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Roeschlin RA, Azad SM, Grove RP, Chuan A, García L, Niñoles R, Uviedo F, Villalobos L, Massimino ME, Marano MR, Boch J, Gadea J. Designer TALEs enable discovery of cell death-inducer genes. PLANT PHYSIOLOGY 2024; 195:2985-2996. [PMID: 38723194 PMCID: PMC11288752 DOI: 10.1093/plphys/kiae230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/26/2024] [Indexed: 08/02/2024]
Abstract
Transcription activator-like effectors (TALEs) in plant-pathogenic Xanthomonas bacteria activate expression of plant genes and support infection or cause a resistance response. PthA4AT is a TALE with a particularly short DNA-binding domain harboring only 7.5 repeats which triggers cell death in Nicotiana benthamiana; however, the genetic basis for this remains unknown. To identify possible target genes of PthA4AT that mediate cell death in N. benthamiana, we exploited the modularity of TALEs to stepwise enhance their specificity and reduce potential target sites. Substitutions of individual repeats suggested that PthA4AT-dependent cell death is sequence specific. Stepwise addition of repeats to the C-terminal or N-terminal end of the repeat region narrowed the sequence requirements in promoters of target genes. Transcriptome profiling and in silico target prediction allowed the isolation of two cell death inducer genes, which encode a patatin-like protein and a bifunctional monodehydroascorbate reductase/carbonic anhydrase protein. These two proteins are not linked to known TALE-dependent resistance genes. Our results show that the aberrant expression of different endogenous plant genes can cause a cell death reaction, which supports the hypothesis that TALE-dependent executor resistance genes can originate from various plant processes. Our strategy further demonstrates the use of TALEs to scan genomes for genes triggering cell death and other relevant phenotypes.
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Affiliation(s)
- Roxana A Roeschlin
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/n, S2002LRK, Rosario, Argentina
| | - Sepideh M Azad
- Instituto de Biología Molecular y celular de Plantas (IBMCP), Universidad Politécnica de Valencia-CSIC, Ingeniero Fausto Elio S/N., 46022, Valencia, España
| | - René P Grove
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Ana Chuan
- Instituto de Biología Molecular y celular de Plantas (IBMCP), Universidad Politécnica de Valencia-CSIC, Ingeniero Fausto Elio S/N., 46022, Valencia, España
| | - Lucila García
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/n, S2002LRK, Rosario, Argentina
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 590, S2002LRK, Rosario, Argentina
| | - Regina Niñoles
- Instituto de Biología Molecular y celular de Plantas (IBMCP), Universidad Politécnica de Valencia-CSIC, Ingeniero Fausto Elio S/N., 46022, Valencia, España
| | - Facundo Uviedo
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/n, S2002LRK, Rosario, Argentina
| | - Liara Villalobos
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/n, S2002LRK, Rosario, Argentina
| | - Maria E Massimino
- Instituto de Biología Molecular y celular de Plantas (IBMCP), Universidad Politécnica de Valencia-CSIC, Ingeniero Fausto Elio S/N., 46022, Valencia, España
| | - María R Marano
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/n, S2002LRK, Rosario, Argentina
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 590, S2002LRK, Rosario, Argentina
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - José Gadea
- Instituto de Biología Molecular y celular de Plantas (IBMCP), Universidad Politécnica de Valencia-CSIC, Ingeniero Fausto Elio S/N., 46022, Valencia, España
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Kumar R, Sinha NR, Mohan RR. Corneal gene therapy: Structural and mechanistic understanding. Ocul Surf 2023; 29:279-297. [PMID: 37244594 DOI: 10.1016/j.jtos.2023.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Cornea, a dome-shaped and transparent front part of the eye, affords 2/3rd refraction and barrier functions. Globally, corneal diseases are the leading cause of vision impairment. Loss of corneal function including opacification involve the complex crosstalk and perturbation between a variety of cytokines, chemokines and growth factors generated by corneal keratocytes, epithelial cells, lacrimal tissues, nerves, and immune cells. Conventional small-molecule drugs can treat mild-to-moderate traumatic corneal pathology but requires frequent application and often fails to treat severe pathologies. The corneal transplant surgery is a standard of care to restore vision in patients. However, declining availability and rising demand of donor corneas are major concerns to maintain ophthalmic care. Thus, the development of efficient and safe nonsurgical methods to cure corneal disorders and restore vision in vivo is highly desired. Gene-based therapy has huge potential to cure corneal blindness. To achieve a nonimmunogenic, safe and sustained therapeutic response, the selection of a relevant genes, gene editing methods and suitable delivery vectors are vital. This article describes corneal structural and functional features, mechanistic understanding of gene therapy vectors, gene editing methods, gene delivery tools, and status of gene therapy for treating corneal disorders, diseases, and genetic dystrophies.
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Affiliation(s)
- Rajnish Kumar
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow campus, UP, 226028, India
| | - Nishant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Rajiv R Mohan
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA; Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
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3
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Zárate-Chaves CA, Audran C, Medina Culma CA, Escalon A, Javegny S, Gagnevin L, Thomas E, Pimparé LL, López CE, Jacobs JM, Noël LD, Koebnik R, Bernal AJ, Szurek B. CRISPRi in Xanthomonas demonstrates functional convergence of transcription activator-like effectors in two divergent pathogens. THE NEW PHYTOLOGIST 2023; 238:1593-1604. [PMID: 36764921 DOI: 10.1111/nph.18808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Functional analysis of large gene families in plant pathogens can be cumbersome using classical insertional mutagenesis. Additionally, Cas9 toxicity has limited the application of CRISPR-Cas9 for directed mutagenesis in bacteria. Here, we successfully applied a CRISPR interference strategy to investigate the cryptic role of the transcription activator-like effector (tale) multigene family in several plant-pathogenic Xanthomonas bacterial species, owing to their contribution to pathogen virulence. Single guide RNAs (sgRNAs) designed against Xanthomonas phaseoli pv manihotis tale conserved gene sequences efficiently silenced expression of all tales, with concomitant decrease in virulence and TALE-induced host gene expression. The system is readily translatable to other Xanthomonas species infecting rice, citrus, Brassica, and cassava, silencing up to 16 tales in a given strain using a single sgRNA. Complementation with plasmid-borne designer tales lacking the sgRNA-targeted sequence restored molecular and virulence phenotypes in all pathosystems. Our results evidenced that X. campestris pv campestris CN08 tales are relevant for symptom development in cauliflower. They also show that the MeSWEET10a sugar transporter is surprisingly targeted by the nonvascular cassava pathogen X. cassavae, highlighting a new example of TALE functional convergence between phylogenetically distant Xanthomonas. Overall, this novel technology provides a platform for discovery and rapid functional understanding of highly conserved gene families.
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Affiliation(s)
| | - Corinne Audran
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, 31326, France
| | - César Augusto Medina Culma
- Laboratorio de interacciones moleculares de microorganismos agrícolas (LIMMA), Universidad de los Andes, Bogotá, 111711, Colombia
| | - Aline Escalon
- CIRAD, UMR PVBMT, Saint-Pierre, 97410, La Réunion, France
| | | | - Lionel Gagnevin
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
| | - Emilie Thomas
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
| | - Léa-Lou Pimparé
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
| | - Camilo E López
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Jonathan M Jacobs
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, 43210-1358, USA
| | - Laurent D Noël
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, 31326, France
| | - Ralf Koebnik
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
| | - Adriana Jimena Bernal
- Laboratorio de interacciones moleculares de microorganismos agrícolas (LIMMA), Universidad de los Andes, Bogotá, 111711, Colombia
| | - Boris Szurek
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
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Díaz-Tatis PA, Ochoa JC, Rico EM, Rodríguez C, Medina A, Szurek B, Chavarriaga P, López CE. RXam2, a NLR from cassava (Manihot esculenta) contributes partially to the quantitative resistance to Xanthomonas phaseoli pv. manihotis. PLANT MOLECULAR BIOLOGY 2022; 109:313-324. [PMID: 34757519 DOI: 10.1007/s11103-021-01211-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
The overexpression of RXam2, a cassava NLR (nucleotide-binding leucine-rich repeat) gene, by stable transformation and gene expression induction mediated by dTALEs, reduce cassava bacterial blight symptoms. Cassava (Manihot esculenta) is a tropical root crop affected by different pathogens including Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of cassava bacterial blight (CBB). Previous studies have reported resistance to CBB as a quantitative and polygenic character. This study sought to validate the functional role of a NLR (nucleotide-binding leucine-rich repeat) associated with a QTL to Xpm strain CIO151 called RXam2. Transgenic cassava plants overexpressing RXam2 were generated and analyzed. Plants overexpressing RXam2 showed a reduction in bacterial growth to Xpm strains CIO151, 232 and 226. In addition, designer TALEs (dTALEs) were developed to specifically bind to the RXam2 promoter region. The Xpm strain transformed with dTALEs allowed the induction of the RXam2 gene expression after inoculation in cassava plants and was associated with a diminution in CBB symptoms. These findings suggest that RXam2 contributes to the understanding of the molecular basis of quantitative disease resistance.
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Affiliation(s)
- Paula A Díaz-Tatis
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
- Grupo de Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Cra1 #47a15, Bogotá D.C., Colombia
| | - Juan C Ochoa
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
- Department of Integrative Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
| | - Edgar M Rico
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
| | - Catalina Rodríguez
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia
- Ludwig Maximilian University of Munich, Biozentrum Martinsried, Grosshaderner Strasse 4, Martinsried, Germany
| | - Adriana Medina
- Transformation Platform, Centro Internacional de Agricultura Tropical (CIAT), Km17 Cali-Palmira, Palmira, Colombia
| | - Boris Szurek
- UMR Interactions Plantes Microorganismes Environnement (IPME), IRD-CIRAD-Université, Montpellier, France
| | - Paul Chavarriaga
- Transformation Platform, Centro Internacional de Agricultura Tropical (CIAT), Km17 Cali-Palmira, Palmira, Colombia
| | - Camilo E López
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá D.C., Colombia.
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Doucouré H, Auguy F, Blanvillain-Baufumé S, Fabre S, Gabriel M, Thomas E, Dambreville F, Sciallano C, Szurek B, Koita O, Verdier V, Cunnac S. The Rice ILI2 Locus Is a Bidirectional Target of the African Xanthomonas oryzae pv. oryzae Major Transcription Activator-like Effector TalC but Does Not Contribute to Disease Susceptibility. Int J Mol Sci 2022; 23:ijms23105559. [PMID: 35628368 PMCID: PMC9142087 DOI: 10.3390/ijms23105559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/16/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription activator-like effectors (TALEs) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed effector binding elements (EBEs). Xoo major TALEs universally target susceptibility genes of the SWEET transporter family. TALE-unresponsive alleles of clade III OsSWEET susceptibility gene promoter created with genome editing confer broad resistance on Asian Xoo strains. African Xoo strains rely primarily on the major TALE TalC, which targets OsSWEET14. Although the virulence of a talC mutant strain is severely impaired, abrogating OsSWEET14 induction with genome editing does not confer equivalent resistance on African Xoo. To address this contradiction, we postulated the existence of a TalC target susceptibility gene redundant with OsSWEET14. Bioinformatics analysis identified a rice locus named ATAC composed of the INCREASED LEAF INCLINATION 2 (ILI2) gene and a putative lncRNA that are shown to be bidirectionally upregulated in a TalC-dependent fashion. Gain-of-function approaches with designer TALEs inducing ATAC sequences did not complement the virulence of a Xoo strain defective for SWEET gene activation. While editing the TalC EBE at the ATAC loci compromised TalC-mediated induction, multiplex edited lines with mutations at the OsSWEET14 and ATAC loci remained essentially susceptible to African Xoo strains. Overall, this work indicates that ATAC is a probable TalC off-target locus but nonetheless documents the first example of divergent transcription activation by a native TALE during infection.
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Affiliation(s)
- Hinda Doucouré
- LBMA, Faculté des Sciences et Techniques, University des Sciences Techniques et Technologiques, Bamako E 3206, Mali; (H.D.); (O.K.)
| | - Florence Auguy
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Servane Blanvillain-Baufumé
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Sandrine Fabre
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Marc Gabriel
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Emilie Thomas
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Fleur Dambreville
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Coline Sciallano
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Boris Szurek
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Ousmane Koita
- LBMA, Faculté des Sciences et Techniques, University des Sciences Techniques et Technologiques, Bamako E 3206, Mali; (H.D.); (O.K.)
| | - Valérie Verdier
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Sébastien Cunnac
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
- Correspondence:
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6
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Wu LB, Eom JS, Isoda R, Li C, Char SN, Luo D, Schepler-Luu V, Nakamura M, Yang B, Frommer WB. OsSWEET11b, a potential sixth leaf blight susceptibility gene involved in sugar transport-dependent male fertility. THE NEW PHYTOLOGIST 2022; 234:975-989. [PMID: 35211968 DOI: 10.1111/nph.18054] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
SWEETs play important roles in intercellular sugar transport. Induction of SWEET sugar transporters by Transcription Activator-Like effectors (TALe) of Xanthomonas ssp. is key for virulence in rice, cassava and cotton. We identified OsSWEET11b with roles in male fertility and potential bacterial blight (BB) susceptibility in rice. While single ossweet11a or 11b mutants were fertile, double mutants were sterile. As clade III SWEETs can transport gibberellin (GA), a key hormone for spikelet fertility, sterility and BB susceptibility might be explained by GA transport deficiencies. However, in contrast with the Arabidopsis homologues, OsSWEET11b did not mediate detectable GA transport. Fertility and susceptibility therefore are likely to depend on sucrose transport activity. Ectopic induction of OsSWEET11b by designer TALe enabled TALe-free Xanthomonas oryzae pv. oryzae (Xoo) to cause disease, identifying OsSWEET11b as a potential BB susceptibility gene and demonstrating that the induction of host sucrose uniporter activity is key to virulence of Xoo. Notably, only three of six clade III SWEETs are targeted by known Xoo strains from Asia and Africa. The identification of OsSWEET11b is relevant for fertility and for protecting rice against emerging Xoo strains that target OsSWEET11b.
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Affiliation(s)
- Lin-Bo Wu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding I, Justus-Liebig University Giessen, Giessen, 35392, Germany
| | - Joon-Seob Eom
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Reika Isoda
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Chenhao Li
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Si Nian Char
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Dangping Luo
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Van Schepler-Luu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Masayoshi Nakamura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Bing Yang
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
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7
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Sivaraman S, Krishnamoorthy D, Arvind K, Grace T, Sharma J, Antony G. TAL effectors and the predicted host targets of pomegranate bacterial blight pathogen Xanthomonas citri pv. punicae. Curr Genet 2022; 68:361-373. [PMID: 35275250 DOI: 10.1007/s00294-022-01232-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
The molecular mechanism of pomegranate susceptibility to bacterial blight, a serious threat to pomegranate production in India, is largely unknown. In the current study, we have used PacBio and Illumina sequencing of Xanthomonas citri pv. punicae (Xcp) strain 119 genome to identify tal genes and RNA-Seq analysis to identify putative host targets in the susceptible pomegranate variety Bhagwa challenged with Xcp119. Xcp119 genome encodes seven transcription activator-like effectors (TALEs), three of which are harbored by a plasmid. RVD-based phylogenetic analysis of TALEs of Xanthomonas citri pathovars indicate the TALEs of Xcp as evolutionarily and functionally close to Xanthomonas citri pv. malvacearum and Xanthomonas citri pv. glycines. Comparative RNA-Seq of Xcp and mock-inoculated leaf tissues revealed Xcp-induced pomegranate transcription modulation. The prediction of TALE binding elements (EBEs) in the promoters of up-regulated genes identified a set of TALE-targeted candidate genes in pomegranate-Xcp interaction. The predicted candidate susceptibility genes include two oxoglutarate-dependent dioxygenase gene, ethylene-responsive transcription factor and flavanone 3-hydroxylase-like gene, and the further characterization of these would enable blight resistance engineering in pomegranate.
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Affiliation(s)
- Sruthi Sivaraman
- Department of Plant Science, Central University of Kerala, Periye, 671320, Kerala, India
| | | | - Kumar Arvind
- Department of Genomic Science, Central University of Kerala, Periye, 671320, Kerala, India
| | - Tony Grace
- Department of Genomic Science, Central University of Kerala, Periye, 671320, Kerala, India
| | - Jyotsana Sharma
- ICAR-National Research Centre On Pomegranate, Kegaon, Solapur, 413255, Maharashtra, India
| | - Ginny Antony
- Department of Plant Science, Central University of Kerala, Periye, 671320, Kerala, India.
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8
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Lachaux M, Thomas E, Bogdanove AJ, Szurek B, Hutin M. TAL Effectors with Avirulence Activity in African Strains of Xanthomonas oryzae pv. oryzae. RICE (NEW YORK, N.Y.) 2022; 15:9. [PMID: 35119567 PMCID: PMC8816977 DOI: 10.1186/s12284-022-00553-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating disease of rice. Among the type-3 effectors secreted by Xoo to support pathogen virulence, the Transcription Activator-Like Effector (TALE) family plays a critical role. Some TALEs are major virulence factors that activate susceptibility (S) genes, overexpression of which contributes to disease development. Host incompatibility can result from TALE-induced expression of so-called executor (E) genes leading to a strong and rapid resistance response that blocks disease development. In that context, the TALE functions as an avirulence (Avr) factor. To date no such avirulence factors have been identified in African strains of Xoo. RESULTS With respect to the importance of TALEs in the Rice-Xoo pathosystem, we aimed at identifying those that may act as Avr factor within African Xoo. We screened 86 rice accessions, and identified 12 that were resistant to two African strains while being susceptible to a well-studied Asian strain. In a gain of function approach based on the introduction of each of the nine tal genes of the avirulent African strain MAI1 into the virulent Asian strain PXO99A, four were found to trigger resistance on specific rice accessions. Loss-of-function mutational analysis further demonstrated the avr activity of two of them, talD and talI, on the rice varieties IR64 and CT13432 respectively. Further analysis of TalI demonstrated the requirement of its activation domain for triggering resistance in CT13432. Resistance in 9 of the 12 rice accessions that were resistant against African Xoo specifically, including CT13432, could be suppressed or largely suppressed by trans-expression of the truncTALE tal2h, similarly to resistance conferred by the Xa1 gene which recognizes TALEs generally independently of their activation domain. CONCLUSION We identified and characterized TalD and TalI as two African Xoo TALEs with avirulence activity on IR64 and CT13432 respectively. Resistance of CT13432 against African Xoo results from the combination of two mechanisms, one relying on the TalI-mediated induction of an unknown executor gene and the other on an Xa1-like gene or allele.
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Affiliation(s)
- Marlène Lachaux
- Plant Health Institute of Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Emilie Thomas
- Plant Health Institute of Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Adam J Bogdanove
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Boris Szurek
- Plant Health Institute of Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - Mathilde Hutin
- Plant Health Institute of Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
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9
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Erkes A, Mücke S, Reschke M, Boch J, Grau J. Epigenetic features improve TALE target prediction. BMC Genomics 2021; 22:914. [PMID: 34965853 PMCID: PMC8717664 DOI: 10.1186/s12864-021-08210-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/25/2021] [Indexed: 11/20/2022] Open
Abstract
Background The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to their target box and determine the specificity of a TALE.All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box. Results To this end, we extend our previously published tool PrediTALE by considering two epigenetic features: (i) chromatin accessibility of potentially bound regions and (ii) DNA methylation of cytosines within target boxes. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS data in rice.We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq data of infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both.Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets. Conclusions Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-08210-z).
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.
| | - Stefanie Mücke
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Maik Reschke
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.
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10
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Wu T, Zhang H, Bi Y, Yu Y, Liu H, Yang H, Yuan B, Ding X, Chu Z. Tal2c Activates the Expression of OsF3H04g to Promote Infection as a Redundant TALE of Tal2b in Xanthomonas oryzae pv. oryzicola. Int J Mol Sci 2021; 22:ijms222413628. [PMID: 34948428 PMCID: PMC8707247 DOI: 10.3390/ijms222413628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
Xanthomonas oryzae delivers transcription activator-like effectors (TALEs) into plant cells to facilitate infection. Following economic principles, the redundant TALEs are rarely identified in Xanthomonas. Previously, we identified the Tal2b, which activates the expression of the rice 2-oxoglutarate-dependent dioxygenase gene OsF3H03g to promote infection in the highly virulent strain of X. oryzae pv. oryzicola HGA4. Here, we reveal that another clustered TALE, Tal2c, also functioned as a virulence factor to target rice OsF3H04g, a homologue of OsF3H03g. Transferring Tal2c into RS105 induced expression of OsF3H04g to coincide with increased susceptibility in rice. Overexpressing OsF3H04g caused higher susceptibility and less salicylic acid (SA) production compared to wild-type plants. Moreover, CRISPR–Cas9 system-mediated editing of the effector-binding element in the promoters of OsF3H03g or OsF3H04g was found to specifically enhance resistance to Tal2b- or Tal2c-transferring strains, but had no effect on resistance to either RS105 or HGA4. Furthermore, transcriptome analysis revealed that several reported SA-related and defense-related genes commonly altered expression in OsF3H04g overexpression line compared with those identified in OsF3H03g overexpression line. Overall, our results reveal a functional redundancy mechanism of pathogenic virulence in Xoc in which tandem Tal2b and Tal2c specifically target homologues of host genes to interfere with rice immunity by reducing SA.
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Affiliation(s)
- Tao Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan 430072, China;
| | - Haimiao Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
| | - Yunya Bi
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan 430072, China;
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Yue Yu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
| | - Haifeng Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
| | - Hong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Bin Yuan
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
- Correspondence: (X.D.); (Z.C.); Tel.: +86-538-8245569 (X.D.); +86-27-68752095 (Z.C.)
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan 430072, China;
- Correspondence: (X.D.); (Z.C.); Tel.: +86-538-8245569 (X.D.); +86-27-68752095 (Z.C.)
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11
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Reshetnyak G, Jacobs JM, Auguy F, Sciallano C, Claude L, Medina C, Perez-Quintero AL, Comte A, Thomas E, Bogdanove A, Koebnik R, Szurek B, Dievart A, Brugidou C, Lacombe S, Cunnac S. An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection. Sci Rep 2021; 11:24141. [PMID: 34921170 PMCID: PMC8683429 DOI: 10.1038/s41598-021-03391-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023] Open
Abstract
Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and xisRNA loci predominantly coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.
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Affiliation(s)
- Ganna Reshetnyak
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jonathan M Jacobs
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43201, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, 43201, USA
| | - Florence Auguy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Coline Sciallano
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Lisa Claude
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Clemence Medina
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Alvaro L Perez-Quintero
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurore Comte
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Emilie Thomas
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Adam Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Ralf Koebnik
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Anne Dievart
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Christophe Brugidou
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Severine Lacombe
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sebastien Cunnac
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
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12
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Duy PN, Lan DT, Pham Thu H, Thi Thu HP, Nguyen Thanh H, Pham NP, Auguy F, Bui Thi Thu H, Manh TB, Cunnac S, Pham XH. Improved bacterial leaf blight disease resistance in the major elite Vietnamese rice cultivar TBR225 via editing of the OsSWEET14 promoter. PLoS One 2021; 16:e0255470. [PMID: 34499670 PMCID: PMC8428762 DOI: 10.1371/journal.pone.0255470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 07/17/2021] [Indexed: 12/05/2022] Open
Abstract
TBR225 is one of the most popular commercial rice varieties in Northern Vietnam. However, this variety is highly susceptible to bacterial leaf blight (BLB), a disease caused by Xanthomonas oryzae pv. oryzae (Xoo) which can lead to important yield losses. OsSWEET14 belongs to the SWEET gene family that encodes sugar transporters. Together with other Clade III members, it behaves as a susceptibility (S) gene whose induction by Asian Xoo Transcription-Activator-Like Effectors (TALEs) is absolutely necessary for disease. In this study, we sought to introduce BLB resistance in the TBR225 elite variety. First, two Vietnamese Xoo strains were shown to up-regulate OsSWEET14 upon TBR225 infection. To investigate if this induction is connected with disease susceptibility, nine TBR225 mutant lines with mutations in the AvrXa7, PthXo3 or TalF TALEs DNA target sequences of the OsSWEET14 promoter were obtained using the CRISPR/Cas9 editing system. Genotyping analysis of T0 and T1 individuals showed that mutations were stably inherited. None of the examined agronomic traits of three transgene-free T2 edited lines were significantly different from those of wild-type TBR225. Importantly, one of these T2 lines, harboring the largest homozygous 6-bp deletion, displayed decreased OsSWEET14 expression as well as a significantly reduced susceptibility to a Vietnamese Xoo strains and complete resistance to another one. Our findings indicate that CRISPR/Cas9 editing conferred an improved BLB resistance to a Vietnamese commercial elite rice variety.
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Affiliation(s)
- Phuong Nguyen Duy
- Department of Molecular Pathology, Institute of Agricultural Genetics, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Dai Tran Lan
- Department of Molecular Pathology, Institute of Agricultural Genetics, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
- Faculty of Natural Sciences, Department of Applied Biology and Agriculture, Quynhon University, Quynhon, Vietnam
| | - Hang Pham Thu
- Department of Molecular Pathology, Institute of Agricultural Genetics, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Huong Phung Thi Thu
- Department of Molecular Pathology, Institute of Agricultural Genetics, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Ha Nguyen Thanh
- Department of Molecular Pathology, Institute of Agricultural Genetics, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Ngoc Phuong Pham
- Department of Molecular Pathology, Institute of Agricultural Genetics, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Florence Auguy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Sebastien Cunnac
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Xuan Hoi Pham
- Department of Molecular Pathology, Institute of Agricultural Genetics, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
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13
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Gupta PK, Balyan HS, Gautam T. SWEET genes and TAL effectors for disease resistance in plants: Present status and future prospects. MOLECULAR PLANT PATHOLOGY 2021; 22:1014-1026. [PMID: 34076324 PMCID: PMC8295518 DOI: 10.1111/mpp.13075] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/13/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
SWEET genes encode sugar transporter proteins and often function as susceptibility (S) genes. Consequently, the recessive alleles of these SWEET genes provide resistance. This review summarizes the available literature on the molecular basis of the role of SWEET genes (as S genes) in the host and corresponding transcription activator-like effectors (TALEs) secreted by the pathogen. The review has four major sections, which follow a brief introduction: The first part gives some details about the occurrence and evolution of SWEET genes in approximately 30 plant species; the second part gives some details about systems where (a) SWEET genes with and without TALEs and (b) TALEs without SWEET genes cause different diseases; the third part summarizes the available information about TALEs along with interfering/truncated TALEs secreted by the pathogens; this section also summarizes the available information on effector-binding elements (EBEs) available in the promoters of either the SWEET genes or the Executor R genes; the code that is used for binding of TALEs to EBEs is also described in this section; the fourth part gives some details about the available approaches that are being used or can be used in the future for exploiting SWEET genes for developing disease-resistant cultivars. The review concludes with a section giving conclusions and future possibilities of using SWEET genes for developing disease-resistant cultivars using different approaches, including conventional breeding and genome editing.
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Affiliation(s)
| | | | - Tinku Gautam
- Department of Genetics and Plant BreedingCCS UniversityMeerutIndia
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14
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Zlobin N, Lebedeva M, Monakhova Y, Ustinova V, Taranov V. An ERF121 transcription factor from Brassica oleracea is a target for the conserved TAL-effectors from different Xanthomonas campestris pv. campestris strains. MOLECULAR PLANT PATHOLOGY 2021; 22:618-624. [PMID: 33650275 PMCID: PMC8035633 DOI: 10.1111/mpp.13048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/19/2021] [Accepted: 02/04/2021] [Indexed: 05/19/2023]
Abstract
Transcription activator-like effectors (TALEs), which induce the expression of specific plant genes to promote infection, are the main pathogenic determinants of various Xanthomonas bacteria. However, investigation of TALEs from Xanthomonas campestris pv. campestris, which causes black rot disease of crucifers, received little attention. In this study, we used PCR-based amplification followed by SMRT amplicon sequencing to identify TALE genes in several X. campestris pv. campestris strains. Computational prediction in conjunction with quantitative reverse transcription PCR analysis was used to find their targets in the Brassica oleracea genome. Transcription factor ERF121, from the AP2/ERF family, was identified as target gene for the conserved TALEs from multiple X. campestris pv. campestris strains. Several members of this family from diverse plants were previously identified as targets of TALEs from different Xanthomonas species. We propose that TALE-dependent activation of AP2/ERF transcription factors promotes susceptibility to Xanthomonas through the misregulation of plant defence pathways.
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Affiliation(s)
- Nikolay Zlobin
- Laboratory of Plant Stress ToleranceAll‐Russia Research Institute of Agricultural BiotechnologyMoscowRussia
| | - Marina Lebedeva
- Laboratory of Plant Stress ToleranceAll‐Russia Research Institute of Agricultural BiotechnologyMoscowRussia
| | - Yuliya Monakhova
- Laboratory of Synthesis and Analysis of Bioorganic CompoundsAll‐Russia Research Institute of Agricultural BiotechnologyMoscowRussia
| | - Vera Ustinova
- Pushchino Scientific Center for Biological Research of the Russian Academy of SciencesG.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of SciencesPushchinoRussia
- Syntol LLCMoscowRussia
| | - Vasiliy Taranov
- Laboratory of Plant Stress ToleranceAll‐Russia Research Institute of Agricultural BiotechnologyMoscowRussia
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TAL Effector Repertoires of Strains of Xanthomonas phaseoli pv. manihotis in Commercial Cassava Crops Reveal High Diversity at the Country Scale. Microorganisms 2021; 9:microorganisms9020315. [PMID: 33557009 PMCID: PMC7913752 DOI: 10.3390/microorganisms9020315] [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: 11/15/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Transcription activator-like effectors (TALEs) play a significant role for pathogenesis in several xanthomonad pathosystems. Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of Cassava Bacterial Blight (CBB), uses TALEs to manipulate host metabolism. Information about Xpm TALEs and their target genes in cassava is scarce, but has been growing in the last few years. We aimed to characterize the TALE diversity in Colombian strains of Xpm and to screen for TALE-targeted gene candidates. We selected eighteen Xpm strains based on neutral genetic diversity at a country scale to depict the TALE diversity among isolates from cassava productive regions. RFLP analysis showed that Xpm strains carry TALomes with a bimodal size distribution, and affinity-based clustering of the sequenced TALEs condensed this variability mainly into five clusters. We report on the identification of 13 novel variants of TALEs in Xpm, as well as a functional variant with 22 repeats that activates the susceptibility gene MeSWEET10a, a previously reported target of TAL20Xam668. Transcriptomics and EBE prediction analyses resulted in the selection of several TALE-targeted candidate genes and two potential cases of functional convergence. This study provides new bases for assessing novel potential TALE targets in the Xpm–cassava interaction, which could be important factors that define the fate of the infection.
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Huerta AI, Delorean EE, Bossa‐Castro AM, Tonnessen BW, Raghavan C, Corral R, Pérez‐Quintero ÁL, Leung H, Verdier V, Leach JE. Resistance and susceptibility QTL identified in a rice MAGIC population by screening with a minor-effect virulence factor from Xanthomonas oryzae pv. oryzae. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:51-63. [PMID: 32594636 PMCID: PMC7769240 DOI: 10.1111/pbi.13438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/02/2020] [Accepted: 06/17/2020] [Indexed: 05/07/2023]
Abstract
Effective and durable disease resistance for bacterial blight (BB) of rice is a continuous challenge due to the evolution and adaptation of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), on cultivated rice varieties. Fundamental to this pathogens' virulence is transcription activator-like (TAL) effectors that activate transcription of host genes and contribute differently to pathogen virulence, fitness or both. Host plant resistance is predicted to be more durable if directed at strategic virulence factors that impact both pathogen virulence and fitness. We characterized Tal7b, a minor-effect virulence factor that contributes incrementally to pathogen virulence in rice, is a fitness factor to the pathogen and is widely present in geographically diverse strains of Xoo. To identify sources of resistance to this conserved effector, we used a highly virulent strain carrying a plasmid borne copy of Tal7b to screen an indica multi-parent advanced generation inter-cross (MAGIC) population. Of 18 QTL revealed by genome-wide association studies and interval mapping analysis, six were specific to Tal7b (qBB-tal7b). Overall, 150 predicted Tal7b gene targets overlapped with qBB-tal7b QTL. Of these, 21 showed polymorphisms in the predicted effector binding element (EBE) site and 23 lost the EBE sequence altogether. Inoculation and bioinformatics studies suggest that the Tal7b target in one of the Tal7b-specific QTL, qBB-tal7b-8, is a disease susceptibility gene and that the resistance mechanism for this locus may be through loss of susceptibility. Our work demonstrates that minor-effect virulence factors significantly contribute to disease and provide a potential new approach to identify effective disease resistance.
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Affiliation(s)
- Alejandra I. Huerta
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Emily E. Delorean
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Ana M. Bossa‐Castro
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | - Bradley W. Tonnessen
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Extension Plant SciencesNew Mexico State UniversityLas CrucesNM88003USA
| | - Chitra Raghavan
- Division Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
- Present address:
Queensland Department of Agriculture and FisheriesHorticulture and Forestry SciencesCairnsQLD4870Australia
| | - Rene Corral
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | | | - Hei Leung
- Division Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
| | | | - Jan E. Leach
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
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To HTM, Le KQ, Van Nguyen H, Duong LV, Kieu HT, Chu QAT, Tran TP, Mai NTP. A genome-wide association study reveals the quantitative trait locus and candidate genes that regulate phosphate efficiency in a Vietnamese rice collection. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2267-2281. [PMID: 33268928 PMCID: PMC7688854 DOI: 10.1007/s12298-020-00902-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/12/2020] [Accepted: 10/17/2020] [Indexed: 05/21/2023]
Abstract
The crucial role of phosphate (Pi) for plant alongside the expected depletion of non-renewable phosphate rock have created an urgent need for phosphate-efficient rice varieties. In this study, 157 greenhouse-grown Vietnamese rice landraces were treated under Pi-deficient conditions to discover the genotypic variation among biochemical traits, including relative efficiency of phosphorus use (REP), relative root to shoot weight ratio (RRSR), relative physiological phosphate use efficiency (RPPUE), and relative phosphate uptake efficiency (RPUpE). Plants were grown in Yoshida nutrient media with either a full (320 μM) or a low Pi supply (10 μM) over six weeks. This genome-wide association study led to the discovery of 31 significant single nucleotide polymorphisms, 18 quantitative trait loci (QTLs), and 85 candidate genes. A common QTL named qRPUUE9.16 was found among the three investigated traits. Some interesting candidate genes, such as PLASMA MEMBRANE PROTEIN1 (OsPM1), CALMODULIN-RELATED CALCIUM SENSOR PROTEIN 15 (OsCML15), phosphatases 2C (PP2C), STRESS-ACTIVATED PROTEIN KINASE (OsSAPK2), and GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASES (GDPD13), were found strongly correlated to the Pi starvation. RNA sequencing transcriptomes revealed that 45 out of 85 candidate genes were significantly regulated under Pi starvation. Furthermore, nearly two-thirds of genotypes did not possess the OsPsTOL1 gene; however, no significant difference was observed in response to Pi deficiency between genotypes with or without this gene, suggesting that other QTLs in rice may resist Pi starvation. These results provide new information on the genetics of nutrient use efficiency in rice and may potentially assist with developing more phosphate-efficient rice plants.
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Affiliation(s)
- Huong Thi Mai To
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Khang Quoc Le
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Hiep Van Nguyen
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Linh Viet Duong
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Hanh Thi Kieu
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Quynh Anh Thi Chu
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Trang Phuong Tran
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nga T. P. Mai
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
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18
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Xue J, Lu Z, Liu W, Wang S, Lu D, Wang X, He X. The genetic arms race between plant and Xanthomonas: lessons learned from TALE biology. SCIENCE CHINA-LIFE SCIENCES 2020; 64:51-65. [PMID: 32661897 DOI: 10.1007/s11427-020-1699-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/29/2020] [Indexed: 10/23/2022]
Abstract
The pathogenic bacterial genus Xanthomonas infects a wide variety of host plants and causes devastating diseases in many crops. Transcription activator-like effectors (TALEs) are important virulence factors secreted by Xanthomonas with the ability to directly bind to the promoters of target genes in plant hosts and activate their expression, which often facilitates the proliferation of pathogens. Understanding how plants cope with TALEs will provide mechanistic insights into crop breeding for Xanthomonas defense. Over the past 30 years, numerous studies have revealed the modes of action of TALEs in plant cells and plant defense strategies to overcome TALE attack. Based on these findings, new technologies were adopted for disease management to optimize crop production. In this article, we will review the most recent advances in the evolutionary arms race between plant resistance and TALEs from Xanthomonas, with a specific focus on TALE applications in the development of novel breeding strategies for durable and broad-spectrum resistance.
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Affiliation(s)
- Jiao Xue
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Dongbai Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China.
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19
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Timilsina S, Potnis N, Newberry EA, Liyanapathiranage P, Iruegas-Bocardo F, White FF, Goss EM, Jones JB. Xanthomonas diversity, virulence and plant-pathogen interactions. Nat Rev Microbiol 2020; 18:415-427. [PMID: 32346148 DOI: 10.1038/s41579-020-0361-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 12/19/2022]
Abstract
Xanthomonas spp. encompass a wide range of plant pathogens that use numerous virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine recent insights into host-pathogen co-evolution, diversity in Xanthomonas populations and host specificity of Xanthomonas spp. that have substantially improved our fundamental understanding of pathogen biology. We emphasize the virulence factors in xanthomonads, such as type III secreted effectors including transcription activator-like effectors, type II secretion systems, diversity resulting in host specificity, evolution of emerging strains, activation of susceptibility genes and strategies of host evasion. We summarize the genomic diversity in several Xanthomonas spp. and implications for disease outbreaks, management strategies and breeding for disease resistance.
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Affiliation(s)
- Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Neha Potnis
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric A Newberry
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | | | | | - Frank F White
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Erica M Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Jeffrey B Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, USA.
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20
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Kremer FS, Guimarães AM, Sanchez CD, da Silva Pinto L. TargeTALE: A Web Resource to Identify TALEs in Xanthomonas Genomes and Their Respective Targets. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1577-1580. [PMID: 31618137 DOI: 10.1094/mpmi-08-19-0227-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The Xanthomonas genus, comprises more than 30 species of gram-negative bacteria, most of which are pathogens of plants with high economic value, such as rice, common bean, and maize. Transcription activator-like effectors (TALEs), which act by regulating the host gene expression, are some of the major virulence factors of these bacteria. We present a novel tool to identify TALE genes in the genome of Xanthomonas strains and their respective targets. The analysis of the results obtained by TargeTALE in a proof-of-concept validation demonstrate that, at optimum setting, approximately 93% of the predicted target genes with available expression data were confirmed as upregulated during the infection, indicating that the tool might be useful for researchers in the field.
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Affiliation(s)
- Frederico Schmitt Kremer
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Amanda Munari Guimarães
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Christian Domingues Sanchez
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Luciano da Silva Pinto
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
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21
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Wan H, Li JM, Ding H, Lin SX, Tu SQ, Tian XH, Hu JP, Chang S. An Overview of Computational Tools of Nucleic Acid Binding Site Prediction for Site-specific Proteins and Nucleases. Protein Pept Lett 2019; 27:370-384. [PMID: 31746287 DOI: 10.2174/0929866526666191028162302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/24/2019] [Accepted: 09/24/2019] [Indexed: 12/26/2022]
Abstract
Understanding the interaction mechanism of proteins and nucleic acids is one of the most fundamental problems for genome editing with engineered nucleases. Due to some limitations of experimental investigations, computational methods have played an important role in obtaining the knowledge of protein-nucleic acid interaction. Over the past few years, dozens of computational tools have been used for identification of nucleic acid binding site for site-specific proteins and design of site-specific nucleases because of their significant advantages in genome editing. Here, we review existing widely-used computational tools for target prediction of site-specific proteins as well as off-target prediction of site-specific nucleases. This article provides a list of on-line prediction tools according to their features followed by the description of computational methods used by these tools, which range from various sequence mapping algorithms (like Bowtie, FetchGWI and BLAST) to different machine learning methods (such as Support Vector Machine, hidden Markov models, Random Forest, elastic network and deep neural networks). We also make suggestions on the further development in improving the accuracy of prediction methods. This survey will provide a reference guide for computational biologists working in the field of genome editing.
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Affiliation(s)
- Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Ming Li
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Huang Ding
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Shuo-Xin Lin
- Department of Electrical and Computer Engineering, James Clark School of Engineering, University of Maryland, College Park, MD 20742, United States
| | - Shu-Qin Tu
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Xu-Hong Tian
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Ping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
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22
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Oliva R, Ji C, Atienza-Grande G, Huguet-Tapia JC, Perez-Quintero A, Li T, Eom JS, Li C, Nguyen H, Liu B, Auguy F, Sciallano C, Luu VT, Dossa GS, Cunnac S, Schmidt SM, Slamet-Loedin IH, Vera Cruz C, Szurek B, Frommer WB, White FF, Yang B. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat Biotechnol 2019; 37:1344-1350. [PMID: 31659337 PMCID: PMC6831514 DOI: 10.1038/s41587-019-0267-z] [Citation(s) in RCA: 305] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/28/2019] [Indexed: 02/01/2023]
Abstract
Bacterial blight of rice is an important disease in Asia and Africa. The pathogen, Xanthomonas oryzae pv. oryzae (Xoo), secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genes SWEET11, SWEET13 and SWEET14, the expression of which is required for disease susceptibility. We used CRISPR-Cas9-mediated genome editing to introduce mutations in all three SWEET gene promoters. Editing was further informed by sequence analyses of TALe genes in 63 Xoo strains, which revealed multiple TALe variants for SWEET13 alleles. Mutations were also created in SWEET14, which is also targeted by two TALes from an African Xoo lineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-edited SWEET promoters endow rice lines with robust, broad-spectrum resistance.
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Affiliation(s)
- Ricardo Oliva
- International Rice Research Institute, Metro Manila, Philippines.
| | - Chonghui Ji
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Genelou Atienza-Grande
- International Rice Research Institute, Metro Manila, Philippines
- College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños, Philippines
| | | | - Alvaro Perez-Quintero
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Ting Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Joon-Seob Eom
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Chenhao Li
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Hanna Nguyen
- International Rice Research Institute, Metro Manila, Philippines
| | - Bo Liu
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Florence Auguy
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | | | - Van T Luu
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | | | - Sarah M Schmidt
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | | | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany.
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, Japan.
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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23
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Wu D, von Roepenack-Lahaye E, Buntru M, de Lange O, Schandry N, Pérez-Quintero AL, Weinberg Z, Lowe-Power TM, Szurek B, Michael AJ, Allen C, Schillberg S, Lahaye T. A Plant Pathogen Type III Effector Protein Subverts Translational Regulation to Boost Host Polyamine Levels. Cell Host Microbe 2019; 26:638-649.e5. [DOI: 10.1016/j.chom.2019.09.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/21/2019] [Accepted: 09/23/2019] [Indexed: 01/21/2023]
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24
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Perez-Quintero AL, Szurek B. A Decade Decoded: Spies and Hackers in the History of TAL Effectors Research. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:459-481. [PMID: 31387457 DOI: 10.1146/annurev-phyto-082718-100026] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transcription activator-like effectors (TALEs) from the genus Xanthomonas are proteins with the remarkable ability to directly bind the promoters of genes in the plant host to induce their expression, which often helps bacterial colonization. Metaphorically, TALEs act as spies that infiltrate the plant disguised as high-ranking civilians (transcription factors) to trick the plant into activating weak points that allow an invasion. Current knowledge of how TALEs operate allows researchers to predict their activity (counterespionage) and exploit their function, engineering them to do our bidding (a Manchurian agent). This has been possible thanks particularly to the discovery of their DNA binding mechanism, which obeys specific amino acid-DNA correspondences (the TALE code). Here, we review the history of how researchers discovered the way these proteins work and what has changed in the ten years since the discovery of the code. Recommended music for reading this review can be found in the Supplemental Material.
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Affiliation(s)
- Alvaro L Perez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523-1177, USA;
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
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25
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Erkes A, Mücke S, Reschke M, Boch J, Grau J. PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting. PLoS Comput Biol 2019; 15:e1007206. [PMID: 31295249 PMCID: PMC6650089 DOI: 10.1371/journal.pcbi.1007206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 07/23/2019] [Accepted: 06/20/2019] [Indexed: 11/18/2022] Open
Abstract
Plant-pathogenic Xanthomonas bacteria secrete transcription activator-like effectors (TALEs) into host cells, where they act as transcriptional activators on plant target genes to support bacterial virulence. TALEs have a unique modular DNA-binding domain composed of tandem repeats. Two amino acids within each tandem repeat, termed repeat-variable diresidues, bind to contiguous nucleotides on the DNA sequence and determine target specificity. In this paper, we propose a novel approach for TALE target prediction to identify potential virulence targets. Our approach accounts for recent findings concerning TALE targeting, including frame-shift binding by repeats of aberrant lengths, and the flexible strand orientation of target boxes relative to the transcription start of the downstream target gene. The computational model can account for dependencies between adjacent RVD positions. Model parameters are learned from the wealth of quantitative data that have been generated over the last years. We benchmark the novel approach, termed PrediTALE, using RNA-seq data after Xanthomonas infection in rice, and find an overall improvement of prediction performance compared with previous approaches. Using PrediTALE, we are able to predict several novel putative virulence targets. However, we also observe that no target genes are predicted by any prediction tool for several TALEs, which we term orphan TALEs for this reason. We postulate that one explanation for orphan TALEs are incomplete gene annotations and, hence, propose to replace promoterome-wide by genome-wide scans for target boxes. We demonstrate that known targets from promoterome-wide scans may be recovered by genome-wide scans, whereas the latter, combined with RNA-seq data, are able to detect putative targets independent of existing gene annotations.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Stefanie Mücke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
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26
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Lang JM, Pérez-Quintero AL, Koebnik R, DuCharme E, Sarra S, Doucoure H, Keita I, Ziegle J, Jacobs JM, Oliva R, Koita O, Szurek B, Verdier V, Leach JE. A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems. FRONTIERS IN PLANT SCIENCE 2019; 10:507. [PMID: 31114597 PMCID: PMC6503118 DOI: 10.3389/fpls.2019.00507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/02/2019] [Indexed: 05/21/2023]
Abstract
Xanthomonas oryzae (Xo) are globally important rice pathogens. Virulent lineages from Africa and Asia and less virulent strains from the United States have been well characterized. Xanthomonas campestris pv. leersiae (Xcl), first described in 1957, causes bacterial streak on the perennial grass, Leersia hexandra, and is a close relative of Xo. L. hexandra, a member of the Poaceae, is highly similar to rice phylogenetically, is globally ubiquitous around rice paddies, and is a reservoir of pathogenic Xo. We used long read, single molecule real time (SMRT) genome sequences of five strains of Xcl from Burkina Faso, China, Mali, and Uganda to determine the genetic relatedness of this organism with Xo. Novel transcription activator-like effectors (TALEs) were discovered in all five strains of Xcl. Predicted TALE target sequences were identified in the Leersia perrieri genome and compared to rice susceptibility gene homologs. Pathogenicity screening on L. hexandra and diverse rice cultivars confirmed that Xcl are able to colonize rice and produce weak but not progressive symptoms. Overall, based on average nucleotide identity (ANI), type III (T3) effector repertoires, and disease phenotype, we propose to rename Xcl to X. oryzae pv. leersiae (Xol) and use this parallel system to improve understanding of the evolution of bacterial pathogenicity in rice agroecosystems.
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Affiliation(s)
- Jillian M. Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Alvaro L. Pérez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Elysa DuCharme
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | - Soungalo Sarra
- Centre Régional de Recherche Agronomique de Niono, Institut d’Economie Rural, Bamako, Mali
| | - Hinda Doucoure
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Ibrahim Keita
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Janet Ziegle
- Pacific Biosciences, Menlo Park, CA, United States
| | - Jonathan M. Jacobs
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
- Department of Plant Pathology, Infectious Disease Institute, Ohio State University, Columbus, OH, United States
| | - Ricardo Oliva
- International Rice Research Institute, Los Baños, Philippines
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Boris Szurek
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Valérie Verdier
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
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27
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Chien CC, Chou MY, Chen CY, Shih MC. Analysis of genetic diversity of Xanthomonas oryzae pv. oryzae populations in Taiwan. Sci Rep 2019; 9:316. [PMID: 30670790 PMCID: PMC6342995 DOI: 10.1038/s41598-018-36575-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/25/2018] [Indexed: 01/22/2023] Open
Abstract
Rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major rice disease. In Taiwan, the tropical indica type of Oryza sativa originally grown in this area is mix-cultivated with the temperate japonica type of O. sativa, and this might have led to adaptive changes of both rice host and Xoo isolates. In order to better understand how Xoo adapts to this unique environment, we collected and analyzed fifty-one Xoo isolates in Taiwan. Three different genetic marker systems consistently identified five groups. Among these groups, two of them had unique sequences in the last acquired ten spacers in the clustered regularly interspaced short palindromic repeats (CRISPR) region, and the other two had sequences that were similar to the Japanese isolate MAFF311018 and the Philippines isolate PXO563, respectively. The genomes of two Taiwanese isolates with unique CRISPR sequence features, XF89b and XM9, were further completely sequenced. Comparison of the genome sequences suggested that XF89b is phylogenetically close to MAFF311018, and XM9 is close to PXO563. Here, documentation of the diversity of groups of Xoo in Taiwan provides evidence of the populations from different sources and hitherto missing information regarding distribution of Xoo populations in East Asia.
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Affiliation(s)
- Chih-Cheng Chien
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Mei-Yi Chou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chun-Yi Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Che Shih
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.
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Zaka A, Grande G, Coronejo T, Quibod IL, Chen CW, Chang SJ, Szurek B, Arif M, Cruz CV, Oliva R. Natural variations in the promoter of OsSWEET13 and OsSWEET14 expand the range of resistance against Xanthomonas oryzae pv. oryzae. PLoS One 2018; 13:e0203711. [PMID: 30212546 PMCID: PMC6136755 DOI: 10.1371/journal.pone.0203711] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/24/2018] [Indexed: 01/21/2023] Open
Abstract
Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the major diseases that impact rice production in Asia. The bacteria use transcription activator-like effectors (TALEs) to hijack the host transcription machinery and activate key susceptibility (S) genes, specifically members of the SWEET sucrose uniporters through the recognition of effector-binding element (EBEs) in the promoter regions. However, natural variations in the EBEs that alter the binding affinity of TALEs usually prevent sufficient induction of SWEET genes, leading to resistance phenotypes. In this study, we identified candidate resistance alleles by mining a rice diversity panel for mutations in the promoter of OsSWEET13 and OsSWEET14, which are direct targets of three major TALEs PthXo2, PthXo3 and AvrXa7. We found natural variations at the EBE of both genes, which appeared to have emerged independently in at least three rice subspecies. For OsSWEET13, a 2-bp deletion at the 5th and 6th positions of the EBE, and a substitution at the 17th position appear to be sufficient to prevent activation by PthXo2. Similarly, a single nucleotide substitution at position 10 compromised the induction of OsSWEET14 by AvrXa7. These findings might increase our opportunities to reduce pathogen virulence by preventing the induction of SWEET transporters. Pyramiding variants along with other resistance genes may provide durable and broad-spectrum resistance to the disease.
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Affiliation(s)
- Abha Zaka
- Agriculture Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang road, Faisalabad, Punjab, Pakistan
- Department of Biological Sciences, Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Punjab, Pakistan
| | - Genelou Grande
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Thea Coronejo
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Ian Lorenzo Quibod
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Chun-Wei Chen
- Taiwan Agricultural Research Institute, Agricultural Research and Extension Station, Council of Agriculture, Guannan, Miaoli District, Taiwan
| | - Su-Jein Chang
- Taiwan Agricultural Research Institute, Agricultural Research and Extension Station, Council of Agriculture, Guannan, Miaoli District, Taiwan
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | - Muhammad Arif
- Agriculture Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang road, Faisalabad, Punjab, Pakistan
- Department of Biological Sciences, Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Punjab, Pakistan
| | - Casiana Vera Cruz
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
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29
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Tran TT, Doucouré H, Hutin M, Jaimes Niño LM, Szurek B, Cunnac S, Koebnik R. Efficient enrichment cloning of TAL effector genes from Xanthomonas. MethodsX 2018; 5:1027-1032. [PMID: 30225203 PMCID: PMC6138780 DOI: 10.1016/j.mex.2018.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/31/2018] [Indexed: 11/29/2022] Open
Abstract
Many plant-pathogenic xanthomonads use a type III secretion system to translocate Transcription Activator-Like (TAL) effectors into eukaryotic host cells where they act as transcription factors. Target genes are induced upon binding of a TAL effector to double-stranded DNA in a sequence-specific manner. DNA binding is governed by a highly repetitive protein domain, which consists of an array of nearly identical repeats of ca. 102 base pairs. Many species and pathovars of Xanthomonas, including pathogens of rice, cereals, cassava, citrus and cotton, encode multiple TAL effectors in their genomes. Some of the TAL effectors have been shown to act as key pathogenicity factors, which induce the expression of susceptibility genes to the benefit of the pathogen. However, due to the repetitive character and the presence of multiple gene copies, high-throughput cloning of TAL effector genes remains a challenge. In order to isolate complete TAL effector gene repertoires, we developed an enrichment cloning strategy based on •genome-informed in silico optimization of restriction digestions,•selective restriction digestion of genomic DNA, and•size fractionation of DNA fragments. Our rapid, cheap and powerful method allows efficient cloning of TAL effector genes from xanthomonads, as demonstrated for two rice-pathogenic strains of Xanthomonas oryzae from Africa.
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Affiliation(s)
- T T Tran
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - H Doucouré
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - M Hutin
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | | | - B Szurek
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - S Cunnac
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - R Koebnik
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
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30
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Doucouré H, Pérez-Quintero AL, Reshetnyak G, Tekete C, Auguy F, Thomas E, Koebnik R, Szurek B, Koita O, Verdier V, Cunnac S. Functional and Genome Sequence-Driven Characterization of tal Effector Gene Repertoires Reveals Novel Variants With Altered Specificities in Closely Related Malian Xanthomonas oryzae pv. oryzae Strains. Front Microbiol 2018; 9:1657. [PMID: 30127769 PMCID: PMC6088199 DOI: 10.3389/fmicb.2018.01657] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/03/2018] [Indexed: 11/13/2022] Open
Abstract
Rice bacterial leaf blight (BLB) is caused by Xanthomonas oryzae pv. oryzae (Xoo) which injects Transcription Activator-Like Effectors (TALEs) into the host cell to modulate the expression of target disease susceptibility genes. Xoo major-virulence TALEs universally target susceptibility genes of the SWEET sugar transporter family. TALE-unresponsive alleles of OsSWEET genes have been identified in the rice germplasm or created by genome editing and confer resistance to BLB. In recent years, BLB has become one of the major biotic constraints to rice cultivation in Mali. To inform the deployment of alternative sources of resistance in this country, rice lines carrying alleles of OsSWEET14 unresponsive to either TalF (formerly Tal5) or TalC, two important TALEs previously identified in West African Xoo, were challenged with a panel of strains recently isolated in Mali and were found to remain susceptible to these isolates. The characterization of TALE repertoires revealed that talF and talC specific molecular markers were simultaneously present in all surveyed Malian strains, suggesting that the corresponding TALEs are broadly deployed by Malian Xoo to redundantly target the OsSWEET14 gene promoter. Consistent with this, the capacity of most Malian Xoo to induce OsSWEET14 was unaffected by either talC- or talF-unresponsive alleles of this gene. Long-read sequencing and assembly of eight Malian Xoo genomes confirmed the widespread occurrence of active TalF and TalC variants and provided a detailed insight into the diversity of TALE repertoires. All sequenced strains shared nine evolutionary related tal effector genes. Notably, a new TalF variant that is unable to induce OsSWEET14 was identified. Furthermore, two distinct TalB variants were shown to have lost the ability to simultaneously induce two susceptibility genes as previously reported for the founding members of this group from strains MAI1 and BAI3. Yet, both new TalB variants retained the ability to induce one or the other of the two susceptibility genes. These results reveal molecular and functional differences in tal repertoires and will be important for the sustainable deployment of broad-spectrum and durable resistance to BLB in West Africa.
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Affiliation(s)
- Hinda Doucouré
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | | | - Ganna Reshetnyak
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Cheick Tekete
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Florence Auguy
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Emilie Thomas
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Boris Szurek
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Valérie Verdier
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Sébastien Cunnac
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
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31
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Denancé N, Szurek B, Doyle EL, Lauber E, Fontaine-Bodin L, Carrère S, Guy E, Hajri A, Cerutti A, Boureau T, Poussier S, Arlat M, Bogdanove AJ, Noël LD. Two ancestral genes shaped the Xanthomonas campestris TAL effector gene repertoire. THE NEW PHYTOLOGIST 2018; 219:391-407. [PMID: 29677397 DOI: 10.1111/nph.15148] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome). The 53 sequenced tal genes encode 21 distinct DNA binding domains that sort into seven major DNA binding specificities. In silico analysis of the Brassica rapa promoterome identified a repertoire of predicted TALE targets, five of which were experimentally validated using quantitative reverse transcription polymerase chain reaction. The Xc TALome shows multiple signs of DNA rearrangements that probably drove its evolution from two ancestral tal genes. We discovered that Tal12a and Tal15a of Xcc strain Xca5 contribute together in the development of disease symptoms on susceptible B. oleracea var. botrytis cv Clovis. This large and polymorphic repertoire of TALEs opens novel perspectives for elucidating TALE-mediated susceptibility of Brassicaceae to black rot disease and for understanding the molecular processes underlying TALE evolution.
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Affiliation(s)
- Nicolas Denancé
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Boris Szurek
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Erin L Doyle
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
- Department of Biology, Doane University, Crete, NE, 68333, USA
| | - Emmanuelle Lauber
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | | | - Sébastien Carrère
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Endrick Guy
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Ahmed Hajri
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Aude Cerutti
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Tristan Boureau
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Stéphane Poussier
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Matthieu Arlat
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Adam J Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Laurent D Noël
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
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32
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Functional analysis of African Xanthomonas oryzae pv. oryzae TALomes reveals a new susceptibility gene in bacterial leaf blight of rice. PLoS Pathog 2018; 14:e1007092. [PMID: 29864161 PMCID: PMC6037387 DOI: 10.1371/journal.ppat.1007092] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 07/09/2018] [Accepted: 05/12/2018] [Indexed: 11/19/2022] Open
Abstract
Most Xanthomonas species translocate Transcription Activator-Like (TAL) effectors into plant cells where they function like plant transcription factors via a programmable DNA-binding domain. Characterized strains of rice pathogenic X. oryzae pv. oryzae harbor 9–16 different tal effector genes, but the function of only a few of them has been decoded. Using sequencing of entire genomes, we first performed comparative analyses of the complete repertoires of TAL effectors, herein referred to as TALomes, in three Xoo strains forming an African genetic lineage different from Asian Xoo. A phylogenetic analysis of the three TALomes combined with in silico predictions of TAL effector targets showed that African Xoo TALomes are highly conserved, genetically distant from Asian ones, and closely related to TAL effectors from the bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc). Nine clusters of TAL effectors could be identified among the three TALomes, including three showing higher levels of variation in their repeat variable diresidues (RVDs). Detailed analyses of these groups revealed recombination events as a possible source of variation among TAL effector genes. Next, to address contribution to virulence, nine TAL effector genes from the Malian Xoo strain MAI1 and four allelic variants from the Burkinabe Xoo strain BAI3, thus representing most of the TAL effector diversity in African Xoo strains, were expressed in the TAL effector-deficient X. oryzae strain X11-5A for gain-of-function assays. Inoculation of the susceptible rice variety Azucena lead to the discovery of three TAL effectors promoting virulence, including two TAL effectors previously reported to target the susceptibility (S) gene OsSWEET14 and a novel major virulence contributor, TalB. RNA profiling experiments in rice and in silico prediction of EBEs were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor. Use of designer TAL effectors demonstrated that induction of either gene resulted in greater susceptibility to strain X11-5A. The induction of OsERF#123 by BAI3Δ1, a talB knockout derivative of BAI3, carrying these designer TAL effectors increased virulence of BAI3Δ1, validating OsERF#123 as a new, bacterial blight S gene. The ability of most Xanthomonas plant pathogenic bacteria to infect their hosts relies on the action of a specific family of proteins called TAL effectors, which are transcriptional activators injected into the plant by the bacteria. TAL effectors enter the plant cell nucleus and bind to the promoters of specific plant genes. Genes that when induced can benefit pathogen multiplication or disease development are called susceptibility (S) genes. Here, we perform a comparative analysis of the TAL effector repertoires of three strains of X. oryzae pv. oryzae, which causes bacterial leaf blight of rice, a major yield constraint in this staple crop. Using sequencing of entire genomes, we compared the large repertoires of TAL effectors in three African Xoo strains which form a genetic lineage distinct from Asian strains. We assessed the individual contribution to pathogen virulence of 13 TAL effector variants represented in the three strains, and identified one that makes a major contribution. By combining host transcriptome profiling and TAL effector binding sites prediction, we identified two targets of this TAL effector that function as S genes, one previously identified, and one, new S gene. We validated the new S gene by functional characterization using designer TAL effectors. Both S genes encode transcription factors and can therefore be considered as susceptibility hubs for pathogen manipulation of the host transcriptome. Our results provide new insights into the diversified strategies underlying the roles of TAL effectors in promoting plant disease.
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33
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Bogdanove AJ, Bohm A, Miller JC, Morgan RD, Stoddard BL. Engineering altered protein-DNA recognition specificity. Nucleic Acids Res 2018; 46:4845-4871. [PMID: 29718463 PMCID: PMC6007267 DOI: 10.1093/nar/gky289] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023] Open
Abstract
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Bohm
- Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Jeffrey C Miller
- Sangamo Therapeutics Inc. 501 Canal Blvd., Richmond, CA 94804, USA
| | - Richard D Morgan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98019, USA
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Erkes A, Reschke M, Boch J, Grau J. Evolution of Transcription Activator-Like Effectors in Xanthomonas oryzae. Genome Biol Evol 2018. [PMID: 28637323 PMCID: PMC5512977 DOI: 10.1093/gbe/evx108] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Transcription activator-like effectors (TALEs) are secreted by plant–pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid (AA) tandem repeats, where AA 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs. Here, we study the evolution of TALEs from the level of RVDs determining target specificity down to the level of DNA sequence with focus on rice-pathogenic Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) strains. We observe that codon pairs coding for individual RVDs are conserved to a similar degree as the flanking repeat sequence. We find strong indications that TALEs may evolve 1) by base substitutions in codon pairs coding for RVDs, 2) by recombination of N-terminal or C-terminal regions of existing TALEs, or 3) by deletion of individual TALE repeats, and we propose possible mechanisms. We find indications that the reassortment of TALE genes in clusters is mediated by an integron-like mechanism in Xoc. We finally study the effect of the presence/absence and evolutionary modifications of TALEs on transcriptional activation of putative target genes in rice, and find that even single RVD swaps may lead to considerable differences in activation. This correlation allowed a refined prediction of TALE targets, which is the crucial step to decipher their virulence activity.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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35
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Pérez-Quintero AL, Lamy L, Zarate CA, Cunnac S, Doyle E, Bogdanove A, Szurek B, Dereeper A. daTALbase: A Database for Genomic and Transcriptomic Data Related to TAL Effectors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:471-480. [PMID: 29143556 DOI: 10.1094/mpmi-06-17-0153-fi] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility genes (S genes), triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs amino acid sequences. New candidate S genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements. By contrasting differential expression data and binding site predictions across different datasets, patterns of TALE diversification or convergence may be unveiled, but this requires the seamless integration of different genomic and transcriptomic data. With this in mind, we present daTALbase, a curated relational database that integrates TALE-related data including bacterial TALE sequences, plant promoter sequences, predicted TALE binding sites, transcriptomic data of host plants in response to TALE-harboring bacteria, and other associated data. The database can be explored to uncover new candidate S genes as well as to study variation in TALE repertories and their corresponding targets. The first version of the database here presented includes data for Oryza sp.-Xanthomonas pv. oryzae interactions. Future versions of the database will incorporate information for other pathosystems involving TALEs.
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Affiliation(s)
- Alvaro L Pérez-Quintero
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
- 2 Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Léo Lamy
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Carlos A Zarate
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Sébastien Cunnac
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Erin Doyle
- 3 Department of Biology, Doane University, 1014 Boswell Avenue, Crete, NE 68333, U.S.A.; and
| | - Adam Bogdanove
- 3 Department of Biology, Doane University, 1014 Boswell Avenue, Crete, NE 68333, U.S.A.; and
- 4 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Boris Szurek
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Alexis Dereeper
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
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36
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Rinaldi FC, Doyle LA, Stoddard BL, Bogdanove AJ. The effect of increasing numbers of repeats on TAL effector DNA binding specificity. Nucleic Acids Res 2017; 45:6960-6970. [PMID: 28460076 PMCID: PMC5499867 DOI: 10.1093/nar/gkx342] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/21/2017] [Indexed: 01/27/2023] Open
Abstract
Transcription activator-like effectors (TALEs) recognize their DNA targets via tandem repeats, each specifying a single nucleotide base in a one-to-one sequential arrangement. Due to this modularity and their ability to bind long DNA sequences with high specificity, TALEs have been used in many applications. Contributions of individual repeat-nucleotide associations to affinity and specificity have been characterized. Here, using in vitro binding assays, we examined the relationship between the number of repeats in a TALE and its affinity, for both target and non-target DNA. Each additional repeat provides extra binding energy for the target DNA, with the gain decaying exponentially such that binding energy saturates. Affinity for non-target DNA also increases non-linearly with the number of repeats, but with a slower decay of gain. The difference between the effect of length on affinity for target versus non-target DNA manifests in specificity increasing then diminishing with increasing TALE length, peaking between 15 and 19 repeats. Modeling across different hypothetical saturation levels and rates of gain decay, reflecting different repeat compositions, yielded a similar range of specificity optima. This range encompasses the mean and median length of native TALEs, suggesting that these proteins as a group have evolved for maximum specificity.
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Affiliation(s)
- Fabio C Rinaldi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research, Seattle, WA 98019, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research, Seattle, WA 98019, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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37
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Ruh M, Briand M, Bonneau S, Jacques MA, Chen NWG. Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors. BMC Genomics 2017; 18:670. [PMID: 28854875 PMCID: PMC5577687 DOI: 10.1186/s12864-017-4087-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/24/2017] [Indexed: 12/25/2022] Open
Abstract
Background Common bacterial blight is a devastating bacterial disease of common bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause similar symptoms on common bean, suggesting that they have acquired common genetic determinants of adaptation to common bean. Transcription Activator-Like (TAL) effectors are bacterial type III effectors that are able to induce the expression of host genes to promote infection or resistance. Their capacity to bind to a specific host DNA sequence suggests that they are potential candidates for host adaption. Results To study the diversity of tal genes from Xanthomonas strains responsible for common bacterial blight of bean, whole genome sequences of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli pv. phaseoli were obtained by single molecule real time sequencing. Analysis of these genomes revealed the existence of four tal genes named tal23A, tal20F, tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A and tal18H were carried on plasmids and shared between phylogenetically distant strains, therefore suggesting recent horizontal transfers of these genes between X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was present in all strains studied, suggesting that it played an important role in adaptation to common bean. In silico predictions of TAL effectors targets in the common bean genome suggested that TAL effectors shared by X. citri pv. fuscans and X. phaseoli pv. phaseoli strains target the promoters of genes of similar functions. This could be a trace of convergent evolution among TAL effectors from different phylogenetic groups, and comforts the hypothesis that TAL effectors have been implied in the adaptation to common bean. Conclusions Altogether, our results favour a model where plasmidic TAL effectors are able to contribute to host adaptation by being horizontally transferred between distant lineages. Electronic supplementary material The online version of this article (10.1186/s12864-017-4087-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mylène Ruh
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France.
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Tollenaere C, Lacombe S, Wonni I, Barro M, Ndougonna C, Gnacko F, Sérémé D, Jacobs JM, Hebrard E, Cunnac S, Brugidou C. Virus-Bacteria Rice Co-Infection in Africa: Field Estimation, Reciprocal Effects, Molecular Mechanisms, and Evolutionary Implications. FRONTIERS IN PLANT SCIENCE 2017; 8:645. [PMID: 28507553 PMCID: PMC5410622 DOI: 10.3389/fpls.2017.00645] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/10/2017] [Indexed: 05/04/2023]
Abstract
Simultaneous infection of a single plant by various pathogen species is increasingly recognized as an important modulator of host resistance and a driver of pathogen evolution. Because plants in agro-ecosystems are the target of a multitude of pathogenic microbes, co-infection could be frequent, and consequently important to consider. This is particularly true for rapidly intensifying crops, such as rice in Africa. This study investigated potential interactions between pathogens causing two of the major rice diseases in Africa: the Rice yellow mottle virus (RYMV) and the bacterium Xanthomonas oryzae pathovar oryzicola (Xoc) in order to: 1/ document virus-bacteria co-infection in rice in the field, 2/ explore experimentally their consequences in terms of symptom development and pathogen multiplication, 3/ test the hypothesis of underlying molecular mechanisms of interactions and 4/ explore potential evolutionary consequences. Field surveys in Burkina Faso revealed that a significant proportion of rice fields were simultaneously affected by the two diseases. Co-infection leads to an increase in bacterial specific symptoms, while a decrease in viral load is observed compared to the mono-infected mock. The lack of effect found when using a bacterial mutant for an effector specifically inducing expression of a small RNA regulatory protein, HEN1, as well as a viral genotype-specific effect, both suggest a role for gene silencing mechanisms mediating the within-plant interaction between RYMV and Xoc. Potential implications for pathogen evolution could not be inferred because genotype-specific effects were found only for pathogens originating from different countries, and consequently not meeting in the agrosystem. We argue that pathogen-pathogen-host interactions certainly deserve more attention, both from a theoretical and applied point of view.
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Affiliation(s)
- Charlotte Tollenaere
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
- Laboratoire Mixte International Patho-Bios, Laboratoire de Bactériologie, Institut de l'Environnement et de Recherches Agricoles (INERA)Bobo-Dioulasso, Burkina Faso
| | - Severine Lacombe
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
- Laboratoire Mixte International Patho-Bios, Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l'Environnement et de Recherches Agricoles (INERA)Kamboinsé, Burkina Faso
| | - Issa Wonni
- Laboratoire Mixte International Patho-Bios, Laboratoire de Bactériologie, Institut de l'Environnement et de Recherches Agricoles (INERA)Bobo-Dioulasso, Burkina Faso
| | - Mariam Barro
- Laboratoire Mixte International Patho-Bios, Laboratoire de Bactériologie, Institut de l'Environnement et de Recherches Agricoles (INERA)Bobo-Dioulasso, Burkina Faso
| | - Cyrielle Ndougonna
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
| | - Fatoumata Gnacko
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
- Laboratoire Mixte International Patho-Bios, Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l'Environnement et de Recherches Agricoles (INERA)Kamboinsé, Burkina Faso
| | - Drissa Sérémé
- Laboratoire Mixte International Patho-Bios, Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l'Environnement et de Recherches Agricoles (INERA)Kamboinsé, Burkina Faso
| | - Jonathan M. Jacobs
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
| | - Eugénie Hebrard
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
| | - Sebastien Cunnac
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
| | - Christophe Brugidou
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
- Laboratoire Mixte International Patho-Bios, Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l'Environnement et de Recherches Agricoles (INERA)Kamboinsé, Burkina Faso
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Streubel J, Baum H, Grau J, Stuttman J, Boch J. Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations. PLoS One 2017; 12:e0173580. [PMID: 28301511 PMCID: PMC5354296 DOI: 10.1371/journal.pone.0173580] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/22/2017] [Indexed: 11/19/2022] Open
Abstract
Plant-pathogenic Xanthomonas bacteria inject transcription activator-like effector proteins (TALEs) into host cells to specifically induce transcription of plant genes and enhance susceptibility. Although the DNA-binding mode is well-understood it is still ambiguous how TALEs initiate transcription and whether additional promoter elements are needed to support this. To systematically dissect prerequisites for transcriptional initiation the activity of one TALE was compared on different synthetic Bs4 promoter fragments. In addition, a large collection of artificial TALEs spanning the OsSWEET14 promoter was compared. We show that the presence of a TALE alone is not sufficient to initiate transcription suggesting the requirement of additional supporting promoter elements. At the OsSWEET14 promoter TALEs can initiate transcription from various positions, in a synergistic manner of multiple TALEs binding in parallel to the promoter, and even by binding in reverse orientation. TALEs are known to shift the transcriptional start site, but our data show that this shift depends on the individual position of a TALE within a promoter context. Our results implicate that TALEs function like classical enhancer-binding proteins and initiate transcription in both orientations which has consequences for in planta target gene prediction and design of artificial activators.
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Affiliation(s)
- Jana Streubel
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Heidi Baum
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Grau
- Institute of Computer Science, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Johannes Stuttman
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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40
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Wang L, Rinaldi FC, Singh P, Doyle EL, Dubrow ZE, Tran TT, Pérez-Quintero AL, Szurek B, Bogdanove AJ. TAL Effectors Drive Transcription Bidirectionally in Plants. MOLECULAR PLANT 2017; 10:285-296. [PMID: 27965000 DOI: 10.1016/j.molp.2016.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 06/06/2023]
Abstract
TAL effectors delivered by phytopathogenic Xanthomonas species are DNA-sequence-specific transcriptional activators of host susceptibility genes and sometimes resistance genes. The modularity of DNA recognition by TAL effectors makes them important also as tools for gene targeting and genome editing. Effector binding elements (EBEs) recognized by native TAL effectors in plants have been identified only on the forward strand of target promoters. Here, we demonstrate that TAL effectors can drive plant transcription from EBEs on either strand and in both directions. Furthermore, we show that a native TAL effector from Xanthomonas oryzae pv. oryzicola drives expression of a target with an EBE on each strand of its promoter. By inserting that promoter and derivatives between two reporter genes oriented head to head, we show that the TAL effector drives expression from either EBE in the respective orientations, and that activity at the reverse-strand EBE also potentiates forward transcription driven by activity at the forward-strand EBE. Our results reveal new modes of action for TAL effectors, suggesting the possibility of yet unrecognized targets important in plant disease, expanding the search space for off-targets of custom TAL effectors, and highlighting the potential of TAL effectors for probing fundamental aspects of plant transcription.
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Affiliation(s)
- Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
| | - Fabio C Rinaldi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
| | - Pallavi Singh
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
| | - Erin L Doyle
- Department of Biology, Doane University, 1014 Boswell Avenue, Crete, NE 68333, USA
| | - Zoe E Dubrow
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
| | - Tuan Tu Tran
- UMR Interactions-Plantes-Microorganismes-Environnement, IRD-Cirad-Université Montpellier, Montpellier, France
| | - Alvaro L Pérez-Quintero
- UMR Interactions-Plantes-Microorganismes-Environnement, IRD-Cirad-Université Montpellier, Montpellier, France
| | - Boris Szurek
- UMR Interactions-Plantes-Microorganismes-Environnement, IRD-Cirad-Université Montpellier, Montpellier, France
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA.
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Hutin M, Césari S, Chalvon V, Michel C, Tran TT, Boch J, Koebnik R, Szurek B, Kroj T. Ectopic activation of the rice NLR heteropair RGA4/RGA5 confers resistance to bacterial blight and bacterial leaf streak diseases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:43-55. [PMID: 27289079 DOI: 10.1111/tpj.13231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 06/01/2016] [Accepted: 06/03/2016] [Indexed: 06/06/2023]
Abstract
Bacterial blight (BB) and bacterial leaf streak (BLS) are important diseases in Oryza sativa caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively. In both bacteria, transcription activator-like (TAL) effectors are major virulence determinants that act by transactivating host genes downstream of effector-binding elements (EBEs) bound in a sequence-specific manner. Resistance to Xoo is mostly related to the action of TAL effectors, either by polymorphisms that prevent the induction of susceptibility (S) genes or by executor (R) genes with EBEs embedded in their promoter, and that induce cell death and resistance. For Xoc, no resistance sources are known in rice. Here, we investigated whether the recognition of effectors by nucleotide binding and leucine-rich repeat domain immune receptors (NLRs), the most widespread resistance mechanism in plants, is also able to stop BB and BLS. In one instance, transgenic rice lines harboring the AVR1-CO39 effector gene from the rice blast fungus Magnaporthe oryzae, under the control of an inducible promoter, were challenged with transgenic Xoo and Xoc strains carrying a TAL effector designed to transactivate the inducible promoter. This induced AVR1-CO39 expression and triggered BB and BLS resistance when the corresponding Pi-CO39 resistance locus was present. In a second example, the transactivation of an auto-active NLR by Xoo-delivered designer TAL effectors resulted in BB resistance, demonstrating that NLR-triggered immune responses efficiently control Xoo. This forms the foundation for future BB and BLS disease control strategies, whereupon endogenous TAL effectors will target synthetic promoter regions of Avr or NLR executor genes.
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Affiliation(s)
- Mathilde Hutin
- UMR Interactions Plantes-Microorganismes-Environnement, IRD-Cirad-UM, Montpellier, France
| | - Stella Césari
- INRA, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- CIRAD, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- SUPAGRO, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
| | - Véronique Chalvon
- INRA, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- CIRAD, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- SUPAGRO, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
| | - Corinne Michel
- INRA, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- CIRAD, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
- SUPAGRO, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France
| | - Tuan Tu Tran
- UMR Interactions Plantes-Microorganismes-Environnement, IRD-Cirad-UM, Montpellier, France
| | - Jens Boch
- Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), 06099, Germany
| | - Ralf Koebnik
- UMR Interactions Plantes-Microorganismes-Environnement, IRD-Cirad-UM, Montpellier, France
| | - Boris Szurek
- UMR Interactions Plantes-Microorganismes-Environnement, IRD-Cirad-UM, Montpellier, France.
| | - Thomas Kroj
- INRA, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France.
- CIRAD, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France.
- SUPAGRO, Biology and Genetics of Plant-Pathogen Interactions Laboratory, Montpellier, France.
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Korostelev YD, Zharov IA, Mironov AA, Rakhmaininova AB, Gelfand MS. Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors. PLoS One 2016; 11:e0162681. [PMID: 27690309 PMCID: PMC5045206 DOI: 10.1371/journal.pone.0162681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 08/26/2016] [Indexed: 11/25/2022] Open
Abstract
The large and increasing volume of genomic data analyzed by comparative methods provides information about transcription factors and their binding sites that, in turn, enables statistical analysis of correlations between factors and sites, uncovering mechanisms and evolution of specific protein-DNA recognition. Here we present an online tool, Prot-DNA-Korr, designed to identify and analyze crucial protein-DNA pairs of positions in a family of transcription factors. Correlations are identified by analysis of mutual information between columns of protein and DNA alignments. The algorithm reduces the effects of common phylogenetic history and of abundance of closely related proteins and binding sites. We apply it to five closely related subfamilies of the MerR family of bacterial transcription factors that regulate heavy metal resistance systems. We validate the approach using known 3D structures of MerR-family proteins in complexes with their cognate DNA binding sites and demonstrate that a significant fraction of correlated positions indeed form specific side-chain-to-base contacts. The joint distribution of amino acids and nucleotides hence may be used to predict changes of specificity for point mutations in transcription factors.
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Affiliation(s)
- Yuriy D. Korostelev
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
- Department of Bioengineering and Bioinformatics, Moscow State University, 1-73 Vorobievy Gory, Moscow, Russia, 119991
| | - Ilya A. Zharov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
| | - Andrey A. Mironov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
- Department of Bioengineering and Bioinformatics, Moscow State University, 1-73 Vorobievy Gory, Moscow, Russia, 119991
| | - Alexandra B. Rakhmaininova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
| | - Mikhail S. Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
- Department of Bioengineering and Bioinformatics, Moscow State University, 1-73 Vorobievy Gory, Moscow, Russia, 119991
- * E-mail:
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Quibod IL, Perez-Quintero A, Booher NJ, Dossa GS, Grande G, Szurek B, Vera Cruz C, Bogdanove AJ, Oliva R. Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment. Sci Rep 2016; 6:34137. [PMID: 27667260 PMCID: PMC5035989 DOI: 10.1038/srep34137] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/07/2016] [Indexed: 01/01/2023] Open
Abstract
Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts. Here, we took advantage of an historical record to examine the adaptation pathway of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) in a semi-isolated environment represented in the Philippine archipelago. By comparing genomes of key Xoo groups we showed that modern populations derived from three Asian lineages. We also showed that diversification of virulence factors occurred within each lineage, most likely driven by host adaptation, and it was essential to shape contemporary pathogen races. This finding is particularly important because it expands our understanding of pathogen adaptation to modern agriculture.
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Affiliation(s)
- Ian Lorenzo Quibod
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Alvaro Perez-Quintero
- Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Gerbert S Dossa
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Genelou Grande
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Boris Szurek
- Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Casiana Vera Cruz
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Ricardo Oliva
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
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Braguy J, Zurbriggen MD. Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:118-38. [PMID: 27227549 DOI: 10.1111/tpj.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 05/15/2023]
Abstract
Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.
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Affiliation(s)
- Justine Braguy
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
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Hu Y, Duan S, Zhang Y, Shantharaj D, Jones JB, Wang N. Temporal Transcription Profiling of Sweet Orange in Response to PthA4-Mediated Xanthomonas citri subsp. citri Infection. PHYTOPATHOLOGY 2016; 106:442-451. [PMID: 26780431 DOI: 10.1094/phyto-09-15-0201-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Citrus canker, caused by Xanthomonas citri subsp. citri, is a devastating disease of most commercial citrus varieties. In our previous study, we analyzed the transcriptional response of 'Valencia' sweet orange to X. citri subsp. citri wild-type and pthA4 mutant infection at 48 h postinoculation (hpi). Using microarray analysis, two PthA4 targets, CsLOB1 and CsSWEET1, were identified. We have shown that PthA4 binds to the effector binding element (EBE) of CsLOB1 and activates gene expression of this susceptibility gene. However, how PthA4 modulates host genes at different stages of infection remains to be determined. In this study, we compared the transcriptional profiles between citrus leaf tissue inoculated with Xcc306 and those inoculated with a pthA4-deletion mutant strain (Xcc306∆pthA4) at 6, 48, and 120 hpi. At both 48 and 120 hpi, the PthA4-mediated infection significantly upregulated expression of a variety of genes involved in cell-wall degradation and modification, DNA packaging, G-protein, protein synthesis, sucrose metabolism, and cell division functions, while the downregulated genes were mainly enriched in photosynthesis, transport, secondary metabolism, cytochrome P450, and various plant defense-associated mechanisms. To validate microarray results, gene expression of 26 genes representing genes associated with cell-wall-associated, immunity system, and carbohydrate metabolism was confirmed using quantitative reverse-transcription polymerase chain reaction. Expression patterns of these genes at 48 and 120 hpi were consistent with the microarray results. We also identified putative EBE for PthA4 (EBEPthA4) in the promoter regions of multiple genes upregulated by PthA4, to which PthA4 might bind directly to control their gene expression. Our study provided a dynamic picture of citrus genes regulated by PthA4 during the X. citri subsp. citri infection of citrus leaves at different stages. This study will be useful in further understanding the virulence mechanism of X. citri subsp. citri and identifying potential targets of PthA4.
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Affiliation(s)
- Yang Hu
- First, fourth, and fifth authors: Department of Plant Pathology, University of Florida, Gainesville 32611; and second, third, and sixth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred 33850
| | - Shuo Duan
- First, fourth, and fifth authors: Department of Plant Pathology, University of Florida, Gainesville 32611; and second, third, and sixth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred 33850
| | - Yunzeng Zhang
- First, fourth, and fifth authors: Department of Plant Pathology, University of Florida, Gainesville 32611; and second, third, and sixth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred 33850
| | - Deepak Shantharaj
- First, fourth, and fifth authors: Department of Plant Pathology, University of Florida, Gainesville 32611; and second, third, and sixth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred 33850
| | - Jeffrey B Jones
- First, fourth, and fifth authors: Department of Plant Pathology, University of Florida, Gainesville 32611; and second, third, and sixth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred 33850
| | - Nian Wang
- First, fourth, and fifth authors: Department of Plant Pathology, University of Florida, Gainesville 32611; and second, third, and sixth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred 33850
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Bhushan K, Pratap D, Sharma PK. Transcription activator‐like effector nucleases (TALENs): An efficient tool for plant genome editing. Eng Life Sci 2016. [DOI: 10.1002/elsc.201500126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Kul Bhushan
- Advanced Centre for Plant Virology Indian Agricultural Research Institute New Delhi India
| | - Dharmendra Pratap
- Department of Genetics & Plant Breeding Ch. Charan Singh University Meerut Uttar Pradesh India
| | - Pradeep K. Sharma
- Department of Genetics & Plant Breeding Ch. Charan Singh University Meerut Uttar Pradesh India
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AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences. Sci Rep 2016; 6:21077. [PMID: 26876161 PMCID: PMC4753510 DOI: 10.1038/srep21077] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 01/18/2016] [Indexed: 12/16/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present ‘AnnoTALE’, a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities.
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Copeland MF, Politz MC, Johnson CB, Markley AL, Pfleger BF. A transcription activator-like effector (TALE) induction system mediated by proteolysis. Nat Chem Biol 2016; 12:254-60. [PMID: 26854666 PMCID: PMC4809019 DOI: 10.1038/nchembio.2021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/31/2015] [Indexed: 12/16/2022]
Abstract
Simple and predictable trans-acting regulatory tools are needed in the fields of synthetic biology and metabolic engineering to build complex genetic circuits and optimize the levels of native and heterologous gene products. Transcription activator-like effectors (TALEs) are bacterial virulence factors that have recently gained traction in biotechnology applications due to their customizable DNA binding specificity. In this work we expand the versatility of these transcription factors to create an inducible TALE system by inserting tobacco-etch virus (TEV) protease recognition sites into the TALE backbone. The resulting engineered TALEs maintain transcriptional repression of their target genes in Escherichia coli, but are degraded following the induction of the TEV protease, thereby promoting expression of the previously repressed target gene of interest. This TALE-TEV technology enables both repression and induction of plasmid or chromosomal target genes in a manner analogous to traditional repressor proteins but with the added flexibility of being operator agnostic.
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Affiliation(s)
- Matthew F Copeland
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
| | - Mark C Politz
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
| | - Charles B Johnson
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
| | - Andrew L Markley
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
| | - Brian F Pfleger
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, Wisconsin, USA
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Abstract
Transcription activator-like effectors (TALEs) are proteins with a unique DNA-binding domain that confers both a predictable and programmable specificity. The DNA-binding domain consists typically of 34-amino acid near-identical repeats. The repeats form a right-handed superhelical structure that wraps around the DNA double helix and exposes the variable amino acids at position 13 of each repeat to the sense strand DNA bases. Each repeat binds one base in a highly specific, non-overlapping, and comma-free fashion. Although TALE specificities are encoded in a simple way, sophisticated rules can be taken into account to build highly efficient DNA-binding modules for biotechnological use.
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50
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Budhagatapalli N, Schedel S, Gurushidze M, Pencs S, Hiekel S, Rutten T, Kusch S, Morbitzer R, Lahaye T, Panstruga R, Kumlehn J, Hensel G. A simple test for the cleavage activity of customized endonucleases in plants. PLANT METHODS 2016; 12:18. [PMID: 26962325 PMCID: PMC4784412 DOI: 10.1186/s13007-016-0118-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/24/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although customized endonucleases [transcription activator-like effector nucleases (TALENs) and RNA-guided endonucleases (RGENs)] are known to be effective agents of mutagenesis in various host plants, newly designed endonuclease constructs require some pre-validation with respect to functionality before investing in the creation of stable transgenic plants. RESULTS A simple, biolistics-based leaf epidermis transient expression test has been developed, based on reconstituting the translational reading frame of a mutated, non-functional yfp reporter gene. Quantification of mutation efficacy was made possible by co-bombarding the explant with a constitutive mCherry expression cassette, thereby allowing the ratio between the number of red and yellow fluorescing cells to serve as a metric for mutation efficiency. Challenging either stable mutant alleles of a compromised version of gfp in tobacco and barley or the barley MLO gene with TALENs/RGENs confirmed the capacity to induce site-directed mutations. CONCLUSIONS A convenient procedure to assay the cleavage activity of customized endonucleases has been established. The system is independent of the endonuclease platform and operates in both di- and monocotyledonous hosts. It not only enables the validation of a TALEN/RGEN's functionality prior to the creation of stable mutants, but also serves as a suitable tool to optimize the design of endonuclease constructs.
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Affiliation(s)
- Nagaveni Budhagatapalli
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Sindy Schedel
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Maia Gurushidze
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Stefanie Pencs
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
- />Chair of Plant Breeding, Martin Luther University, Betty-Heimann-Str. 3, 06120 Halle (Saale), Germany
| | - Stefan Hiekel
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Twan Rutten
- />Structural Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Stefan Kusch
- />Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
| | - Robert Morbitzer
- />ZMBP-General Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Thomas Lahaye
- />ZMBP-General Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Ralph Panstruga
- />Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
| | - Jochen Kumlehn
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Goetz Hensel
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
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