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9
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Qi M, Berry JC, Veley KW, O'Connor L, Finkel OM, Salas-González I, Kuhs M, Jupe J, Holcomb E, Glavina Del Rio T, Creech C, Liu P, Tringe SG, Dangl JL, Schachtman DP, Bart RS. Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. ISME J 2022; 16:1957-1969. [PMID: 35523959 PMCID: PMC9296637 DOI: 10.1038/s41396-022-01245-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022]
Abstract
Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.
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Affiliation(s)
- Mingsheng Qi
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Kira W Veley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Lily O'Connor
- Donald Danforth Plant Science Center, St. Louis, MO, USA.,Washington University, St. Louis, MO, USA
| | - Omri M Finkel
- 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.,Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- 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.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Molly Kuhs
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Emily Holcomb
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Cody Creech
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - 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.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.,Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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10
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Abstract
In the 20th century, researchers studying animal and plant signaling pathways discovered a protein domain shared across diverse innate immune systems: the Toll/Interleukin-1/Resistance-gene (TIR) domain. The TIR domain is found in several protein architectures and was defined as an adaptor mediating protein-protein interactions in animal innate immunity and developmental signaling pathways. However, studies of nerve degeneration in animals, and subsequent breakthroughs in plant, bacterial and archaeal systems, revealed that TIR domains possess enzymatic activities. We provide a synthesis of TIR functions and the role of various related TIR enzymatic products in evolutionarily diverse immune systems. These studies may ultimately guide interventions that would span the tree of life, from treating human neurodegenerative disorders and bacterial infections, to preventing plant diseases.
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Affiliation(s)
- Kow Essuman
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marc T. Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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11
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Kim NH, Jacob P, Dangl JL. Con-Ca 2+ -tenating plant immune responses via calcium-permeable cation channels. New Phytol 2022; 234:813-818. [PMID: 35181918 PMCID: PMC9994437 DOI: 10.1111/nph.18044] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/06/2022] [Indexed: 05/24/2023]
Abstract
Calcium serves as a second messenger in a variety of developmental and physiological processes and has long been identified as important for plant immune responses. We discuss recent discoveries regarding plant immune-related calcium-permeable channels and how the two intertwined branches of the plant immune system are intricately linked to one another through calcium signalling. Cell surface immune receptors carefully tap the immense calcium gradient that exists between apoplast and cytoplasm in a short burst via tightly regulated plasma membrane (PM)-resident cation channels. Intracellular immune receptors form atypical calcium-permeable cation channels at the PM and mediate a prolonged calcium influx, overcoming the deleterious influence of pathogen effectors and enhancing plant immune responses.
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Affiliation(s)
- Nak Hyun Kim
- Department of Biology and Howard Hughes Medical InstituteUniversity of North Carolina at Chapel HillChapel HillNC27599USA
| | - Pierre Jacob
- Department of Biology and Howard Hughes Medical InstituteUniversity of North Carolina at Chapel HillChapel HillNC27599USA
| | - Jeffery L. Dangl
- Department of Biology and Howard Hughes Medical InstituteUniversity of North Carolina at Chapel HillChapel HillNC27599USA
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12
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Saile SC, Ackermann FM, Sunil S, Keicher J, Bayless A, Bonardi V, Wan L, Doumane M, Stöbbe E, Jaillais Y, Caillaud MC, Dangl JL, Nishimura MT, Oecking C, El Kasmi F. Arabidopsis ADR1 helper NLR immune receptors localize and function at the plasma membrane in a phospholipid dependent manner. New Phytol 2021; 232:2440-2456. [PMID: 34628646 DOI: 10.1111/nph.17788] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Activation of nucleotide-binding leucine-rich repeat receptors (NLRs) results in immunity and a localized cell death. NLR cell death activity requires oligomerization and in some cases plasma membrane (PM) localization. The exact mechanisms underlying PM localization of NLRs lacking predicted transmembrane domains or recognizable lipidation motifs remain elusive. We used confocal microscopy, genetically encoded molecular tools and protein-lipid overlay assays to determine whether PM localization of members of the Arabidopsis HeLo-/RPW8-like domain 'helper' NLR (RNL) family is mediated by the interaction with negatively charged phospholipids of the PM. Our results show that PM localization and stability of some RNLs and one CC-type NLR (CNL) depend on the direct interaction with PM phospholipids. Depletion of phosphatidylinositol-4-phosphate from the PM led to a mis-localization of the analysed NLRs and consequently inhibited their cell death activity. We further demonstrate homo- and hetero-association of members of the RNL family. Our results provide new insights into the molecular mechanism of NLR localization and defines an important role of phospholipids for CNL and RNL PM localization and consequently, for their function. We propose that RNLs interact with anionic PM phospholipids and that RNL-mediated cell death and immune responses happen at the PM.
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Affiliation(s)
- Svenja C Saile
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Frank M Ackermann
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Sruthi Sunil
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Jutta Keicher
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Adam Bayless
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Vera Bonardi
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Li Wan
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Mehdi Doumane
- Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69264, Lyon, France
| | - Eva Stöbbe
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69264, Lyon, France
| | - Marie-Cécile Caillaud
- Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69264, Lyon, France
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Marc T Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Claudia Oecking
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Farid El Kasmi
- Centre for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
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13
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Tzipilevich E, Russ D, Dangl JL, Benfey PN. Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria. Cell Host Microbe 2021; 29:1507-1520.e4. [PMID: 34610294 DOI: 10.1016/j.chom.2021.09.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/07/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022]
Abstract
Although plant roots encounter a plethora of microorganisms in the surrounding soil, at the rhizosphere, plants exert selective forces on their bacterial colonizers. Unlike immune recognition of pathogenic bacteria, the mechanisms by which beneficial bacteria are selected and how they interact with the plant immune system are not well understood. To better understand this process, we studied the interaction of auxin-producing Bacillus velezensis FZB42 with Arabidopsis roots and found that activation of the plant immune system is necessary for efficient bacterial colonization and auxin secretion. A feedback loop is established in which bacterial colonization triggers an immune reaction and production of reactive oxygen species, which, in turn, stimulate auxin production by the bacteria. Auxin promotes bacterial survival and efficient root colonization, allowing the bacteria to inhibit fungal infection and promote plant health. Thus, a feedback loop between bacteria and the plant immune system promotes the fitness of both partners.
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Affiliation(s)
- Elhanan Tzipilevich
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute Duke University, Durham, NC 27708, USA
| | - Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Howard Hughes Medical Institute. University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Howard Hughes Medical Institute. University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute Duke University, Durham, NC 27708, USA.
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14
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Pruitt RN, Locci F, Wanke F, Zhang L, Saile SC, Joe A, Karelina D, Hua C, Fröhlich K, Wan WL, Hu M, Rao S, Stolze SC, Harzen A, Gust AA, Harter K, Joosten MHAJ, Thomma BPHJ, Zhou JM, Dangl JL, Weigel D, Nakagami H, Oecking C, Kasmi FE, Parker JE, Nürnberger T. The EDS1-PAD4-ADR1 node mediates Arabidopsis pattern-triggered immunity. Nature 2021; 598:495-499. [PMID: 34497423 DOI: 10.1038/s41586-021-03829-0] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/16/2021] [Indexed: 02/08/2023]
Abstract
Plants deploy cell-surface and intracellular leucine rich-repeat domain (LRR) immune receptors to detect pathogens1. LRR receptor kinases and LRR receptor proteins at the plasma membrane recognize microorganism-derived molecules to elicit pattern-triggered immunity (PTI), whereas nucleotide-binding LRR proteins detect microbial effectors inside cells to confer effector-triggered immunity (ETI). Although PTI and ETI are initiated in different host cell compartments, they rely on the transcriptional activation of similar sets of genes2, suggesting pathway convergence upstream of nuclear events. Here we report that PTI triggered by the Arabidopsis LRR receptor protein RLP23 requires signalling-competent dimers of the lipase-like proteins EDS1 and PAD4, and of ADR1 family helper nucleotide-binding LRRs, which are all components of ETI. The cell-surface LRR receptor kinase SOBIR1 links RLP23 with EDS1, PAD4 and ADR1 proteins, suggesting the formation of supramolecular complexes containing PTI receptors and transducers at the inner side of the plasma membrane. We detected similar evolutionary patterns in LRR receptor protein and nucleotide-binding LRR genes across Arabidopsis accessions; overall higher levels of variation in LRR receptor proteins than in LRR receptor kinases are consistent with distinct roles of these two receptor families in plant immunity. We propose that the EDS1-PAD4-ADR1 node is a convergence point for defence signalling cascades, activated by both surface-resident and intracellular LRR receptors, in conferring pathogen immunity.
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Affiliation(s)
- Rory N Pruitt
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Federica Locci
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Friederike Wanke
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Lisha Zhang
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Svenja C Saile
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Anna Joe
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Darya Karelina
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chenlei Hua
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Katja Fröhlich
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Wei-Lin Wan
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Meijuan Hu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shaofei Rao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Sara C Stolze
- Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anne Harzen
- Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrea A Gust
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Klaus Harter
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | | | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands.,Cluster of Excellence on Plant Sciences (CEPLAS), Cologne University, Cologne, Germany
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jeffery L Dangl
- Department of Biology, Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hirofumi Nakagami
- Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Claudia Oecking
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Farid El Kasmi
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Cluster of Excellence on Plant Sciences (CEPLAS), Cologne University, Cologne, Germany.
| | - Thorsten Nürnberger
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany. .,Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
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15
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Jones JDG, Dangl JL. Editorial overview: An embarrassment of riches. Curr Opin Plant Biol 2021; 62:102105. [PMID: 34479723 DOI: 10.1016/j.pbi.2021.102105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Jonathan D G Jones
- The Sainsbury Lab, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Jeffery L Dangl
- Howard Hughes Medical Institute and Dept. of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.
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16
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Jacob P, Kim NH, Wu F, El-Kasmi F, Chi Y, Walton WG, Furzer OJ, Lietzan AD, Sunil S, Kempthorn K, Redinbo MR, Pei ZM, Wan L, Dangl JL. Plant "helper" immune receptors are Ca 2+-permeable nonselective cation channels. Science 2021; 373:420-425. [PMID: 34140391 PMCID: PMC8939002 DOI: 10.1126/science.abg7917] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022]
Abstract
Plant nucleotide-binding leucine-rich repeat receptors (NLRs) regulate immunity and cell death. In Arabidopsis, a subfamily of "helper" NLRs is required by many "sensor" NLRs. Active NRG1.1 oligomerized, was enriched in plasma membrane puncta, and conferred cytoplasmic calcium ion (Ca2+) influx in plant and human cells. NRG1.1-dependent Ca2+ influx and cell death were sensitive to Ca2+ channel blockers and were suppressed by mutations affecting oligomerization or plasma membrane enrichment. Ca2+ influx and cell death mediated by NRG1.1 and ACTIVATED DISEASE RESISTANCE 1 (ADR1), another helper NLR, required conserved negatively charged N-terminal residues. Whole-cell voltage-clamp recordings demonstrated that Arabidopsis helper NLRs form Ca2+-permeable cation channels to directly regulate cytoplasmic Ca2+ levels and consequent cell death. Thus, helper NLRs transduce cell death signals directly.
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Affiliation(s)
- Pierre Jacob
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nak Hyun Kim
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Feihua Wu
- Department of Biology, Duke University, Durham, NC 27708, USA
- Department of Horticulture, Foshan University, Foshan, China
| | - Farid El-Kasmi
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Yuan Chi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oliver J Furzer
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adam D Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sruthi Sunil
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Korina Kempthorn
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhen-Ming Pei
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | - Li Wan
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
- 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 and Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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17
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Teixeira PJPL, Colaianni NR, Law TF, Conway JM, Gilbert S, Li H, Salas-González I, Panda D, Del Risco NM, Finkel OM, Castrillo G, Mieczkowski P, Jones CD, Dangl JL. Specific modulation of the root immune system by a community of commensal bacteria. Proc Natl Acad Sci U S A 2021; 118:e2100678118. [PMID: 33879573 PMCID: PMC8072228 DOI: 10.1073/pnas.2100678118] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plants have an innate immune system to fight off potential invaders that is based on the perception of nonself or modified-self molecules. Microbe-associated molecular patterns (MAMPs) are evolutionarily conserved microbial molecules whose extracellular detection by specific cell surface receptors initiates an array of biochemical responses collectively known as MAMP-triggered immunity (MTI). Well-characterized MAMPs include chitin, peptidoglycan, and flg22, a 22-amino acid epitope found in the major building block of the bacterial flagellum, FliC. The importance of MAMP detection by the plant immune system is underscored by the large diversity of strategies used by pathogens to interfere with MTI and that failure to do so is often associated with loss of virulence. Yet, whether or how MTI functions beyond pathogenic interactions is not well understood. Here we demonstrate that a community of root commensal bacteria modulates a specific and evolutionarily conserved sector of the Arabidopsis immune system. We identify a set of robust, taxonomically diverse MTI suppressor strains that are efficient root colonizers and, notably, can enhance the colonization capacity of other tested commensal bacteria. We highlight the importance of extracellular strategies for MTI suppression by showing that the type 2, not the type 3, secretion system is required for the immunomodulatory activity of one robust MTI suppressor. Our findings reveal that root colonization by commensals is controlled by MTI, which, in turn, can be selectively modulated by specific members of a representative bacterial root microbiota.
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Affiliation(s)
- Paulo J P L Teixeira
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nicholas R Colaianni
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Theresa F Law
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jonathan M Conway
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Sarah Gilbert
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Haofan Li
- Department of Biology, Kenyon College, Gambier, OH 43022
| | - Isai Salas-González
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Darshana Panda
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nicole M Del Risco
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Omri M Finkel
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Gabriel Castrillo
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Piotr Mieczkowski
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jeffery L Dangl
- HHMI, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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18
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Parys K, Colaianni NR, Lee HS, Hohmann U, Edelbacher N, Trgovcevic A, Blahovska Z, Lee D, Mechtler A, Muhari-Portik Z, Madalinski M, Schandry N, Rodríguez-Arévalo I, Becker C, Sonnleitner E, Korte A, Bläsi U, Geldner N, Hothorn M, Jones CD, Dangl JL, Belkhadir Y. Signatures of antagonistic pleiotropy in a bacterial flagellin epitope. Cell Host Microbe 2021; 29:620-634.e9. [DOI: 10.1016/j.chom.2021.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/04/2021] [Accepted: 02/11/2021] [Indexed: 12/20/2022]
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19
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Colaianni NR, Parys K, Lee HS, Conway JM, Kim NH, Edelbacher N, Mucyn TS, Madalinski M, Law TF, Jones CD, Belkhadir Y, Dangl JL. A complex immune response to flagellin epitope variation in commensal communities. Cell Host Microbe 2021; 29:635-649.e9. [PMID: 33713602 DOI: 10.1016/j.chom.2021.02.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/05/2021] [Accepted: 02/09/2021] [Indexed: 10/21/2022]
Abstract
Immune systems restrict microbial pathogens by identifying "non-self" molecules called microbe-associated molecular patterns (MAMPs). It is unclear how immune responses are tuned to or by MAMP diversity present in commensal microbiota. We systematically studied the variability of commensal peptide derivatives of flagellin (flg22), a MAMP detected by plants. We define substantial functional diversity. Most flg22 peptides evade recognition, while others contribute to evasion by manipulating immunity through antagonism and signal modulation. We establish a paradigm of signal integration, wherein the sequential signaling outputs of the flagellin receptor are separable and allow for reprogramming by commensal-derived flg22 epitope variants. Plant-associated communities are enriched for immune evading flg22 epitopes, but upon physiological stress that represses the immune system, immune-activating flg22 epitopes become enriched. The existence of immune-manipulating epitopes suggests that they evolved to either communicate or utilize the immune system for host colonization and thus can influence commensal microbiota community composition.
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Affiliation(s)
- Nicholas R Colaianni
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational 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
| | - Katarzyna Parys
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Ho-Seok Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Jonathan M Conway
- 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
| | - 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
| | - Natalie Edelbacher
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Tatiana S Mucyn
- 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
| | - Mathias Madalinski
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Theresa F Law
- 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
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria.
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational 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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Salas-González I, Reyt G, Flis P, Custódio V, Gopaulchan D, Bakhoum N, Dew TP, Suresh K, Franke RB, Dangl JL, Salt DE, Castrillo G. Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis. Science 2021; 371:science.abd0695. [DOI: 10.1126/science.abd0695] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Isai Salas-González
- Curriculum in Bioinformatics and Computational Biology, 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
| | - Guilhem Reyt
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Paulina Flis
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Valéria Custódio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidad de Nova de Lisboa, Lisboa, Portugal
| | - David Gopaulchan
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Niokhor Bakhoum
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Tristan P. Dew
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Kiran Suresh
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Rochus Benni Franke
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Jeffery L. Dangl
- Curriculum in Bioinformatics and Computational Biology, 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
| | - David E. Salt
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington, UK
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21
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Finkel OM, Salas-González I, Castrillo G, Conway JM, Law TF, Teixeira PJPL, Wilson ED, Fitzpatrick CR, Jones CD, Dangl JL. A single bacterial genus maintains root growth in a complex microbiome. Nature 2020. [PMID: 32999461 DOI: 10.1101/645655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Plants grow within a complex web of species that interact with each other and with the plant1-10. These interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development7-9,11-18. Here, to understand how interactions between microorganisms influence root growth in Arabidopsis, we established a model system for interactions between plants, microorganisms and the environment. We inoculated seedlings with a 185-member bacterial synthetic community, manipulated the abiotic environment and measured bacterial colonization of the plant. This enabled us to classify the synthetic community into four modules of co-occurring strains. We deconstructed the synthetic community on the basis of these modules, and identified interactions between microorganisms that determine root phenotype. These interactions primarily involve a single bacterial genus (Variovorax), which completely reverses the severe inhibition of root growth that is induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulates plant hormone levels to balance the effects of our ecologically realistic synthetic root community on root growth. We identify an auxin-degradation operon that is conserved in all available genomes of Variovorax and is necessary and sufficient for the reversion of root growth inhibition. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the stereotypic developmental programme of the root. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising ecological strategy for developing more resilient and productive crops.
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Affiliation(s)
- Omri M Finkel
- 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
- Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- 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
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriel Castrillo
- 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
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Jonathan M Conway
- 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
| | - Theresa F Law
- 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
| | - Paulo José Pereira Lima Teixeira
- 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
- Department of Biology, 'Luiz de Queiroz' College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Ellie D Wilson
- 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
| | - Connor R Fitzpatrick
- 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
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - 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.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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22
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Finkel OM, Salas-González I, Castrillo G, Conway JM, Law TF, Teixeira PJPL, Wilson ED, Fitzpatrick CR, Jones CD, Dangl JL. A single bacterial genus maintains root growth in a complex microbiome. Nature 2020; 587:103-108. [PMID: 32999461 DOI: 10.1038/s41586-020-2778-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/03/2020] [Indexed: 12/17/2022]
Abstract
Plants grow within a complex web of species that interact with each other and with the plant1-10. These interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development7-9,11-18. Here, to understand how interactions between microorganisms influence root growth in Arabidopsis, we established a model system for interactions between plants, microorganisms and the environment. We inoculated seedlings with a 185-member bacterial synthetic community, manipulated the abiotic environment and measured bacterial colonization of the plant. This enabled us to classify the synthetic community into four modules of co-occurring strains. We deconstructed the synthetic community on the basis of these modules, and identified interactions between microorganisms that determine root phenotype. These interactions primarily involve a single bacterial genus (Variovorax), which completely reverses the severe inhibition of root growth that is induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulates plant hormone levels to balance the effects of our ecologically realistic synthetic root community on root growth. We identify an auxin-degradation operon that is conserved in all available genomes of Variovorax and is necessary and sufficient for the reversion of root growth inhibition. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the stereotypic developmental programme of the root. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising ecological strategy for developing more resilient and productive crops.
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Affiliation(s)
- Omri M Finkel
- 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.,Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- 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.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriel Castrillo
- 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.,Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Jonathan M Conway
- 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
| | - Theresa F Law
- 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
| | - Paulo José Pereira Lima Teixeira
- 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.,Department of Biology, 'Luiz de Queiroz' College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Ellie D Wilson
- 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
| | - Connor R Fitzpatrick
- 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
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - 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. .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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23
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Wang B, Zhao Z, Jabusch LK, Chiniquy DM, Ono K, Conway JM, Zhang Z, Wang G, Robinson D, Cheng JF, Dangl JL, Northen TR, Yoshikuni Y. CRAGE-Duet Facilitates Modular Assembly of Biological Systems for Studying Plant-Microbe Interactions. ACS Synth Biol 2020; 9:2610-2615. [PMID: 32786359 DOI: 10.1021/acssynbio.0c00280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Developing sustainable agricultural practices will require increasing our understanding of plant-microbe interactions. To study these interactions, new genetic tools for manipulating nonmodel microbes will be needed. To help meet this need, we recently reported development of chassis-independent recombinase-assisted genome engineering (CRAGE). CRAGE relies on cassette exchange between two pairs of mutually exclusive lox sites and allows direct, single-step chromosomal integration of large, complex gene constructs into diverse bacterial species. We then extended CRAGE by introducing a third mutually exclusive lox site, creating CRAGE-Duet, which allows modular integration of two constructs. CRAGE-Duet offers advantages over CRAGE, especially when a cumbersome recloning step is required to build single-integration constructs. To demonstrate the utility of CRAGE-Duet, we created a set of strains from the plant-growth-promoting rhizobacterium Pseudomonas simiae WCS417r that expressed various fluorescence marker genes. We visualized these strains simultaneously under a confocal microscope, demonstrating the usefulness of CRAGE-Duet for creating biological systems to study plant-microbe interactions.
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Affiliation(s)
- Bing Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lauren K. Jabusch
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Dawn M. Chiniquy
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Koyo Ono
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jonathan M. Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Zheyun Zhang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Gaoyan Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David Robinson
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Trent R. Northen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido 060-8589, Japan
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24
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Saile SC, Jacob P, Castel B, Jubic LM, Salas-Gonzáles I, Bäcker M, Jones JDG, Dangl JL, El Kasmi F. Two unequally redundant "helper" immune receptor families mediate Arabidopsis thaliana intracellular "sensor" immune receptor functions. PLoS Biol 2020; 18:e3000783. [PMID: 32925907 PMCID: PMC7514072 DOI: 10.1371/journal.pbio.3000783] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 09/24/2020] [Accepted: 08/17/2020] [Indexed: 01/08/2023] Open
Abstract
Plant nucleotide-binding (NB) leucine-rich repeat (LRR) receptor (NLR) proteins function as intracellular immune receptors that perceive the presence of pathogen-derived virulence proteins (effectors) to induce immune responses. The 2 major types of plant NLRs that “sense” pathogen effectors differ in their N-terminal domains: these are Toll/interleukin-1 receptor resistance (TIR) domain-containing NLRs (TNLs) and coiled-coil (CC) domain-containing NLRs (CNLs). In many angiosperms, the RESISTANCE TO POWDERY MILDEW 8 (RPW8)-CC domain containing NLR (RNL) subclass of CNLs is encoded by 2 gene families, ACTIVATED DISEASE RESISTANCE 1 (ADR1) and N REQUIREMENT GENE 1 (NRG1), that act as “helper” NLRs during multiple sensor NLR-mediated immune responses. Despite their important role in sensor NLR-mediated immunity, knowledge of the specific, redundant, and synergistic functions of helper RNLs is limited. We demonstrate that the ADR1 and NRG1 families act in an unequally redundant manner in basal resistance, effector-triggered immunity (ETI) and regulation of defense gene expression. We define RNL redundancy in ETI conferred by some TNLs and in basal resistance against virulent pathogens. We demonstrate that, in Arabidopsis thaliana, the 2 RNL families contribute specific functions in ETI initiated by specific CNLs and TNLs. Time-resolved whole genome expression profiling revealed that RNLs and “classical” CNLs trigger similar transcriptome changes, suggesting that RNLs act like other CNLs to mediate ETI downstream of sensor NLR activation. Together, our genetic data confirm that RNLs contribute to basal resistance, are fully required for TNL signaling, and can also support defense activation during CNL-mediated ETI. This study shows that two intracellular plant Nod-like immune receptor (NLR-) subfamilies act with unequal redundancy in their roles in plant disease resistance to virulent and avirulent pathogens, in effector-triggered immunity induced gene expression and in immunity-associated cell death. This function is most likely in parallel with, and not downstream of, other canonical intracellular plant immune receptors.
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Affiliation(s)
- Svenja C. Saile
- Center for Plant Molecular Biology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Pierre Jacob
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Baptiste Castel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Lance M. Jubic
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isai Salas-Gonzáles
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Marcel Bäcker
- Center for Plant Molecular Biology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | | | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Farid El Kasmi
- Center for Plant Molecular Biology, Eberhard Karls University of Tübingen, Tübingen, Germany
- * E-mail:
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25
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Ramirez-Villacis DX, Finkel OM, Salas-González I, Fitzpatrick CR, Dangl JL, Jones CD, Leon-Reyes A. Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate. mSphere 2020; 5:5/4/e00484-20. [PMID: 32817451 DOI: 10.46678/pb.20.1383160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis We found that a dose of 3.6 × 10-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.
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Affiliation(s)
- Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Galapagos Science Center, USFQ-UNC, San Cristobal, Galápagos, Ecuador
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26
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Ramirez-Villacis DX, Finkel OM, Salas-González I, Fitzpatrick CR, Dangl JL, Jones CD, Leon-Reyes A. Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate. mSphere 2020; 5:e00484-20. [PMID: 32817451 PMCID: PMC7426167 DOI: 10.1128/msphere.00484-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/23/2020] [Indexed: 01/22/2023] Open
Abstract
Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis We found that a dose of 3.6 × 10-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.
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Affiliation(s)
- Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Galapagos Science Center, USFQ-UNC, San Cristobal, Galápagos, Ecuador
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Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, Teixeira PJPL, Dangl JL. The Plant Microbiome: From Ecology to Reductionism and Beyond. Annu Rev Microbiol 2020; 74:81-100. [PMID: 32530732 DOI: 10.1146/annurev-micro-022620-014327] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.
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Affiliation(s)
- Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Sarah Gilbert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Paulo José Pereira Lima Teixeira
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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28
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Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones JDG, Dangl JL, Weigel D, Bemm F. A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell 2020; 178:1260-1272.e14. [PMID: 31442410 PMCID: PMC6709784 DOI: 10.1016/j.cell.2019.07.038] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/13/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022]
Abstract
Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes. Species-wide NLR diversity is high but not unlimited A large fraction of NLR diversity is recovered with 40–50 accessions Presence/absence variation in NLRs is widespread, resulting in a mosaic population A high diversity of NLR-integrated domains favor known virulence targets
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Affiliation(s)
- Anna-Lena Van de Weyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Freddy Monteiro
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Oliver J Furzer
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Marc T Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Milner Centre for Evolution & Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Jeffery L Dangl
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Wan L, Essuman K, Anderson RG, Sasaki Y, Monteiro F, Chung EH, Osborne Nishimura E, DiAntonio A, Milbrandt J, Dangl JL, Nishimura MT. TIR domains of plant immune receptors are NAD +-cleaving enzymes that promote cell death. Science 2020; 365:799-803. [PMID: 31439793 DOI: 10.1126/science.aax1771] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022]
Abstract
Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors activate cell death and confer disease resistance by unknown mechanisms. We demonstrate that plant Toll/interleukin-1 receptor (TIR) domains of NLRs are enzymes capable of degrading nicotinamide adenine dinucleotide in its oxidized form (NAD+). Both cell death induction and NAD+ cleavage activity of plant TIR domains require known self-association interfaces and a putative catalytic glutamic acid that is conserved in both bacterial TIR NAD+-cleaving enzymes (NADases) and the mammalian SARM1 (sterile alpha and TIR motif containing 1) NADase. We identify a variant of cyclic adenosine diphosphate ribose as a biomarker of TIR enzymatic activity. TIR enzymatic activity is induced by pathogen recognition and functions upstream of the genes enhanced disease susceptibility 1 (EDS1) and N requirement gene 1 (NRG1), which encode regulators required for TIR immune function. Thus, plant TIR-NLR receptors require NADase function to transduce recognition of pathogens into a cell death response.
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Affiliation(s)
- Li Wan
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kow Essuman
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ryan G Anderson
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Freddy Monteiro
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, USA.,Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Eui-Hwan Chung
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA. .,Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine, St. Louis, MO 63110, USA.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Marc T Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
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30
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Prokchorchik M, Choi S, Chung EH, Won K, Dangl JL, Sohn KH. A host target of a bacterial cysteine protease virulence effector plays a key role in convergent evolution of plant innate immune system receptors. New Phytol 2020; 225:1327-1342. [PMID: 31550400 DOI: 10.1111/nph.16218] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Some virulence effectors secreted from pathogens target host proteins and induce biochemical modifications that are monitored by nucleotide-binding and leucine-rich repeat (NLR) immune receptors. Arabidopsis RIN4 protein (AtRIN4: RPM1-interacting protein 4) homologs are present in diverse plant species and targeted by several bacterial type III effector proteins including the cysteine protease AvrRpt2. RIN4 is 'guarded' by several independently evolved NLRs from various plant species, including Arabidopsis RPS2. Recently, it was shown that the MR5 NLR from a wild apple relative can recognize the AvrRpt2 effector from Erwinia amylovora, but the details of this recognition remained unclear. The present contribution reports the mechanism of AvrRpt2 recognition by independently evolved NLRs, MR5 from apple and RPS2, both of which require proteolytically processed RIN4 for activation. It shows that the C-terminal cleaved product of apple RIN4 (MdRIN4) but not AtRIN4 is necessary and sufficient for MR5 activation. Additionally, two polymorphic residues in AtRIN4 and MdRIN4 are identified that are crucial in the regulation of and physical association with NLRs. It is proposed that polymorphisms in RIN4 from distantly related plant species allow it to remain an effector target while maintaining compatibility with multiple NLRs.
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Affiliation(s)
- Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- Bioprotection Research Centre, Institute of Agriculture and Environment, Massey University, Palmerston North, 4474, New Zealand
| | - Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Eui-Hwan Chung
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, 54875, Korea
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Korea
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31
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Redditt TJ, Chung EH, Karimi HZ, Rodibaugh N, Zhang Y, Trinidad JC, Kim JH, Zhou Q, Shen M, Dangl JL, Mackey D, Innes RW. AvrRpm1 Functions as an ADP-Ribosyl Transferase to Modify NOI Domain-Containing Proteins, Including Arabidopsis and Soybean RPM1-Interacting Protein4. Plant Cell 2019; 31:2664-2681. [PMID: 31727786 PMCID: PMC6881136 DOI: 10.1105/tpc.19.00020r2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 08/26/2019] [Accepted: 09/22/2019] [Indexed: 06/10/2023]
Abstract
The Pseudomonas syringae effector protein AvrRpm1 activates the Arabidopsis (Arabidopsis thaliana) intracellular innate immune receptor protein RESISTANCE TO PSEUDOMONAS MACULICOLA1 (RPM1) via modification of a second Arabidopsis protein, RPM1-INTERACTING PROTEIN4 (AtRIN4). Prior work has shown that AvrRpm1 induces phosphorylation of AtRIN4, but homology modeling indicated that AvrRpm1 may be an ADP-ribosyl transferase. Here, we show that AvrRpm1 induces ADP-ribosylation of RIN4 proteins from both Arabidopsis and soybean (Glycine max) within two highly conserved nitrate-induced (NOI) domains. It also ADP ribosylates at least 10 additional Arabidopsis NOI domain-containing proteins. The ADP-ribosylation activity of AvrRpm1 is required for subsequent phosphorylation on Thr-166 of AtRIN4, an event that is necessary and sufficient for RPM1 activation. We also show that the C-terminal NOI domain of AtRIN4 interacts with the exocyst subunits EXO70B1, EXO70E1, EXO70E2, and EXO70F1. Mutation of either EXO70B1 or EXO70E2 inhibited secretion of callose induced by the bacterial flagellin-derived peptide flg22. Substitution of RIN4 Thr-166 with Asp enhanced the association of AtRIN4 with EXO70E2, which we posit inhibits its callose deposition function. Collectively, these data indicate that AvrRpm1 ADP-ribosyl transferase activity contributes to virulence by promoting phosphorylation of RIN4 Thr-166, which inhibits the secretion of defense compounds by promoting the inhibitory association of RIN4 with EXO70 proteins.plantcell;31/11/2664/FX1F1fx1.
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Affiliation(s)
- Thomas J Redditt
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Eui-Hwan Chung
- Department of Biology, and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Hana Zand Karimi
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Natalie Rodibaugh
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Yixiang Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | | | - Jin Hee Kim
- Department of Horticulture and Crop Science, Ohio State University, Columbus, Ohio 43210
| | - Qian Zhou
- Department of Horticulture and Crop Science, Ohio State University, Columbus, Ohio 43210
| | - Mingzhe Shen
- Department of Horticulture and Crop Science, Ohio State University, Columbus, Ohio 43210
| | - Jeffery L Dangl
- Department of Biology, and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Microbiology and Immunology, and Curriculum in Genetics and Molecular Biology, and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David Mackey
- Department of Horticulture and Crop Science, Ohio State University, Columbus, Ohio 43210
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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32
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Finkel OM, Salas-González I, Castrillo G, Spaepen S, Law TF, Teixeira PJPL, Jones CD, Dangl JL. The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response. PLoS Biol 2019; 17:e3000534. [PMID: 31721759 PMCID: PMC6876890 DOI: 10.1371/journal.pbio.3000534] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/25/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Phosphate starvation response (PSR) in nonmycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms-the plant microbiota-are exposed to direct influence by the soil's phosphorus (P) content itself as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient and compared the composition of their shoot and root microbiota to wild-type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota than soil P concentrations in both roots and shoots. To dissect plant-microbe interactions under variable P conditions, we conducted a microbiota reconstitution experiment. Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift was accompanied by changes in microbiota composition: the genus Burkholderia was specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrated that in the absence of Burkholderia from the SynCom, plant shoots accumulated higher ortophosphate (Pi) levels than shoots colonized with the full SynCom but only under Pi starvation conditions. Therefore, Pi-stressed plants are susceptible to colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant's Pi starvation.
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Affiliation(s)
- Omri M. Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stijn Spaepen
- Department Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Theresa F. Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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33
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Teixeira PJP, Colaianni NR, Fitzpatrick CR, Dangl JL. Beyond pathogens: microbiota interactions with the plant immune system. Curr Opin Microbiol 2019; 49:7-17. [PMID: 31563068 DOI: 10.1016/j.mib.2019.08.003] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/15/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022]
Abstract
Plant immune receptors perceive microbial molecules and initiate an array of biochemical responses that are effective against most invaders. The role of the plant immune system in detecting and controlling pathogenic microorganism has been well described. In contrast, much less is known about plant immunity in the context of the wealth of commensals that inhabit plants. Recent research indicates that, just like pathogens, commensals in the plant microbiome can suppress or evade host immune responses. Moreover, the plant immune system has an active role in microbiome assembly and controls microbial homeostasis in response to environmental variation. We propose that the plant immune system shapes the microbiome, and that the microbiome expands plant immunity and acts as an additional layer of defense against pathogenic organisms.
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Affiliation(s)
- Paulo José Pl Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nicholas R Colaianni
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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Redditt TJ, Chung EH, Zand Karimi H, Rodibaugh N, Zhang Y, Trinidad JC, Kim JH, Zhou Q, Shen M, Dangl JL, Mackey DM, Innes RW. AvrRpm1 Functions as an ADP-Ribosyl Transferase to Modify NOI-domain Containing Proteins, Including Arabidopsis and Soybean RPM1-interacting Protein 4. Plant Cell 2019; 31:tpc.00020.2019. [PMID: 31548257 PMCID: PMC6881136 DOI: 10.1105/tpc.19.00020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 08/26/2019] [Accepted: 09/22/2019] [Indexed: 05/19/2023]
Abstract
The Pseudomonas syringae effector protein AvrRpm1 activates the Arabidopsis intracellular innate immune receptor protein RPM1 via modification of a second Arabidopsis protein, RIN4. Prior work has shown that AvrRpm1 induces phosphorylation of AtRIN4, but homology modeling indicated that AvrRpm1 may be an ADP-ribosyl transferase. Here we show that AvrRpm1 induces ADP-ribosylation of RIN4 proteins from both Arabidopsis and soybean within two highly conserved nitrate-induced (NOI) domains. It also ADP-ribosylates at least ten additional Arabidopsis NOI domain-containing proteins. The ADP-ribosylation activity of AvrRpm1 is required for subsequent phosphorylation on threonine 166 of Arabidopsis RIN4, an event that is necessary and sufficient for RPM1 activation. We also show that the C-terminal NOI domain of AtRIN4 interacts with the exocyst subunits EXO70B1, EXO70E1, EXO70E2 and EXO70F1. Mutation of either EXO70B1 or EXO70E2 inhibited secretion of callose induced by the bacterial flagellin-derived peptide flg22. Substitution of RIN4 threonine 166 with aspartate enhanced the association of AtRIN4 with EXO70E2, which we posit inhibits its callose deposition function. Collectively, these data indicate that AvrRpm1 ADP-ribosyl transferase activity contributes to virulence by promoting phosphorylation of RIN4 threonine 166, which inhibits the secretion of defense compounds by promoting the inhibitory association of RIN4 with EXO70 proteins.
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Affiliation(s)
- Thomas J Redditt
- Indiana University CITY: Bloomington STATE: IN United States Of America [US]
| | - Eui-Hwan Chung
- University of North Carolina CITY: Chappel Hill STATE: NC United States Of America [US]
| | - Hana Zand Karimi
- Indiana University CITY: Bloomington STATE: Indiana United States Of America [US]
| | - Natalie Rodibaugh
- Indiana University CITY: Bloomington STATE: IN United States Of America [US]
| | - Yixiang Zhang
- Indiana University CITY: Bloomington STATE: IN United States Of America [US]
| | - Jonathan C Trinidad
- Indiana University CITY: Bloomington STATE: IN United States Of America [US]
| | - Jin Hee Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS) CITY: Daegu Korea (South), Republic Of
| | - Qian Zhou
- Ohio State University CITY: Columbus STATE: OH United States Of America [US]
| | - Mingzhe Shen
- Gyeongsang National University CITY: Jinju Korea (South), Republic Of
| | - Jeffery L Dangl
- University of North Carolina CITY: Chapel Hill STATE: North Carolina POSTAL_CODE: 27599-3280 United States Of America [US]
| | - David M Mackey
- Ohio State University CITY: Columbus STATE: Ohio POSTAL_CODE: 43210 United States Of America [US]
| | - Roger W Innes
- Indiana University CITY: Bloomington STATE: Indiana POSTAL_CODE: 47405-7107 United States Of America [US]
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Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones JDG, Dangl JL, Weigel D, Bemm F. A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell 2019. [PMID: 31442410 DOI: 10.1101/537001v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes.
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Affiliation(s)
- Anna-Lena Van de Weyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Freddy Monteiro
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Oliver J Furzer
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Marc T Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Milner Centre for Evolution & Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Jeffery L Dangl
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Jubic LM, Saile S, Furzer OJ, El Kasmi F, Dangl JL. Help wanted: helper NLRs and plant immune responses. Curr Opin Plant Biol 2019; 50:82-94. [PMID: 31063902 DOI: 10.1016/j.pbi.2019.03.013] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/13/2019] [Accepted: 03/25/2019] [Indexed: 05/09/2023]
Abstract
Plant nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins function as intracellular receptors in response to pathogens and activate effector-triggered immune responses (ETI). The activation of some sensor NLRs (sNLR) by their corresponding pathogen effector is well studied. However, the mechanisms by which the recently defined helper NLRs (hNLR) function to transduce sNLR activation into ETI-associated cell death and disease resistance remains poorly understood. We briefly summarize recent examples of sNLR activation and we then focus on hNLR requirements in sNLR-initiated immune responses. We further discuss how shared sequence homology with fungal self-incompatibility proteins and the mammalian mixed lineage kinase domain like pseudokinase (MLKL) proteins informs a plausible model for the structure and function of an ancient clade of plant hNLRs, called RNLs.
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Affiliation(s)
- Lance M Jubic
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Svenja Saile
- ZMBP-Plant Physiology, University of Tübingen, Tübingen, Germany
| | - Oliver J Furzer
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Farid El Kasmi
- ZMBP-Plant Physiology, University of Tübingen, Tübingen, Germany.
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, USA; Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, USA.
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Sasse J, Kant J, Cole BJ, Klein AP, Arsova B, Schlaepfer P, Gao J, Lewald K, Zhalnina K, Kosina S, Bowen BP, Treen D, Vogel J, Visel A, Watt M, Dangl JL, Northen TR. Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass. New Phytol 2019. [PMID: 30585637 DOI: 10.1101/435818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate-sufficient and -deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits.
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Affiliation(s)
- Joelle Sasse
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Josefine Kant
- Institut für Bio- & Geowissenschaften, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Benjamin J Cole
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Andrew P Klein
- Department of Biology, Howard Hughes Medical Institute, University of North Carolina Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC, 27599, USA
| | - Borjana Arsova
- Institut für Bio- & Geowissenschaften, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Pascal Schlaepfer
- Institute of Molecular Plant Biology, ETH Zürich, Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Jian Gao
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Kyle Lewald
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Kateryna Zhalnina
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Suzanne Kosina
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Benjamin P Bowen
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Daniel Treen
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - John Vogel
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- School of Natural Sciences, University of California, Merced, CA, 95343, USA
| | - Michelle Watt
- Institut für Bio- & Geowissenschaften, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Jeffery L Dangl
- Department of Biology, Howard Hughes Medical Institute, University of North Carolina Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC, 27599, USA
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
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Sasse J, Kant J, Cole BJ, Klein AP, Arsova B, Schlaepfer P, Gao J, Lewald K, Zhalnina K, Kosina S, Bowen BP, Treen D, Vogel J, Visel A, Watt M, Dangl JL, Northen TR. Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass. New Phytol 2019; 222:1149-1160. [PMID: 30585637 PMCID: PMC6519027 DOI: 10.1111/nph.15662] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 05/12/2023]
Abstract
There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate-sufficient and -deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits.
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Affiliation(s)
- Joelle Sasse
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Josefine Kant
- Institut für Bio‐ & GeowissenschaftenForschungszentrum JülichWilhelm‐Johnen‐Straße52428JülichGermany
| | - Benjamin J. Cole
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Andrew P. Klein
- Department of BiologyHoward Hughes Medical InstituteUniversity of North Carolina Chapel Hill250 Bell Tower DriveChapel HillNC27599USA
| | - Borjana Arsova
- Institut für Bio‐ & GeowissenschaftenForschungszentrum JülichWilhelm‐Johnen‐Straße52428JülichGermany
| | - Pascal Schlaepfer
- Institute of Molecular Plant BiologyETH ZürichUniversitätsstrasse 28092ZürichSwitzerland
| | - Jian Gao
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Kyle Lewald
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Kateryna Zhalnina
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Suzanne Kosina
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Benjamin P. Bowen
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Daniel Treen
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - John Vogel
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
- School of Natural SciencesUniversity of CaliforniaMercedCA95343USA
| | - Michelle Watt
- Institut für Bio‐ & GeowissenschaftenForschungszentrum JülichWilhelm‐Johnen‐Straße52428JülichGermany
| | - Jeffery L. Dangl
- Department of BiologyHoward Hughes Medical InstituteUniversity of North Carolina Chapel Hill250 Bell Tower DriveChapel HillNC27599USA
| | - Trent R. Northen
- Lawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
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41
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Coates RC, Bowen BP, Oberortner E, Thomashow L, Hadjithomas M, Zhao Z, Ke J, Silva L, Louie K, Wang G, Robinson D, Tarver A, Hamilton M, Lubbe A, Feltcher M, Dangl JL, Pati A, Weller D, Northen TR, Cheng JF, Mouncey NJ, Deutsch S, Yoshikuni Y. An integrated workflow for phenazine-modifying enzyme characterization. ACTA ACUST UNITED AC 2018; 45:567-577. [DOI: 10.1007/s10295-018-2025-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/09/2018] [Indexed: 02/04/2023]
Abstract
Abstract
Increasing availability of new genomes and putative biosynthetic gene clusters (BGCs) has extended the opportunity to access novel chemical diversity for agriculture, medicine, environmental and industrial purposes. However, functional characterization of BGCs through heterologous expression is limited because expression may require complex regulatory mechanisms, specific folding or activation. We developed an integrated workflow for BGC characterization that integrates pathway identification, modular design, DNA synthesis, assembly and characterization. This workflow was applied to characterize multiple phenazine-modifying enzymes. Phenazine pathways are useful for this workflow because all phenazines are derived from a core scaffold for modification by diverse modifying enzymes (PhzM, PhzS, PhzH, and PhzO) that produce characterized compounds. We expressed refactored synthetic modules of previously uncharacterized phenazine BGCs heterologously in Escherichia coli and were able to identify metabolic intermediates they produced, including a previously unidentified metabolite. These results demonstrate how this approach can accelerate functional characterization of BGCs.
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Affiliation(s)
- R Cameron Coates
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Benjamin P Bowen
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Ernst Oberortner
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Linda Thomashow
- 0000 0001 2157 6568 grid.30064.31 USDA Agricultural Research Service, Wheat Health, Genetics and Quality Washington State University Pullman WA USA
- 0000 0001 2157 6568 grid.30064.31 Department of Plant Pathology Washington State University Pullman WA USA
| | - Michalis Hadjithomas
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Zhiying Zhao
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Jing Ke
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Leslie Silva
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Katherine Louie
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Gaoyan Wang
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - David Robinson
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Angela Tarver
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Matthew Hamilton
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Andrea Lubbe
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Meghan Feltcher
- 0000000122483208 grid.10698.36 Department of Biology University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - Jeffery L Dangl
- 0000000122483208 grid.10698.36 Department of Biology University of North Carolina at Chapel Hill Chapel Hill NC USA
- 0000000122483208 grid.10698.36 Howard Hughes Medical Institute University of North Carolina at Chapel Hill Chapel Hill NC USA
- 0000000122483208 grid.10698.36 Curriculum in Genetics and Molecular Biology University of North Carolina at Chapel Hill Chapel Hill NC USA
- 0000000122483208 grid.10698.36 Department of Microbiology and Immunology University of North Carolina at Chapel Hill Chapel Hill NC USA
- 0000000122483208 grid.10698.36 Carolina Center for Genome Sciences University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - Amrita Pati
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - David Weller
- 0000 0001 2157 6568 grid.30064.31 USDA Agricultural Research Service, Wheat Health, Genetics and Quality Washington State University Pullman WA USA
- 0000 0001 2157 6568 grid.30064.31 Department of Plant Pathology Washington State University Pullman WA USA
| | - Trent R Northen
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Jan-Fang Cheng
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Nigel J Mouncey
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Samuel Deutsch
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
- 0000 0001 2231 4551 grid.184769.5 Biological Systems and Engineering Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Yasuo Yoshikuni
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
- 0000 0001 2231 4551 grid.184769.5 Biological Systems and Engineering Division Lawrence Berkeley National Laboratory Berkeley CA USA
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Lema Asqui S, Vercammen D, Serrano I, Valls M, Rivas S, Van Breusegem F, Conlon FL, Dangl JL, Coll NS. AtSERPIN1 is an inhibitor of the metacaspase AtMC1-mediated cell death and autocatalytic processing in planta. New Phytol 2018; 218:1156-1166. [PMID: 28157265 DOI: 10.1111/nph.14446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 12/16/2016] [Indexed: 05/10/2023]
Abstract
The hypersensitive response (HR) is a localized programmed cell death phenomenon that occurs in response to pathogen recognition at the site of attempted invasion. Despite more than a century of research on HR, little is known about how it is so tightly regulated and how it can be contained spatially to a few cells. AtMC1 is an Arabidopsis thaliana plant metacaspase that positively regulates the HR. Here, we used an unbiased approach to identify new AtMC1 regulators. Immunoaffinity purification of AtMC1-containing complexes led us to the identification of the protease inhibitor AtSerpin1. Our data clearly showed that coimmunoprecipitation between AtMC1 and AtSerpin1 and formation of a complex between them was lost upon mutation of the AtMC1 catalytic site, and that the AtMC1 prodomain was not required for the interaction. AtSerpin1 blocked AtMC1 self-processing and inhibited AtMC1-mediated cell death. Our results constitute an in vivo example of a Serpin acting as a suicide inhibitor in plants, reminiscent of the activity of animal or viral serpins on immune/cell death regulators, including caspase-1. These results indicate a conserved function of a protease inhibitor on cell death regulators from different kingdoms with unrelated modes of action (i.e. caspases vs metacaspases).
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Affiliation(s)
- Saul Lema Asqui
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Dominique Vercammen
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
| | - Irene Serrano
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Marc Valls
- Department of Genetics, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, Catalonia, 08193, Spain
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Department of Medical Protein Research, VIB, Ghent, 9000, Belgium
- Department of Biochemistry, Ghent University, Ghent, 9000, Belgium
| | - Frank L Conlon
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
| | - Núria S Coll
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
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Herrera Paredes S, Gao T, Law TF, Finkel OM, Mucyn T, Teixeira PJPL, Salas González I, Feltcher ME, Powers MJ, Shank EA, Jones CD, Jojic V, Dangl JL, Castrillo G. Design of synthetic bacterial communities for predictable plant phenotypes. PLoS Biol 2018; 16:e2003962. [PMID: 29462153 PMCID: PMC5819758 DOI: 10.1371/journal.pbio.2003962] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/17/2018] [Indexed: 01/01/2023] Open
Abstract
Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant-bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation-responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.
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Affiliation(s)
- Sur Herrera Paredes
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tianxiang Gao
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Theresa F. Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Omri M. Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tatiana Mucyn
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isaí Salas González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Meghan E. Feltcher
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Matthew J. Powers
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elizabeth A. Shank
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Park M, Krause C, Karnahl M, Reichardt I, El Kasmi F, Mayer U, Stierhof YD, Hiller U, Strompen G, Bayer M, Kientz M, Sato MH, Nishimura MT, Dangl JL, Sanderfoot AA, Jürgens G. Concerted Action of Evolutionarily Ancient and Novel SNARE Complexes in Flowering-Plant Cytokinesis. Dev Cell 2018; 44:500-511.e4. [PMID: 29396117 DOI: 10.1016/j.devcel.2017.12.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 11/29/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022]
Abstract
Membrane vesicles delivered to the cell-division plane fuse with one another to form the partitioning membrane during plant cytokinesis, starting in the cell center. In Arabidopsis, this requires SNARE complexes involving the cytokinesis-specific Qa-SNARE KNOLLE. However, cytokinesis still occurs in knolle mutant embryos, suggesting contributions from KNOLLE-independent SNARE complexes. Here we show that Qa-SNARE SYP132, having counterparts in lower plants, functionally overlaps with the flowering plant-specific KNOLLE. SYP132 mutation causes cytokinesis defects, knolle syp132 double mutants consist of only one or a few multi-nucleate cells, and SYP132 has the same SNARE partners as KNOLLE. SYP132 and KNOLLE also have non-overlapping functions in secretion and in cellularization of the embryo-nourishing endosperm resulting from double fertilization unique to flowering plants. Evolutionarily ancient non-specialized SNARE complexes originating in algae were thus amended by the appearance of cytokinesis-specific SNARE complexes, meeting the high demand for membrane-fusion capacity during endosperm cellularization in angiosperms.
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Affiliation(s)
- Misoon Park
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Cornelia Krause
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Matthias Karnahl
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Ilka Reichardt
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Farid El Kasmi
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Ulrike Mayer
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany; Center for Plant Molecular Biology (ZMBP), Microscopy, University of Tübingen, 72076 Tübingen, Germany
| | - York-Dieter Stierhof
- Center for Plant Molecular Biology (ZMBP), Microscopy, University of Tübingen, 72076 Tübingen, Germany
| | - Ulrike Hiller
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany; Center for Plant Molecular Biology (ZMBP), Microscopy, University of Tübingen, 72076 Tübingen, Germany
| | - Georg Strompen
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Martin Bayer
- Department of Cell Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Marika Kientz
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Masa H Sato
- Laboratory of Cellular Dynamics, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Marc T Nishimura
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anton A Sanderfoot
- Biology Department, University of Wisconsin La Crosse, La Crosse, WI 54601, USA
| | - Gerd Jürgens
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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45
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Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, Wang K, Devescovi G, Stillman K, Monteiro F, Rangel Alvarez B, Lundberg DS, Lu TY, Lebeis S, Jin Z, McDonald M, Klein AP, Feltcher ME, Rio TG, Grant SR, Doty SL, Ley RE, Zhao B, Venturi V, Pelletier DA, Vorholt JA, Tringe SG, Woyke T, Dangl JL. Genomic features of bacterial adaptation to plants. Nat Genet 2017; 50:138-150. [PMID: 29255260 PMCID: PMC5957079 DOI: 10.1038/s41588-017-0012-9] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 11/10/2017] [Indexed: 01/10/2023]
Abstract
Plants intimately associate with diverse bacteria. Plant-associated (PA) bacteria have ostensibly evolved genes enabling adaptation to the plant environment. However, the identities of such genes are mostly unknown and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3837 bacterial genomes to identify thousands of PA gene clusters. Genomes of PA bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant associated genomes. We experimentally validated candidates from two sets of PA genes, one involved in plant colonization, the other serving in microbe-microbe competition between PA bacteria. We also identified 64 PA protein domains that potentially mimic plant domains; some are shared with PA fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides leads for efficient and sustainable agriculture through microbiome engineering.
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Affiliation(s)
- Asaf Levy
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Isai Salas Gonzalez
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Jiamin Miao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.,The Grassland College, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Kunru Wang
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA
| | - Giulia Devescovi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Freddy Monteiro
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Derek S Lundberg
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tse-Yuan Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sarah Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Zhao Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Meredith McDonald
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Andrew P Klein
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Meghan E Feltcher
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,BD Technologies and Innovation, Research Triangle Park, NC, USA
| | | | - Sarah R Grant
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Sharon L Doty
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA
| | - Ruth E Ley
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Susannah G Tringe
- DOE Joint Genome Institute, Walnut Creek, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, USA. .,Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
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46
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Cole BJ, Feltcher ME, Waters RJ, Wetmore KM, Mucyn TS, Ryan EM, Wang G, Ul-Hasan S, McDonald M, Yoshikuni Y, Malmstrom RR, Deutschbauer AM, Dangl JL, Visel A. Genome-wide identification of bacterial plant colonization genes. PLoS Biol 2017; 15:e2002860. [PMID: 28938018 PMCID: PMC5627942 DOI: 10.1371/journal.pbio.2002860] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 10/04/2017] [Accepted: 09/05/2017] [Indexed: 01/09/2023] Open
Abstract
Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system. Among the genes we identified were some with obvious colonization-related roles in motility and carbon metabolism, as well as 44 other genes that had no or vague functional predictions. Independent validation assays of individual genes confirmed colonization functions for 20 of 22 (91%) cases tested. To further characterize genes identified by our screen, we compared the functional contributions of P. simiae genes to growth in 90 distinct in vitro conditions by RB-TnSeq, highlighting specific metabolic functions associated with root colonization genes. Our analysis of bacterial genes by sequence-driven saturation mutagenesis revealed a genome-wide map of the genetic determinants of plant root colonization and offers a starting point for targeted improvement of the colonization capabilities of plant-beneficial microbes. Plants fix carbon to create an abundance of sugars and amino acids, thus providing an enticing environment for microorganisms that reside in soil. Once these microorganisms have colonized the root environment, they can dramatically influence plant growth and development. We set out to identify a comprehensive set of microbial genes that control or influence root colonization, using a genome-wide transposon mutagenesis approach (randomly barcoded transposon sequencing [RB-TnSeq]). By using this method, we identified several hundred genes that, when mutated, affect the ability of the bacterium P. simiae to competitively colonize the root system of the model plant A. thaliana. These included many genes purported to be involved in carbohydrate metabolism, cell wall biosynthesis, and motility, underscoring the notion that sugar metabolism, defense, and motility are all key features of a root-colonizing microbe. We also identified several amino acid transport and metabolism genes with mutations that confer a fitness advantage in root colonization. Lastly, we identified several genes with no known function that significantly alter root colonization ability when mutated. These findings suggest novel engineering strategies to improve biological product development, and will facilitate the mechanistic exploration of the root colonization process.
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Affiliation(s)
- Benjamin J. Cole
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Meghan E. Feltcher
- Department of Biology, Department of Microbiology and Immunology, Curriculum in Genetics and Molecular Biology, Howard Hughes Medical Institute, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Robert J. Waters
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Tatiana S. Mucyn
- Department of Biology, Department of Microbiology and Immunology, Curriculum in Genetics and Molecular Biology, Howard Hughes Medical Institute, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elizabeth M. Ryan
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Gaoyan Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Sabah Ul-Hasan
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Meredith McDonald
- Department of Biology, Department of Microbiology and Immunology, Curriculum in Genetics and Molecular Biology, Howard Hughes Medical Institute, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rex R. Malmstrom
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jeffery L. Dangl
- Department of Biology, Department of Microbiology and Immunology, Curriculum in Genetics and Molecular Biology, Howard Hughes Medical Institute, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (JLD); (AV)
| | - Axel Visel
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
- * E-mail: (JLD); (AV)
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47
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El Kasmi F, Chung EH, Anderson RG, Li J, Wan L, Eitas TK, Gao Z, Dangl JL. Signaling from the plasma-membrane localized plant immune receptor RPM1 requires self-association of the full-length protein. Proc Natl Acad Sci U S A 2017; 114:E7385-E7394. [PMID: 28808003 PMCID: PMC5584451 DOI: 10.1073/pnas.1708288114] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Plants evolved intracellular immune receptors that belong to the NOD-like receptor (NLR) family to recognize the presence of pathogen-derived effector proteins. NLRs possess an N-terminal Toll-like/IL-1 receptor (TIR) or a non-TIR domain [some of which contain coiled coils (CCs)], a central nucleotide-binding (NB-ARC) domain, and a C-terminal leucine-rich repeat (LRR). Activation of NLR proteins results in a rapid and high-amplitude immune response, eventually leading to host cell death at the infection site, the so-called hypersensitive response. Despite their important contribution to immunity, the exact mechanisms of NLR activation and signaling remain unknown and are likely heterogenous. We undertook a detailed structure-function analysis of the plasma membrane (PM)-localized CC NLR Resistance to Pseudomonas syringae pv. maculicola 1 (RPM1) using both stable transgenic Arabidopsis and transient expression in Nicotiana benthamiana We report that immune signaling is induced only by activated full-length PM-localized RPM1. Our interaction analyses demonstrate the importance of a functional P-loop for in planta interaction of RPM1 with the small host protein RPM1-interacting protein 4 (RIN4), for constitutive preactivation and postactivation self-association of RPM1 and for proper PM localization. Our results reveal an additive effect of hydrophobic conserved residues in the CC domain for RPM1 function and RPM1 self-association and their necessity for RPM1-RIN4 interaction. Thus, our findings considerably extend our understanding of the mechanisms regulating NLR activation at, and signaling from, the PM.
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Affiliation(s)
- Farid El Kasmi
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Eui-Hwan Chung
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Ryan G Anderson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Jinyue Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, P. R. China 430072
| | - Li Wan
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Timothy K Eitas
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Zhiyong Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, P. R. China 430072;
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280;
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
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48
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Finkel OM, Castrillo G, Herrera Paredes S, Salas González I, Dangl JL. Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol 2017; 38:155-163. [PMID: 28622659 PMCID: PMC5561662 DOI: 10.1016/j.pbi.2017.04.018] [Citation(s) in RCA: 275] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/25/2017] [Indexed: 05/18/2023]
Abstract
After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.
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Affiliation(s)
- Omri M Finkel
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Isai Salas González
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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49
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Abstract
Many microbes associate with higher eukaryotes and impact their vitality. To engineer microbiomes for host benefit, we must understand the rules of community assembly and maintenance that, in large part, demand an understanding of the direct interactions among community members. Toward this end, we have developed a Poisson-multivariate normal hierarchical model to learn direct interactions from the count-based output of standard metagenomics sequencing experiments. Our model controls for confounding predictors at the Poisson layer and captures direct taxon-taxon interactions at the multivariate normal layer using an ℓ1 penalized precision matrix. We show in a synthetic experiment that our method handily outperforms state-of-the-art methods such as SparCC and the graphical lasso (glasso). In a real in planta perturbation experiment of a nine-member bacterial community, we show our model, but not SparCC or glasso, correctly resolves a direct interaction structure among three community members that associates with Arabidopsis thaliana roots. We conclude that our method provides a structured, accurate, and distributionally reasonable way of modeling correlated count-based random variables and capturing direct interactions among them.
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Affiliation(s)
- Surojit Biswas
- 1 Department of Statistics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Meredith Mcdonald
- 2 Department of Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Derek S Lundberg
- 2 Department of Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Jeffery L Dangl
- 2 Department of Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,3 Howard Hughes Medical Institute, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,4 Department of Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Vladimir Jojic
- 5 Department of Computer Science, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
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50
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Biswas S, Kerner K, Teixeira PJPL, Dangl JL, Jojic V, Wigge PA. Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes. Nat Commun 2017; 8:15309. [PMID: 28474674 PMCID: PMC5424156 DOI: 10.1038/ncomms15309] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/15/2017] [Indexed: 12/21/2022] Open
Abstract
Transcript levels are a critical determinant of the proteome and hence cellular function. Because the transcriptome is an outcome of the interactions between genes and their products, it may be accurately represented by a subset of transcript abundances. We develop a method, Tradict (transcriptome predict), capable of learning and using the expression measurements of a small subset of 100 marker genes to predict transcriptome-wide gene abundances and the expression of a comprehensive, but interpretable list of transcriptional programs that represent the major biological processes and pathways of the cell. By analyzing over 23,000 publicly available RNA-Seq data sets, we show that Tradict is robust to noise and accurate. Coupled with targeted RNA sequencing, Tradict may therefore enable simultaneous transcriptome-wide screening and mechanistic investigation at large scales.
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Affiliation(s)
- Surojit Biswas
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Konstantin Kerner
- Botanical Institute, Biocenter, University of Cologne, D-50674 Cologne, Germany
| | - Paulo José Pereira Lima Teixeira
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jeffery L. Dangl
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Philip A. Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
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