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Aparicio Chacón MV, Hernández Luelmo S, Devlieghere V, Robichez L, Leroy T, Stuer N, De Keyser A, Ceulemans E, Goossens A, Goormachtig S, Van Dingenen J. Exploring the potential role of four Rhizophagus irregularis nuclear effectors: opportunities and technical limitations. FRONTIERS IN PLANT SCIENCE 2024; 15:1384496. [PMID: 38736443 PMCID: PMC11085264 DOI: 10.3389/fpls.2024.1384496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate symbionts that interact with the roots of most land plants. The genome of the AMF model species Rhizophagus irregularis contains hundreds of predicted small effector proteins that are secreted extracellularly but also into the plant cells to suppress plant immunity and modify plant physiology to establish a niche for growth. Here, we investigated the role of four nuclear-localized putative effectors, i.e., GLOIN707, GLOIN781, GLOIN261, and RiSP749, in mycorrhization and plant growth. We initially intended to execute the functional studies in Solanum lycopersicum, a host plant of economic interest not previously used for AMF effector biology, but extended our studies to the model host Medicago truncatula as well as the non-host Arabidopsis thaliana because of the technical advantages of working with these models. Furthermore, for three effectors, the implementation of reverse genetic tools, yeast two-hybrid screening and whole-genome transcriptome analysis revealed potential host plant nuclear targets and the downstream triggered transcriptional responses. We identified and validated a host protein interactors participating in mycorrhization in the host.S. lycopersicum and demonstrated by transcriptomics the effectors possible involvement in different molecular processes, i.e., the regulation of DNA replication, methylglyoxal detoxification, and RNA splicing. We conclude that R. irregularis nuclear-localized effector proteins may act on different pathways to modulate symbiosis and plant physiology and discuss the pros and cons of the tools used.
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Affiliation(s)
- María Victoria Aparicio Chacón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Sofía Hernández Luelmo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Viktor Devlieghere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Louis Robichez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Toon Leroy
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Naomi Stuer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Evi Ceulemans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
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Raheem A, Lu D, Khalid AK, Zhao G, Fu Y, Chen Y, Chen X, Hu C, Chen J, Chen H, Guo A. The Identification of a Novel Nucleomodulin MbovP467 of Mycoplasmopsis bovis and Its Potential Contribution in Pathogenesis. Cells 2024; 13:604. [PMID: 38607043 PMCID: PMC11011252 DOI: 10.3390/cells13070604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Mycoplasmopsis bovis is a causative agent of crucial diseases in both dairy and beef cattle leading to substantial economic losses. However, limited control measures for M. bovis-related diseases exist due to a lack of understanding about the virulence factors of this pathogen, a common challenge in mycoplasma research. Consequently, this study aimed to characterize a novel nucleomodulin as a virulence-related factor of M. bovis. Employing bioinformatic tools, we initially predicted MbovP467 to be a secreted protein with a nuclear localization signal based on SignalP scores and the cNLS (Nuclear Localization Signal) Mapper, respectively. Subsequently, the MbovP467 gene was synthesized and cloned into a pEGFP plasmid with EGFP labeling to obtain a recombinant plasmid (rpEGFP-MbovP467) and then was also cloned in pET-30a with a consideration for an Escherichia coli codon bias and expressed and purified for the production of polyclonal antibodies against the recombinant MbovP467 protein. Confocal microscopy and a Western blotting assay confirmed the nuclear location of MbovP467 in bovine macrophages (BoMacs). RNA-seq data revealed 220 up-regulated and 20 down-regulated genes in the rpEGFP-MbovP467-treated BoMac group compared to the control group (pEGFP). A GO- and KEGG-enrichment analysis identified associations with inflammatory responses, G protein-coupled receptor signaling pathways, nuclear receptor activity, sequence-specific DNA binding, the regulation of cell proliferation, IL-8, apoptotic processes, cell growth and death, the TNF signaling pathway, the NF-κB signaling pathway, pathways in cancer, and protein families of signaling and cellular processes among the differentially expressed up-regulated mRNAs. Further experiments, investigating cell viability and the inflammatory response, demonstrated that MbovP467 reduces BoMac cell viability and induces the mRNA expression of IL-1β, IL-6, IL-8, TNF-α, and apoptosis in BoMac cells. Further, MbovP467 increased the promoter activity of TNF-α. In conclusion, this study identified a new nucleomodulin, MbovP467, for M. bovis, which might have an important role in M. bovis pathogenesis.
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Affiliation(s)
- Abdul Raheem
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Doukun Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Abdul Karim Khalid
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Gang Zhao
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, School of Life Sciences, Ningxia University, Yinchuan 750021, China;
| | - Yingjie Fu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingyu Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianguo Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.R.); (D.L.); (A.K.K.); (Y.F.); (Y.C.); (X.C.); (C.H.); (J.C.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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3
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do Nascimento Soares T, Silva Valadares V, Cardoso Amorim G, de Mattos Lacerda de Carvalho M, Berrêdo‐Pinho M, Ceneviva Lacerda Almeida F, Mascarello Bisch P, Batista PR, Miranda Santos Lery L. The C‐terminal extension of
VgrG4
from
Klebsiella pneumoniae
remodels host cell microfilaments. Proteins 2022; 90:1655-1668. [PMID: 35430767 PMCID: PMC9542434 DOI: 10.1002/prot.26344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/11/2022] [Accepted: 04/07/2022] [Indexed: 12/12/2022]
Abstract
Klebsiella pneumoniae is an opportunistic pathogen, which concerns public health systems worldwide, as multiple antibiotic‐resistant strains are frequent. One of its pathogenicity factors is the Type VI Secretion System (T6SS), a macromolecular complex assembled through the bacterial membranes. T6SS injects effector proteins inside target cells. Such effectors confer competitive advantages or modulate the target cell signaling and metabolism to favor bacterial infection. The VgrG protein is a T6SS core component. It may present a variable C‐terminal domain carrying an additional effector function. Kp52.145 genome encodes three VgrG proteins, one of them with a C‐terminal extension (VgrG4‐CTD). VgrG4‐CTD is 138 amino acids long, does not contain domains of known function, but is conserved in some Klebsiella, and non‐Klebsiella species. To get insights into its function, recombinant VgrG4‐CTD was used in pulldown experiments to capture ligands from macrophages and lung epithelial cells. A total of 254 proteins were identified: most of them are ribosomal proteins. Cytoskeleton‐associated and proteins involved in the phagosome maturation pathway were also identified. We further showed that VgrG4‐CTD binds actin and induces actin remodeling in macrophages. This study presents novel clues on the role of K. pneumoniae T6SS in pathogenesis.
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Affiliation(s)
| | | | | | | | - Marcia Berrêdo‐Pinho
- Laboratório de Microbiologia Celular Instituto Oswaldo Cruz Rio de Janeiro Brazil
| | - Fábio Ceneviva Lacerda Almeida
- Centro Nacional de Ressonância Magnética Nuclear Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Paulo Mascarello Bisch
- Laboratório de Física‐Biológica Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
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4
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Smith KP, Lee W, Tonelli M, Lee Y, Light SH, Cornilescu G, Chakravarthy S. Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach. Protein Sci 2022; 31:e4282. [PMID: 35137487 PMCID: PMC9047041 DOI: 10.1002/pro.4282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 11/11/2022]
Abstract
The bacterial pathogen Vibrio cholerae use a type III secretion system to inject effector proteins into a host cell. Recently, a putative Toxic GTPase Activating Protein (ToxGAP) called Vibrio outer protein E (VopE) was identified as a T3SS substrate and virulence factor that affected host mitochondrial dynamics and immune response. However, biophysical and structural characterization has been absent. Here, we describe solution NMR structure of the putative GTPase-activating protein (GAP) domain (73-204) of VopE. Using size exclusion chromatography coupled with small-angle x-ray scattering and residual dipolar coupling data, we restrained the MD process to efficiently determine the overall fold and improve the quality of the output calculated structures. Comparing the structure of VopE with other ToxGAP's revealed a similar overall fold with several features unique to VopE. Specifically, the "Bulge 1," α1 helix, and noteworthy "backside linker" elements on the N-terminus are dissimilar to the other ToxGAP's. By using NMR relaxation dispersion experiments, we demonstrate that these regions undergo motions on a > 6 s-1 timescale. Based on the disposition of these mobile regions relative to the putative catalytic arginine residue, we hypothesize that the protein may undergo structural changes to bind cognate GTPases.
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Affiliation(s)
- Kyle P. Smith
- Department of Cell & Developmental BiologyNorthwestern University ChicagoIllinoisUSA
- Xilio TherapeuticsWalthamMassachusettsUSA
| | - Woonghee Lee
- Department of ChemistryUniversity of Colorado‐DenverDenverColoradoUSA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Yeongjoon Lee
- Department of ChemistryUniversity of Colorado‐DenverDenverColoradoUSA
| | - Samuel H. Light
- Department of MicrobiologyUniversity of ChicagoChicagoIllinoisUSA
| | - Gabriel Cornilescu
- Advanced Technology Research Facility, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research, Inc., National Cancer Institute, National Institutes of HealthFrederickMarylandUSA
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5
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Khan AA, Khan Z. Bacterial nucleomodulins and cancer: An unresolved enigma. Transl Oncol 2021; 14:100922. [PMID: 33137543 PMCID: PMC7644672 DOI: 10.1016/j.tranon.2020.100922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 01/07/2023] Open
Abstract
Recent studies in microbial pathogenesis have identified several bacterial proteins with the potential to influence host cell nuclei. This field of research is in its infancy, however it is rapidly growing. In particular, the role of bacterial nucleomodulins in animal oncogenesis is an area that requires attention. Earlier research has suggested the role of nucleomodulins in plant tumor development and these findings may provide us with a better understanding of the role of these proteins in human cancer development. This proposition is further supported by previous identification of nucleomodulins present in bacteria that have been associated with cancer development, but their role in human cancer is unclear. In this article, we provide an update on the status of these nucleomodulins and their role in cancer etiology. We collected information about known bacterial nucleomodulins and tried to relate their mechanistic implication with already known plant tumor development model. The present research indicates that bacterial nucleomodulins may be an important target in cancer etiology and knowledge of their role in human oncogenesis may help us to create suitable alternative cancer management strategies.
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Affiliation(s)
- Abdul Arif Khan
- Indian Council of Medical Research-National AIDS Research Institute, Pune, Maharashtra 411026, India.
| | - Zakir Khan
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Davis Bldg. Rm. 2008, 8700 Beverly Blvd. Los Angeles, CA 90048, United States
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6
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Hanford HE, Von Dwingelo J, Abu Kwaik Y. Bacterial nucleomodulins: A coevolutionary adaptation to the eukaryotic command center. PLoS Pathog 2021; 17:e1009184. [PMID: 33476322 PMCID: PMC7819608 DOI: 10.1371/journal.ppat.1009184] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Through long-term interactions with their hosts, bacterial pathogens have evolved unique arsenals of effector proteins that interact with specific host targets and reprogram the host cell into a permissive niche for pathogen proliferation. The targeting of effector proteins into the host cell nucleus for modulation of nuclear processes is an emerging theme among bacterial pathogens. These unique pathogen effector proteins have been termed in recent years as "nucleomodulins." The first nucleomodulins were discovered in the phytopathogens Agrobacterium and Xanthomonas, where their nucleomodulins functioned as eukaryotic transcription factors or integrated themselves into host cell DNA to promote tumor induction, respectively. Numerous nucleomodulins were recently identified in mammalian pathogens. Bacterial nucleomodulins are an emerging family of pathogen effector proteins that evolved to target specific components of the host cell command center through various mechanisms. These mechanisms include: chromatin dynamics, histone modification, DNA methylation, RNA splicing, DNA replication, cell cycle, and cell signaling pathways. Nucleomodulins may induce short- or long-term epigenetic modifications of the host cell. In this extensive review, we discuss the current knowledge of nucleomodulins from plant and mammalian pathogens. While many nucleomodulins are already identified, continued research is instrumental in understanding their mechanisms of action and the role they play during the progression of pathogenesis. The continued study of nucleomodulins will enhance our knowledge of their effects on nuclear chromatin dynamics, protein homeostasis, transcriptional landscapes, and the overall host cell epigenome.
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Affiliation(s)
- Hannah E. Hanford
- Department of Microbiology and Immunology, University of Louisville, Kentucky, United States of America
| | - Juanita Von Dwingelo
- Department of Microbiology and Immunology, University of Louisville, Kentucky, United States of America
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Kentucky, United States of America
- Center for Predicative Medicine, College of Medicine, University of Louisville, Kentucky, United States of America
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Nissan G, Chalupowicz L, Sessa G, Manulis‐Sasson S, Barash I. Two Pantoea agglomerans type III effectors can transform nonpathogenic and phytopathogenic bacteria into host-specific gall-forming pathogens. MOLECULAR PLANT PATHOLOGY 2019; 20:1582-1587. [PMID: 31368647 PMCID: PMC6804341 DOI: 10.1111/mpp.12860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Pantoea agglomerans (Pa), a widespread commensal bacterium, has evolved into a host-specific gall-forming pathogen on gypsophila and beet by acquiring a plasmid harbouring a type III secretion system (T3SS) and effectors (T3Es). Pantoea agglomerans pv. gypsophilae (Pag) elicits galls on gypsophila and a hypersensitive response on beet, whereas P. agglomerans pv. betae (Pab) elicits galls on beet and gypsophila. HsvG and HsvB are two paralogous T3Es present in both pathovars and act as host-specific transcription activators on gypsophila and beet, respectively. PthG and PseB are major T3Es that contribute to gall development of Pag and Pab, respectively. To establish the minimal combinations of T3Es that are sufficient to elicit gall symptoms, strains of the nonpathogenic bacteria Pseudomonas fluorescens 55, Pa 3-1, Pa 98 and Escherichia coli, transformed with pHIR11 harbouring a T3SS, and the phytopathogenic bacteria Erwinia amylovora, Dickeya solani and Xanthomonas campestris pv. campestris were transformed with the T3Es hsvG, hsvB, pthG and pseB, either individually or in pairs, and used to infect gypsophila and beet. Strikingly, all the tested nonpathogenic and phytopathogenic bacterial strains harbouring hsvG and pthG incited galls on gypsophila, whereas strains harbouring hsvB and pseB, with the exception of E. coli, incited galls on beet.
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Affiliation(s)
- Gal Nissan
- School of Plant Sciences and Security, Faculty of Life SciencesTel‐Aviv UniversityTel AvivIsrael
- Department of Plant Pathology and Weed ResearchARO the Volcani CenterRishon LeZion7528809Israel
| | - Laura Chalupowicz
- Department of Plant Pathology and Weed ResearchARO the Volcani CenterRishon LeZion7528809Israel
| | - Guido Sessa
- School of Plant Sciences and Security, Faculty of Life SciencesTel‐Aviv UniversityTel AvivIsrael
| | - Shulamit Manulis‐Sasson
- Department of Plant Pathology and Weed ResearchARO the Volcani CenterRishon LeZion7528809Israel
| | - Isaac Barash
- School of Plant Sciences and Security, Faculty of Life SciencesTel‐Aviv UniversityTel AvivIsrael
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8
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Cao FY, Khan M, Taniguchi M, Mirmiran A, Moeder W, Lumba S, Yoshioka K, Desveaux D. A host-pathogen interactome uncovers phytopathogenic strategies to manipulate plant ABA responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:187-198. [PMID: 31148337 DOI: 10.1111/tpj.14425] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 04/05/2018] [Accepted: 05/22/2019] [Indexed: 05/21/2023]
Abstract
The phytopathogen Pseudomonas syringae delivers into host cells type III secreted effectors (T3SEs) that promote virulence. One virulence mechanism employed by T3SEs is to target hormone signaling pathways to perturb hormone homeostasis. The phytohormone abscisic acid (ABA) influences interactions between various phytopathogens and their plant hosts, and has been shown to be a target of P. syringae T3SEs. In order to provide insight into how T3SEs manipulate ABA responses, we generated an ABA-T3SE interactome network (ATIN) between P. syringae T3SEs and Arabidopsis proteins encoded by ABA-regulated genes. ATIN consists of 476 yeast-two-hybrid interactions between 97 Arabidopsis ABA-regulated proteins and 56 T3SEs from four pathovars of P. syringae. We demonstrate that T3SE interacting proteins are significantly enriched for proteins associated with transcription. In particular, the ETHYLENE RESPONSIVE FACTOR (ERF) family of transcription factors is highly represented. We show that ERF105 and ERF8 displayed a role in defense against P. syringae, supporting our overall observation that T3SEs of ATIN converge on proteins that influence plant immunity. In addition, we demonstrate that T3SEs that interact with a large number of ABA-regulated proteins can influence ABA responses. One of these T3SEs, HopF3Pph6 , inhibits the function of ERF8, which influences both ABA-responses and plant immunity. These results provide a potential mechanism for how HopF3Pph6 manipulates ABA-responses to promote P. syringae virulence, and also demonstrate the utility of ATIN as a resource to study the ABA-T3SE interface.
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Affiliation(s)
- Feng Y Cao
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Madiha Khan
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Masatoshi Taniguchi
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Armand Mirmiran
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Wolfgang Moeder
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Shelley Lumba
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Keiko Yoshioka
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
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9
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van de Vossenberg BTLH, Warris S, Nguyen HDT, van Gent-Pelzer MPE, Joly DL, van de Geest HC, Bonants PJM, Smith DS, Lévesque CA, van der Lee TAJ. Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum. Sci Rep 2019; 9:8672. [PMID: 31209237 PMCID: PMC6572847 DOI: 10.1038/s41598-019-45128-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 01/09/2023] Open
Abstract
Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.
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Affiliation(s)
- Bart T L H van de Vossenberg
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands.
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands.
| | - Sven Warris
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Hai D T Nguyen
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Marga P E van Gent-Pelzer
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - David L Joly
- Université de Moncton, 18 avenue Antonine-Maillet, Moncton, Canada
| | - Henri C van de Geest
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Peter J M Bonants
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Donna S Smith
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, Canada
| | - C André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Theo A J van der Lee
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
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10
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Ahmed MB, Santos KCGD, Sanchez IB, Petre B, Lorrain C, Plourde MB, Duplessis S, Desgagné-Penix I, Germain H. A rust fungal effector binds plant DNA and modulates transcription. Sci Rep 2018; 8:14718. [PMID: 30283062 PMCID: PMC6170375 DOI: 10.1038/s41598-018-32825-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/21/2018] [Indexed: 02/08/2023] Open
Abstract
The basidiomycete Melampsora larici-populina causes poplar rust disease by invading leaf tissues and secreting effector proteins through specialized infection structures known as haustoria. The mechanisms by which rust effectors promote pathogen virulence are poorly understood. The present study characterized Mlp124478, a candidate effector of M. larici-populina. We used the models Arabidopsis thaliana and Nicotiana benthamiana to investigate the function of Mlp124478 in plant cells. We established that Mlp124478 accumulates in the nucleus and nucleolus, however its nucleolar accumulation is not required to promote growth of the oomycete pathogen Hyaloperonospora arabidopsidis. Stable constitutive expression of Mlp124478 in A. thaliana repressed the expression of genes involved in immune responses, and also altered leaf morphology by increasing the waviness of rosette leaves. Chip-PCR experiments showed that Mlp124478 associats'e with the TGA1a-binding DNA sequence. Our results suggest that Mlp124478 exerts a virulence activity and binds the TGA1a promoter to suppress genes induced in response to pathogen infection.
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Affiliation(s)
- Md Bulbul Ahmed
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Karen Cristine Gonçalves Dos Santos
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Ingrid Benerice Sanchez
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
- Department of Biotechnology and Engineering in Chemistry, Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Estado de México (ITESM CEM), Margarita Maza de Juárez, 52926, Cd, López Mateos, Mexico
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Faculté des Sciences et Technologies - Campus Aiguillettes, BP, 70239-54506, Vandoeuvre-lès-Nancy, France
| | - Cécile Lorrain
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
| | - Mélodie B Plourde
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada.
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada.
| | - Sébastien Duplessis
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada.
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada.
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11
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The role of chloroplasts in plant pathology. Essays Biochem 2018; 62:21-39. [PMID: 29273582 DOI: 10.1042/ebc20170020] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/22/2017] [Accepted: 11/28/2017] [Indexed: 12/13/2022]
Abstract
Plants have evolved complex tolerance systems to survive abiotic and biotic stresses. Central to these programmes is a sophisticated conversation of signals between the chloroplast and the nucleus. In this review, we examine the antagonism between abiotic stress tolerance (AST) and immunity: we propose that to generate immunogenic signals, plants must disable AST systems, in particular those that manage reactive oxygen species (ROS), while the pathogen seeks to reactivate or enhance those systems to achieve virulence. By boosting host systems of AST, pathogens trick the plant into suppressing chloroplast immunogenic signals and steer the host into making an inappropriate immune response. Pathogens disrupt chloroplast function, both transcriptionally-by secreting effectors that alter host gene expression by interacting with defence-related kinase cascades, with transcription factors, or with promoters themselves-and post-transcriptionally, by delivering effectors that enter the chloroplast or alter the localization of host proteins to change chloroplast activities. These mechanisms reconfigure the chloroplast proteome and chloroplast-originating immunogenic signals in order to promote infection.
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12
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Nissan G, Gershovits M, Morozov M, Chalupowicz L, Sessa G, Manulis‐Sasson S, Barash I, Pupko T. Revealing the inventory of type III effectors in Pantoea agglomerans gall-forming pathovars using draft genome sequences and a machine-learning approach. MOLECULAR PLANT PATHOLOGY 2018; 19:381-392. [PMID: 28019708 PMCID: PMC6638007 DOI: 10.1111/mpp.12528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/06/2016] [Accepted: 12/14/2016] [Indexed: 05/03/2023]
Abstract
Pantoea agglomerans, a widespread epiphytic bacterium, has evolved into a hypersensitive response and pathogenicity (hrp)-dependent and host-specific gall-forming pathogen by the acquisition of a pathogenicity plasmid containing a type III secretion system (T3SS) and its effectors (T3Es). Pantoea agglomerans pv. betae (Pab) elicits galls on beet (Beta vulgaris) and gypsophila (Gypsophila paniculata), whereas P. agglomerans pv. gypsophilae (Pag) incites galls on gypsophila and a hypersensitive response (HR) on beet. Draft genome sequences were generated and employed in combination with a machine-learning approach and a translocation assay into beet roots to identify the pools of T3Es in the two pathovars. The genomes of the sequenced Pab4188 and Pag824-1 strains have a similar size (∼5 MB) and GC content (∼55%). Mutational analysis revealed that, in Pab4188, eight T3Es (HsvB, HsvG, PseB, DspA/E, HopAY1, HopX2, HopAF1 and HrpK) contribute to pathogenicity on beet and gypsophila. In Pag824-1, nine T3Es (HsvG, HsvB, PthG, DspA/E, HopAY1, HopD1, HopX2, HopAF1 and HrpK) contribute to pathogenicity on gypsophila, whereas the PthG effector triggers HR on beet. HsvB, HsvG, PthG and PseB appear to endow pathovar specificities to Pab and Pag, and no homologous T3Es were identified for these proteins in other phytopathogenic bacteria. Conversely, the remaining T3Es contribute to the virulence of both pathovars, and homologous T3Es were found in other phytopathogenic bacteria. Remarkably, HsvG and HsvB, which act as host-specific transcription factors, displayed the largest contribution to disease development.
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Affiliation(s)
- Gal Nissan
- Department of Molecular Biology and Ecology of Plants, Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv69978Israel
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, The Volcani CenterRishonLeZion7528809Israel
| | - Michael Gershovits
- Department of Cell Research and Immunology, Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv69978Israel
| | - Michael Morozov
- Department of Molecular Biology and Ecology of Plants, Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv69978Israel
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, The Volcani CenterRishonLeZion7528809Israel
| | - Laura Chalupowicz
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, The Volcani CenterRishonLeZion7528809Israel
| | - Guido Sessa
- Department of Molecular Biology and Ecology of Plants, Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv69978Israel
| | - Shulamit Manulis‐Sasson
- Department of Plant Pathology and Weed ResearchAgricultural Research Organization, The Volcani CenterRishonLeZion7528809Israel
| | - Isaac Barash
- Department of Molecular Biology and Ecology of Plants, Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv69978Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv69978Israel
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13
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Büttner D. Behind the lines-actions of bacterial type III effector proteins in plant cells. FEMS Microbiol Rev 2018; 40:894-937. [PMID: 28201715 PMCID: PMC5091034 DOI: 10.1093/femsre/fuw026] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/31/2016] [Accepted: 07/03/2016] [Indexed: 01/30/2023] Open
Abstract
Pathogenicity of most Gram-negative plant-pathogenic bacteria depends on the type III secretion (T3S) system, which translocates bacterial effector proteins into plant cells. Type III effectors modulate plant cellular pathways to the benefit of the pathogen and promote bacterial multiplication. One major virulence function of type III effectors is the suppression of plant innate immunity, which is triggered upon recognition of pathogen-derived molecular patterns by plant receptor proteins. Type III effectors also interfere with additional plant cellular processes including proteasome-dependent protein degradation, phytohormone signaling, the formation of the cytoskeleton, vesicle transport and gene expression. This review summarizes our current knowledge on the molecular functions of type III effector proteins with known plant target molecules. Furthermore, plant defense strategies for the detection of effector protein activities or effector-triggered alterations in plant targets are discussed.
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Affiliation(s)
- Daniela Büttner
- Genetics Department, Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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14
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Ramirez-Prado JS, Piquerez SJM, Bendahmane A, Hirt H, Raynaud C, Benhamed M. Modify the Histone to Win the Battle: Chromatin Dynamics in Plant-Pathogen Interactions. FRONTIERS IN PLANT SCIENCE 2018; 9:355. [PMID: 29616066 PMCID: PMC5868138 DOI: 10.3389/fpls.2018.00355] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/02/2018] [Indexed: 05/02/2023]
Abstract
Relying on an immune system comes with a high energetic cost for plants. Defense responses in these organisms are therefore highly regulated and fine-tuned, permitting them to respond pertinently to the attack of a microbial pathogen. In recent years, the importance of the physical modification of chromatin, a highly organized structure composed of genomic DNA and its interacting proteins, has become evident in the research field of plant-pathogen interactions. Several processes, including DNA methylation, changes in histone density and variants, and various histone modifications, have been described as regulators of various developmental and defense responses. Herein, we review the state of the art in the epigenomic aspects of plant immunity, focusing on chromatin modifications, chromatin modifiers, and their physiological consequences. In addition, we explore the exciting field of understanding how plant pathogens have adapted to manipulate the plant epigenomic regulation in order to weaken their immune system and thrive in their host, as well as how histone modifications in eukaryotic pathogens are involved in the regulation of their virulence.
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Affiliation(s)
- Juan S. Ramirez-Prado
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Sophie J. M. Piquerez
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Abdelhafid Bendahmane
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Heribert Hirt
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Cécile Raynaud
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Moussa Benhamed
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
- *Correspondence: Moussa Benhamed,
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15
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Howden AJM, Stam R, Martinez Heredia V, Motion GB, ten Have S, Hodge K, Marques Monteiro Amaro TM, Huitema E. Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity. THE NEW PHYTOLOGIST 2017; 215:309-322. [PMID: 28394025 PMCID: PMC5637918 DOI: 10.1111/nph.14540] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/22/2017] [Indexed: 05/20/2023]
Abstract
Plant-pathogen interactions are complex associations driven by the interplay of host and microbe-encoded factors. With secreted pathogen proteins (effectors) and immune signalling components found in the plant nucleus, this compartment is a battleground where susceptibility is specified. We hypothesized that, by defining changes in the nuclear proteome during infection, we can pinpoint vital components required for immunity or susceptibility. We tested this hypothesis by documenting dynamic changes in the tomato (Solanum lycopersicum) nuclear proteome during infection by the oomycete pathogen Phytophthora capsici. We enriched nuclei from infected and noninfected tissues and quantitatively assessed changes in the nuclear proteome. We then tested the role of candidate regulators in immunity through functional assays. We demonstrated that the host nuclear proteome dynamically changes during P. capsici infection. We observed that known nuclear immunity factors were differentially expressed and, based on this observation, selected a set of candidate regulators that we successfully implicated in immunity to P. capsici. Our work exemplifies a powerful strategy to gain rapid insight into important nuclear processes that underpin complex crop traits such as resistance. We have identified a large set of candidate nuclear factors that may underpin immunity to pathogens in crops.
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Affiliation(s)
- Andrew J. M. Howden
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
| | - Remco Stam
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
- Section of Population GeneticsTechnische Universität München85354FreisingGermany
| | - Victor Martinez Heredia
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
| | - Graham B. Motion
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
- Cell and Molecular SciencesJHIInvergowrieDundeeDD2 5DAUK
| | - Sara ten Have
- Wellcome Trust Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | - Kelly Hodge
- Wellcome Trust Centre for Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | - Tiago M. Marques Monteiro Amaro
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
| | - Edgar Huitema
- Division of Plant ScienceSchool of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI)InvergowrieDundeeDD2 5DAUK
- Dundee Effector ConsortiumJHIInvergowrieDundeeDD2 5DAUK
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16
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17
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Sperschneider J, Catanzariti AM, DeBoer K, Petre B, Gardiner DM, Singh KB, Dodds PN, Taylor JM. LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell. Sci Rep 2017; 7:44598. [PMID: 28300209 PMCID: PMC5353544 DOI: 10.1038/srep44598] [Citation(s) in RCA: 247] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/09/2017] [Indexed: 12/17/2022] Open
Abstract
Pathogens secrete effector proteins and many operate inside plant cells to enable infection. Some effectors have been found to enter subcellular compartments by mimicking host targeting sequences. Although many computational methods exist to predict plant protein subcellular localization, they perform poorly for effectors. We introduce LOCALIZER for predicting plant and effector protein localization to chloroplasts, mitochondria, and nuclei. LOCALIZER shows greater prediction accuracy for chloroplast and mitochondrial targeting compared to other methods for 652 plant proteins. For 107 eukaryotic effectors, LOCALIZER outperforms other methods and predicts a previously unrecognized chloroplast transit peptide for the ToxA effector, which we show translocates into tobacco chloroplasts. Secretome-wide predictions and confocal microscopy reveal that rust fungi might have evolved multiple effectors that target chloroplasts or nuclei. LOCALIZER is the first method for predicting effector localisation in plants and is a valuable tool for prioritizing effector candidates for functional investigations. LOCALIZER is available at http://localizer.csiro.au/.
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Affiliation(s)
- Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - Ann-Maree Catanzariti
- Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Kathleen DeBoer
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Donald M. Gardiner
- Queensland Bioscience Precinct, CSIRO Agriculture and Food, Brisbane, QLD, Australia
| | - Karam B. Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - Peter N. Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Jennifer M. Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
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18
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Khan AA, Khan Z, Kalam MA, Khan AA. Inter-kingdom prediction certainty evaluation of protein subcellular localization tools: microbial pathogenesis approach for deciphering host microbe interaction. Brief Bioinform 2016; 19:12-22. [DOI: 10.1093/bib/bbw093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 12/19/2022] Open
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19
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Garner CM, Kim SH, Spears BJ, Gassmann W. Express yourself: Transcriptional regulation of plant innate immunity. Semin Cell Dev Biol 2016; 56:150-162. [PMID: 27174437 DOI: 10.1016/j.semcdb.2016.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
The plant immune system is a complex network of components that function together to sense the presence and activity of potential biotic threats, and integrate these signals into an appropriate output, namely the transcription of genes that activate an immune response that is commensurate with the perceived threat. Given the variety of biotic threats a plant must face the immune response must be plastic, but because an immune response is costly to the plant in terms of energy expenditure and development it must also be under tight control. To meet these needs transcriptional control is exercised at multiple levels. In this article we will review some of the latest developments in understanding how the plant immune response is regulated at the level of transcription. New roles are being discovered for the long-studied WRKY and TGA transcription factor families, while additional critical defense functions are being attributed to TCPs and other transcription factors. Dynamically controlling access to DNA through post-translational modification of histones is emerging as an essential component of priming, maintaining, attenuating, and repressing transcription in response to biotic stress. Unsurprisingly, the plant's transcriptional response is targeted by pathogen effectors, and in turn resistance proteins stand guard over and participate in transcriptional regulation. Together, these multiple layers lead to the observed complexity of the plant transcriptional immune response, with different transcription factors or chromatin components playing a prominent role depending on the plant-pathogen interaction being studied.
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Affiliation(s)
- Christopher M Garner
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA; C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Sang Hee Kim
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA; C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Benjamin J Spears
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA; C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Walter Gassmann
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA; C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA.
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20
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Inada N, Higaki T, Hasezawa S. Nuclear Function of Subclass I Actin-Depolymerizing Factor Contributes to Susceptibility in Arabidopsis to an Adapted Powdery Mildew Fungus. PLANT PHYSIOLOGY 2016; 170:1420-34. [PMID: 26747284 PMCID: PMC4775110 DOI: 10.1104/pp.15.01265] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/05/2016] [Indexed: 05/19/2023]
Abstract
Actin-depolymerizing factors (ADFs) are conserved proteins that function in regulating the structure and dynamics of actin microfilaments in eukaryotes. In this study, we present evidence that Arabidopsis (Arabidopsis thaliana) subclass I ADFs, particularly ADF4, functions as a susceptibility factor for an adapted powdery mildew fungus. The null mutant of ADF4 significantly increased resistance against the adapted powdery mildew fungus Golovinomyces orontii. The degree of resistance was further enhanced in transgenic plants in which the expression of all subclass I ADFs (i.e. ADF1-ADF4) was suppressed. Microscopic observations revealed that the enhanced resistance of adf4 and ADF1-4 knockdown plants (ADF1-4Ri) was associated with the accumulation of hydrogen peroxide and cell death specific to G. orontii-infected cells. The increased resistance and accumulation of hydrogen peroxide in ADF1-4Ri were suppressed by the introduction of mutations in the salicylic acid- and jasmonic acid-signaling pathways but not by a mutation in the ethylene-signaling pathway. Quantification by microscopic images detected an increase in the level of actin microfilament bundling in ADF1-4Ri but not in adf4 at early G. orontii infection time points. Interestingly, complementation analysis revealed that nuclear localization of ADF4 was crucial for susceptibility to G. orontii. Based on its G. orontii-infected-cell-specific phenotype, we suggest that subclass I ADFs are susceptibility factors that function in a direct interaction between the host plant and the powdery mildew fungus.
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Affiliation(s)
- Noriko Inada
- Laboratory of Plant Function Analysis, Plant Global Educational Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (N.I.); andDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan (T.H., S.H.)
| | - Takumi Higaki
- Laboratory of Plant Function Analysis, Plant Global Educational Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (N.I.); andDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan (T.H., S.H.)
| | - Seiichiro Hasezawa
- Laboratory of Plant Function Analysis, Plant Global Educational Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan (N.I.); andDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan (T.H., S.H.)
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Targeting of host organelles by pathogenic bacteria: a sophisticated subversion strategy. Nat Rev Microbiol 2015; 14:5-19. [PMID: 26594043 DOI: 10.1038/nrmicro.2015.1] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many bacterial pathogens have evolved the ability to subvert and exploit host functions in order to enter and replicate in eukaryotic cells. For example, bacteria have developed specific mechanisms to target eukaryotic organelles such as the nucleus, the mitochondria, the endoplasmic reticulum and the Golgi apparatus. In this Review, we highlight the most recent advances in our understanding of the mechanisms that bacterial pathogens use to target these organelles. We also discuss how these strategies allow bacteria to manipulate host functions and to ultimately enable bacterial infection.
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The intracellular Scots pine shoot symbiont Methylobacterium extorquens DSM13060 aggregates around the host nucleus and encodes eukaryote-like proteins. mBio 2015; 6:mBio.00039-15. [PMID: 25805725 PMCID: PMC4453540 DOI: 10.1128/mbio.00039-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Endophytes are microbes that inhabit plant tissues without any apparent signs of infection, often fundamentally altering plant phenotypes. While endophytes are typically studied in plant roots, where they colonize the apoplast or dead cells, Methylobacterium extorquens strain DSM13060 is a facultatively intracellular symbiont of the meristematic cells of Scots pine (Pinus sylvestris L.) shoot tips. The bacterium promotes host growth and development without the production of known plant growth-stimulating factors. Our objective was to examine intracellular colonization by M. extorquens DSM13060 of Scots pine and sequence its genome to identify novel molecular mechanisms potentially involved in intracellular colonization and plant growth promotion. Reporter construct analysis of known growth promotion genes demonstrated that these were only weakly active inside the plant or not expressed at all. We found that bacterial cells accumulate near the nucleus in intact, living pine cells, pointing to host nuclear processes as the target of the symbiont’s activity. Genome analysis identified a set of eukaryote-like functions that are common as effectors in intracellular bacterial pathogens, supporting the notion of intracellular bacterial activity. These include ankyrin repeats, transcription factors, and host-defense silencing functions and may be secreted by a recently imported type IV secretion system. Potential factors involved in host growth include three copies of phospholipase A2, an enzyme that is rare in bacteria but implicated in a range of plant cellular processes, and proteins putatively involved in gibberellin biosynthesis. Our results describe a novel endophytic niche and create a foundation for postgenomic studies of a symbiosis with potential applications in forestry and agriculture. All multicellular eukaryotes host communities of essential microbes, but most of these interactions are still poorly understood. In plants, bacterial endophytes are found inside all tissues. M. extorquens DSM13060 occupies an unusual niche inside cells of the dividing shoot tissues of a pine and stimulates seedling growth without producing cytokinin, auxin, or other plant hormones commonly synthesized by plant-associated bacteria. Here, we tracked the bacteria using a fluorescent tag and confocal laser scanning microscopy and found that they localize near the nucleus of the plant cell. This prompted us to sequence the genome and identify proteins that may affect host growth by targeting processes in the host cytoplasm and nucleus. We found many novel genes whose products may modulate plant processes from within the plant cell. Our results open up new avenues to better understand how bacteria assist in plant growth, with broad implications for plant science, forestry, and agriculture.
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Shi Y, Lee LY, Gelvin SB. Is VIP1 important for Agrobacterium-mediated transformation? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:848-60. [PMID: 24953893 DOI: 10.1111/tpj.12596] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 05/07/2014] [Accepted: 06/09/2014] [Indexed: 05/05/2023]
Abstract
Agrobacterium genetically transforms plants by transferring and integrating T-(transferred) DNA into the host genome. This process requires both Agrobacterium and host proteins. VirE2 interacting protein 1 (VIP1), an Arabidopsis bZIP protein, has been suggested to mediate transformation through interaction with and targeting of VirE2 to nuclei. We examined the susceptibility of Arabidopsis vip1 mutant and VIP1 overexpressing plants to transformation by numerous Agrobacterium strains. In no instance could we detect altered transformation susceptibility. We also used confocal microscopy to examine the subcellular localization of Venus-tagged VirE2 or Venus-tagged VIP1, in the presence or absence of the other untagged protein, in different plant cell systems. We found that VIP1-Venus localized in both the cytoplasm and the nucleus of Arabidopsis roots, agroinfiltrated Nicotiana benthamiana leaves, Arabidopsis mesophyll protoplasts and tobacco BY-2 protoplasts, regardless of whether VirE2 was co-expressed. VirE2 localized exclusively to the cytoplasm of tobacco and Arabidopsis protoplasts, whether in the absence or presence of VIP1 overexpression. In transgenic Arabidopsis plants and agroinfiltrated N. benthamina leaves we could occasionally detect small aggregates of the Venus signal in nuclei, but these were likely to be imagining artifacts. The vast majority of VirE2 remained in the cytoplasm. We conclude that VIP1 is not important for Agrobacterium-mediated transformation or VirE2 subcellular localization.
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Affiliation(s)
- Yong Shi
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi, 712100, China; Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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Lohou D, Turner M, Lonjon F, Cazalé AC, Peeters N, Genin S, Vailleau F. HpaP modulates type III effector secretion in Ralstonia solanacearum and harbours a substrate specificity switch domain essential for virulence. MOLECULAR PLANT PATHOLOGY 2014; 15:601-14. [PMID: 24405562 PMCID: PMC6638691 DOI: 10.1111/mpp.12119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Many pathogenic bacteria have evolved a type III secretion system (T3SS) to successfully invade their host. This extracellular apparatus allows the translocation of proteins, called type III effectors (T3Es), directly into the host cells. T3Es are virulence factors that have been shown to interfere with the host's immunity or to provide nutrients from the host to the bacteria. The Gram-negative bacterium Ralstonia solanacearum is a worldwide major crop pest whose virulence strongly relies on the T3SS. In R. solanacearum, transcriptional regulation has been extensively studied. However, very few data are available concerning the role played by type III-associated regulators, such as type III chaperones and T3SS control proteins. Here, we characterized HpaP, a putative type III secretion substrate specificity switch (T3S4) protein of R. solanacearum which is not secreted by the bacterium or translocated in the plant cells. HpaP self-interacts and interacts with the PopP1 T3E. HpaP modulates the secretion of early (HrpY pilin) and late (AvrA and PopP1 T3Es) type III substrates. HpaP is dispensable for the translocation of T3Es into the host cells. Finally, we identified two regions of five amino acids in the T3S4 domain that are essential for efficient PopP1 secretion and for HpaP's role in virulence on tomato and Arabidopsis thaliana, but not required for HpaP-HpaP and HpaP-PopP1 interactions. Taken together, our results indicate that HpaP is a putative R. solanacearum T3S4 protein important for full pathogenicity on several hosts, acting as a helper for PopP1 secretion, and repressing AvrA and HrpY secretion.
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Affiliation(s)
- David Lohou
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, F-31326, Castanet-Tolosan, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, F-31326, Castanet-Tolosan, France
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Kazan K, Lyons R. Intervention of Phytohormone Pathways by Pathogen Effectors. THE PLANT CELL 2014; 26:2285-2309. [PMID: 24920334 PMCID: PMC4114936 DOI: 10.1105/tpc.114.125419] [Citation(s) in RCA: 267] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/16/2014] [Accepted: 05/24/2014] [Indexed: 05/18/2023]
Abstract
The constant struggle between plants and microbes has driven the evolution of multiple defense strategies in the host as well as offense strategies in the pathogen. To defend themselves from pathogen attack, plants often rely on elaborate signaling networks regulated by phytohormones. In turn, pathogens have adopted innovative strategies to manipulate phytohormone-regulated defenses. Tactics frequently employed by plant pathogens involve hijacking, evading, or disrupting hormone signaling pathways and/or crosstalk. As reviewed here, this is achieved mechanistically via pathogen-derived molecules known as effectors, which target phytohormone receptors, transcriptional activators and repressors, and other components of phytohormone signaling in the host plant. Herbivores and sap-sucking insects employ obligate pathogens such as viruses, phytoplasma, or symbiotic bacteria to intervene with phytohormone-regulated defenses. Overall, an improved understanding of phytohormone intervention strategies employed by pests and pathogens during their interactions with plants will ultimately lead to the development of new crop protection strategies.
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Affiliation(s)
- Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Queensland Bioscience Precinct, Brisbane 4069, Queensland, Australia
| | - Rebecca Lyons
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Queensland Bioscience Precinct, Brisbane 4069, Queensland, Australia
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Lefeuvre P, Cellier G, Remenant B, Chiroleu F, Prior P. Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species. PLoS One 2013; 8:e63155. [PMID: 23723974 PMCID: PMC3665557 DOI: 10.1371/journal.pone.0063155] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/28/2013] [Indexed: 01/11/2023] Open
Abstract
Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.
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Affiliation(s)
- Pierre Lefeuvre
- CIRAD UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France.
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Gimenez-Ibanez S, Solano R. Nuclear jasmonate and salicylate signaling and crosstalk in defense against pathogens. FRONTIERS IN PLANT SCIENCE 2013; 4:72. [PMID: 23577014 PMCID: PMC3617366 DOI: 10.3389/fpls.2013.00072] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 03/15/2013] [Indexed: 05/20/2023]
Abstract
An extraordinary progress has been made over the last two decades on understanding the components and mechanisms governing plant innate immunity. After detection of a pathogen, effective plant resistance depends on the activation of a complex signaling network integrated by small signaling molecules and hormonal pathways, and the balance of these hormone systems determines resistance to particular pathogens. The discovery of new components of hormonal signaling pathways, including plant nuclear hormone receptors, is providing a picture of complex crosstalk and induced hormonal changes that modulate disease and resistance through several protein families that perceive hormones within the nucleus and lead to massive gene induction responses often achieved by de-repression. This review highlights recent advances in our understanding of positive and negative regulators of these hormones signaling pathways that are crucial regulatory targets of hormonal crosstalk in disease and defense. We focus on the most recent discoveries on the jasmonate and salicylate pathway components that explain their crosstalk with other hormonal pathways in the nucleus. We discuss how these components fine-tune defense responses to build a robust plant immune system against a great number of different microbes and, finally, we summarize recent discoveries on specific nuclear hormonal manipulation by microbes which exemplify the ingenious ways by which pathogens can take control over the plant's hormone signaling network to promote disease.
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Affiliation(s)
| | - Roberto Solano
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones CientíficasMadrid, Spain
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