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Read AC, Rinaldi FC, Hutin M, He YQ, Triplett LR, Bogdanove AJ. Suppression of Xo1-Mediated Disease Resistance in Rice by a Truncated, Non-DNA-Binding TAL Effector of Xanthomonas oryzae. FRONTIERS IN PLANT SCIENCE 2016; 7:1516. [PMID: 27790231 PMCID: PMC5062187 DOI: 10.3389/fpls.2016.01516] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/26/2016] [Indexed: 05/19/2023]
Abstract
Delivered into plant cells by type III secretion from pathogenic Xanthomonas species, TAL (transcription activator-like) effectors are nuclear-localized, DNA-binding proteins that directly activate specific host genes. Targets include genes important for disease, genes that confer resistance, and genes inconsequential to the host-pathogen interaction. TAL effector specificity is encoded by polymorphic repeats of 33-35 amino acids that interact one-to-one with nucleotides in the recognition site. Activity depends also on N-terminal sequences important for DNA binding and C-terminal nuclear localization signals (NLS) and an acidic activation domain (AD). Coding sequences missing much of the N- and C-terminal regions due to conserved, in-frame deletions are present and annotated as pseudogenes in sequenced strains of Xanthomonas oryzae pv. oryzicola (Xoc) and pv. oryzae (Xoo), which cause bacterial leaf streak and bacterial blight of rice, respectively. Here we provide evidence that these sequences encode proteins we call "truncTALEs," for "truncated TAL effectors." We show that truncTALE Tal2h of Xoc strain BLS256, and by correlation truncTALEs in other strains, specifically suppress resistance mediated by the Xo1 locus recently described in the heirloom rice variety Carolina Gold. Xo1-mediated resistance is triggered by different TAL effectors from diverse X. oryzae strains, irrespective of their DNA binding specificity, and does not require the AD. This implies a direct protein-protein rather than protein-DNA interaction. Similarly, truncTALEs exhibit diverse predicted DNA recognition specificities. And, in vitro, Tal2h did not bind any of several potential recognition sites. Further, a single candidate NLS sequence in Tal2h was dispensable for resistance suppression. Many truncTALEs have one 28 aa repeat, a length not observed previously. Tested in an engineered TAL effector, this repeat required a single base pair deletion in the DNA, suggesting that it or a neighbor disengages. The presence of the 28 aa repeat, however, was not required for resistance suppression. TruncTALEs expand the paradigm for TAL effector-mediated effects on plants. We propose that Tal2h and other truncTALEs act as dominant negative ligands for an immune receptor encoded by the Xo1 locus, likely a nucleotide binding, leucine-rich repeat protein. Understanding truncTALE function and distribution will inform strategies for disease control.
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Affiliation(s)
- Andrew C. Read
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Fabio C. Rinaldi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Mathilde Hutin
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Yong-Qiang He
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi UniversityNanning, China
| | - Lindsay R. Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment StationNew Haven, CT, USA
| | - Adam J. Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
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Poulin L, Grygiel P, Magne M, Gagnevin L, Rodriguez-R LM, Forero Serna N, Zhao S, El Rafii M, Dao S, Tekete C, Wonni I, Koita O, Pruvost O, Verdier V, Vernière C, Koebnik R. New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae. Appl Environ Microbiol 2015; 81:688-98. [PMID: 25398857 PMCID: PMC4277570 DOI: 10.1128/aem.02768-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/04/2014] [Indexed: 12/12/2022] Open
Abstract
Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales.
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Affiliation(s)
- L Poulin
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - P Grygiel
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - M Magne
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - L Gagnevin
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - L M Rodriguez-R
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - N Forero Serna
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - S Zhao
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - M El Rafii
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - S Dao
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), Université des Sciences Techniques et Technologie, Bamako, Mali
| | - C Tekete
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), Université des Sciences Techniques et Technologie, Bamako, Mali
| | - I Wonni
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France Institut de l'Environnement et de Recherches Agricoles, Bobo Dioulasso, Burkina Faso
| | - O Koita
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), Université des Sciences Techniques et Technologie, Bamako, Mali
| | - O Pruvost
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - V Verdier
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - C Vernière
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - R Koebnik
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
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