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Denancé N, Szurek B, Noël LD. Emerging functions of nodulin-like proteins in non-nodulating plant species. PLANT & CELL PHYSIOLOGY 2014; 55:469-74. [PMID: 24470637 DOI: 10.1093/pcp/pct198] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plant genes whose expression is induced in legumes by Rhizobium bacteria upon nodulation were initially referred to as nodulins. Several of them play a key role in the establishment of symbiosis. Yet, nodulin-like proteins are also found in non-nodulating plant species such as Arabidopsis, rice, maize or poplar. For instance, 132 are predicted in the Arabidopsis thaliana Col-0 genome. Recent studies now highlight the importance of nodulin-like proteins for the transport of nutrients, solutes, amino acids or hormones and for major aspects of plant development. Interestingly, nodulin-like activities at the plant-microbe interface are also important for pathogens to enhance their fitness during host colonization. This work presents a genomic and functional overview of nodulin-like proteins in non-leguminous plant species, with a particular focus on Arabidopsis and rice.
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Affiliation(s)
- Nicolas Denancé
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR 441, F-31326 Castanet-Tolosan, France
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Cernadas RA, Doyle EL, Niño-Liu DO, Wilkins KE, Bancroft T, Wang L, Schmidt CL, Caldo R, Yang B, White FF, Nettleton D, Wise RP, Bogdanove AJ. Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene. PLoS Pathog 2014; 10:e1003972. [PMID: 24586171 PMCID: PMC3937315 DOI: 10.1371/journal.ppat.1003972] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 01/17/2014] [Indexed: 12/17/2022] Open
Abstract
Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. oryzae pv. oryzae (Xoo), which invades xylem to cause bacterial blight of rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that transactivate effector-specific host genes. A TAL effector finds its target(s) via a partially degenerate code whereby the modular effector amino acid sequence identifies nucleotide sequences to which the protein binds. Virulence contributions of some Xoo TAL effectors have been shown, and their relevant targets, susceptibility (S) genes, identified, but the role of TAL effectors in leaf streak is uncharacterized. We used host transcript profiling to compare leaf streak to blight and to probe functions of Xoc TAL effectors. We found that Xoc and Xoo induce almost completely different host transcriptional changes. Roughly one in three genes upregulated by the pathogens is preceded by a candidate TAL effector binding element. Experimental analysis of the 44 such genes predicted to be Xoc TAL effector targets verified nearly half, and identified most others as false predictions. None of the Xoc targets is a known bacterial blight S gene. Mutational analysis revealed that Tal2g, which activates two genes, contributes to lesion expansion and bacterial exudation. Use of designer TAL effectors discriminated a sulfate transporter gene as the S gene. Across all targets, basal expression tended to be higher than genome-average, and induction moderate. Finally, machine learning applied to real vs. falsely predicted targets yielded a classifier that recalled 92% of the real targets with 88% precision, providing a tool for better target prediction in the future. Our study expands the number of known TAL effector targets, identifies a new class of S gene, and improves our ability to predict functional targeting. Many crop and ornamental plants suffer losses due to bacterial pathogens in the genus Xanthomonas. Pathogen manipulation of host gene expression by injected proteins called TAL effectors is important in many of these diseases. A TAL effector finds its gene target(s) by virtue of structural repeats in the protein that differ one from another at two amino acids that together identify one DNA base. The number of repeats and those amino acids thereby code for the DNA sequence the protein binds. This code allows target prediction and engineering TAL effectors for custom gene activation. By combining genome-wide analysis of gene expression with TAL effector binding site prediction and verification using designer TAL effectors, we identified 19 targets of TAL effectors in bacterial leaf streak of rice, a disease of growing importance worldwide caused by X. oryzae pv. oryzicola. Among these was a sulfate transport gene that plays a major role. Comparison of true vs. false predictions using machine learning yielded a classifier that will streamline TAL effector target identification in the future. Probing the diversity and functions of such plant genes is critical to expand our knowledge of disease and defense mechanisms, and open new avenues for effective disease control.
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Affiliation(s)
- Raul A. Cernadas
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Erin L. Doyle
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | - David O. Niño-Liu
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Katherine E. Wilkins
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Timothy Bancroft
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Li Wang
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Clarice L. Schmidt
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Rico Caldo
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Bing Yang
- Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Frank F. White
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Roger P. Wise
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
- Corn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, Iowa, United States of America
| | - Adam J. Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Liu W, Liu J, Triplett L, Leach JE, Wang GL. Novel insights into rice innate immunity against bacterial and fungal pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:213-41. [PMID: 24906128 DOI: 10.1146/annurev-phyto-102313-045926] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rice feeds more than half of the world's population. Rice blast, caused by the fungal pathogen Magnaporthe oryzae, and bacterial blight, caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae, are major constraints to rice production worldwide. Genome sequencing and extensive molecular analysis has led to the identification of many new pathogen-associated molecular patterns (PAMPs) and avirulence and virulence effectors in both pathogens, as well as effector targets and receptors in the rice host. Characterization of these effectors, host targets, and resistance genes has provided new insight into innate immunity in plants. Some of the new findings, such as the binding activity of X. oryzae transcriptional activator-like (TAL) effectors to specific rice genomic sequences, are being used for the development of effective disease control methods and genome modification tools. This review summarizes the recent progress toward understanding the recognition and signaling events that govern rice innate immunity.
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Affiliation(s)
- Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Doyle EL, Hummel AW, Demorest ZL, Starker CG, Voytas DF, Bradley P, Bogdanove AJ. TAL effector specificity for base 0 of the DNA target is altered in a complex, effector- and assay-dependent manner by substitutions for the tryptophan in cryptic repeat -1. PLoS One 2013; 8:e82120. [PMID: 24312634 PMCID: PMC3849474 DOI: 10.1371/journal.pone.0082120] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 10/21/2013] [Indexed: 12/20/2022] Open
Abstract
TAL effectors are re-targetable transcription factors used for tailored gene regulation and, as TAL effector-nuclease fusions (TALENs), for genome engineering. Their hallmark feature is a customizable central string of polymorphic amino acid repeats that interact one-to-one with individual DNA bases to specify the target. Sequences targeted by TAL effector repeats in nature are nearly all directly preceded by a thymine (T) that is required for maximal activity, and target sites for custom TAL effector constructs have typically been selected with this constraint. Multiple crystal structures suggest that this requirement for T at base 0 is encoded by a tryptophan residue (W232) in a cryptic repeat N-terminal to the central repeats that exhibits energetically favorable van der Waals contacts with the T. We generated variants based on TAL effector PthXo1 with all single amino acid substitutions for W232. In a transcriptional activation assay, many substitutions altered or relaxed the specificity for T and a few were as active as wild type. Some showed higher activity. However, when replicated in a different TAL effector, the effects of the substitutions differed. Further, the effects differed when tested in the context of a TALEN in a DNA cleavage assay, and in a TAL effector-DNA binding assay. Substitution of the N-terminal region of the PthXo1 construct with that of one of the TAL effector-like proteins of Ralstonia solanacearum, which have arginine in place of the tryptophan, resulted in specificity for guanine as the 5' base but low activity, and several substitutions for the arginine, including tryptophan, destroyed activity altogether. Thus, the effects on specificity and activity generated by substitutions at the W232 (or equivalent) position are complex and context dependent. Generating TAL effector scaffolds with high activity that robustly accommodate sites without a T at position 0 may require larger scale re-engineering.
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Affiliation(s)
- Erin L. Doyle
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Aaron W. Hummel
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Zachary L. Demorest
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- Cellectis Plant Sciences, New Brighton, Minnesota, United States of America
| | - Colby G. Starker
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Philip Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Adam J. Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States of America
- Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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55
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Streubel J, Pesce C, Hutin M, Koebnik R, Boch J, Szurek B. Five phylogenetically close rice SWEET genes confer TAL effector-mediated susceptibility to Xanthomonas oryzae pv. oryzae. THE NEW PHYTOLOGIST 2013; 200:808-819. [PMID: 23879865 DOI: 10.1111/nph.12411] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/03/2013] [Indexed: 05/03/2023]
Abstract
Bacterial plant-pathogenic Xanthomonas strains translocate transcription activator-like (TAL) effectors into plant cells to function as specific transcription factors. Only a few plant target genes of TAL effectors have been identified, so far. Three plant SWEET genes encoding putative sugar transporters are known to be induced by TAL effectors from rice-pathogenic Xanthomonas oryzae pv. oryzae (Xoo). We predict and validate that expression of OsSWEET14 is induced by a novel TAL effector, Tal5, from an African Xoo strain. Artificial TAL effectors (ArtTALs) were constructed to individually target 20 SWEET orthologs in rice. They were used as designer virulence factors to study which rice SWEET genes can support Xoo virulence. The Tal5 target box differs from those of the already known TAL effectors TalC, AvrXa7 and PthXo3, which also induce expression of OsSWEET14, suggesting evolutionary convergence on key targets. ArtTALs efficiently complemented an Xoo talC mutant, demonstrating that specific induction of OsSWEET14 is the key target of TalC. ArtTALs that specifically target individual members of the rice SWEET family revealed three known and two novel SWEET genes to support bacterial virulence. Our results demonstrate that five phylogenetically close SWEET proteins, which presumably act as sucrose transporters, can support Xoo virulence.
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Affiliation(s)
- Jana Streubel
- Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120, Halle (Saale), Germany
| | - Céline Pesce
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
- Earth and Life Institute, Applied Microbiology Phytopathology, Université Catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Mathilde Hutin
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
| | - Ralf Koebnik
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
| | - Jens Boch
- Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, D-06120, Halle (Saale), Germany
| | - Boris Szurek
- UMR 186 IRD-UM2-Cirad 'Résistance des Plantes aux Bioagresseurs', BP 64501, 34394, Montpellier Cedex 5, France
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56
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Cheong H, Kim CY, Jeon JS, Lee BM, Sun Moon J, Hwang I. Xanthomonas oryzae pv. oryzae type III effector XopN targets OsVOZ2 and a putative thiamine synthase as a virulence factor in rice. PLoS One 2013; 8:e73346. [PMID: 24019919 PMCID: PMC3760903 DOI: 10.1371/journal.pone.0073346] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 07/18/2013] [Indexed: 01/13/2023] Open
Abstract
Xanthomonasoryzae pv. oryzae (Xoo) is spread systemically through the xylem tissue and causes bacterial blight in rice. We evaluated the roles of Xanthomonas outer proteins (Xop) in the Xoo strain KXO85 in a Japonica-type rice cultivar, Dongjin. Five xop gene knockout mutants (xopQKXO85, xopXKXO85, xopP1KXO85, xopP2KXO85, and xopNKXO85) were generated by EZ-Tn5 mutagenesis, and their virulence was assessed in 3-month-old rice leaves. Among these mutants, the xopNKXO85 mutant appeared to be less virulent than the wild-type KXO85; however, the difference was not statistically significant. In contrast, the xopNKXO85 mutant exhibited significantly less virulence in flag leaves after flowering than the wild-type KXO85. These observations indicate that the roles of Xop in Xoo virulence are dependent on leaf stage. We chose the xopN gene for further characterization because the xopNKXO85 mutant showed the greatest influence on virulence. We confirmed that XopNKXO85 is translocated into rice cells, and its gene expression is positively regulated by HrpX. Two rice proteins, OsVOZ2 and a putative thiamine synthase (OsXNP), were identified as targets of XopNKXO85 by yeast two-hybrid screening. Interactions between XopNKXO85 and OsVOZ2 and OsXNP were further confirmed in planta by bimolecular fluorescence complementation and in vivo pull-down assays. To investigate the roles of OsVOZ2 in interactions between rice and Xoo, we evaluated the virulence of the wild-type KXO85 and xopNKXO85 mutant in the OsVOZ2 mutant line PFG_3A-07565 of Dongjin. The wild-type KXO85 and xopNKXO85 mutant were significantly less virulent in the mutant rice line. These results indicate that XopNKXO85 and OsVOZ2 play important roles both individually and together for Xoo virulence in rice.
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Affiliation(s)
- Hoon Cheong
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Chi-Yeol Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Byoung-Moo Lee
- National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- * E-mail:
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57
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Ye G, Hong N, Zou LF, Zou HS, Zakria M, Wang GP, Chen GY. tale-Based Genetic Diversity of Chinese Isolates of the Citrus Canker Pathogen Xanthomonas citri subsp. citri. PLANT DISEASE 2013; 97:1187-1194. [PMID: 30722424 DOI: 10.1094/pdis-12-12-1201-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Pathotype A of Xanthomonas citri subsp. citri, the cause of citrus bacterial canker (CBC), is assumed to have originated in southern China. PthA, a type III secreted transcriptional activator-like effector (TALE), is a major pathogenicity determinant in X. citri subsp. citri. To investigate the diversity of X. citri subsp. citri in China, genomic and plasmid DNA of 105 X. citri subsp. citri isolates, collected from nine citrus-growing provinces of China, were digested by BamHI and hybridized with an internal repeat region of pthA. Strains were classified into 14 different genotypes (designated A to N) based on the number and size of pthA homologues. Genotypes B and G represented 19 and 62% of the isolate collection, respectively. Genotypes J and L lacked pthA or a pthA-hybridizing fragment and were less virulent on grapefruit (C. paradisi) and sweet orange (C. sinensis) compared with strains containing pthA or a pthA homologue. The virulence of genotypes J and L was increased when the wild-type pthA was introduced. Genotype I, which was isolated from sweet orange in Jiangxi province, caused typical canker symptoms and may contain a novel pthA-like gene. To our knowledge, this is the first description of genetic diversity in Chinese CBC strains based on tale gene analysis.
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Affiliation(s)
- Gang Ye
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Li-Fang Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua-Song Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Zakria
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guo-Ping Wang
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University
| | - Gong-You Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University
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Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ. TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol 2013; 23:390-8. [PMID: 23707478 PMCID: PMC3729746 DOI: 10.1016/j.tcb.2013.04.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/19/2022]
Abstract
Transcription activator-like (TAL) effectors are transcription factors injected into plant cells by pathogenic bacteria of the genus Xanthomonas. They function as virulence factors by activating host genes important for disease, or as avirulence factors by turning on genes that provide resistance. DNA-binding specificity is encoded by polymorphic repeats in each protein that correspond one-to-one with different nucleotides. This code has facilitated target identification and opened new avenues for engineering disease resistance. It has also enabled TAL effector customization for targeted gene control, genome editing, and other applications. This article reviews the structural basis for TAL effector-DNA specificity, the impact of the TAL effector-DNA code on plant pathology and engineered resistance, and recent accomplishments and future challenges in TAL effector-based DNA targeting.
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Affiliation(s)
- Erin L. Doyle
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. A3-025, Seattle WA 98109
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, 321 Church Street SE, University of Minnesota, Minneapolis, MN 55455
| | - Adam J. Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, 334 Plant Science, Ithaca NY 14853
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59
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Pérez-Quintero AL, Rodriguez-R LM, Dereeper A, López C, Koebnik R, Szurek B, Cunnac S. An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. PLoS One 2013; 8:e68464. [PMID: 23869221 PMCID: PMC3711819 DOI: 10.1371/journal.pone.0068464] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/30/2013] [Indexed: 11/19/2022] Open
Abstract
Transcription Activators-Like Effectors (TALEs) belong to a family of virulence proteins from the Xanthomonas genus of bacterial plant pathogens that are translocated into the plant cell. In the nucleus, TALEs act as transcription factors inducing the expression of susceptibility genes. A code for TALE-DNA binding specificity and high-resolution three-dimensional structures of TALE-DNA complexes were recently reported. Accurate prediction of TAL Effector Binding Elements (EBEs) is essential to elucidate the biological functions of the many sequenced TALEs as well as for robust design of artificial TALE DNA-binding domains in biotechnological applications. In this work a program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions. To gain a systems perspective on the large TALE repertoires from X. oryzae strains, this program was used to predict rice gene targets for 99 sequenced family members. Integrating predictions and available expression data in a TALE-gene network revealed multiple candidate transcriptional targets for many TALEs as well as several possible instances of functional convergence among TALEs.
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Affiliation(s)
- Alvaro L. Pérez-Quintero
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
- Biology Department, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Luis M. Rodriguez-R
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Alexis Dereeper
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Camilo López
- Biology Department, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Ralf Koebnik
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Boris Szurek
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Sebastien Cunnac
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
- * E-mail: .
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60
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Zhang F, Du Z, Huang L, Cruz CV, Zhou Y, Li Z. Comparative transcriptome profiling reveals different expression patterns in Xanthomonas oryzae pv. oryzae strains with putative virulence-relevant genes. PLoS One 2013; 8:e64267. [PMID: 23734193 PMCID: PMC3667120 DOI: 10.1371/journal.pone.0064267] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/10/2013] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice bacterial blight, which is a major rice disease in tropical Asian countries. An attempt has been made to investigate gene expression patterns of three Xoo strains on the minimal medium XOM2, PXO99 (P6) and PXO86 (P2) from the Philippines, and GD1358 (C5) from China, which exhibited different virulence in 30 rice varieties, with putative virulence factors using deep sequencing. In total, 4,781 transcripts were identified in this study, and 1,151 and 3,076 genes were differentially expressed when P6 was compared with P2 and with C5, respectively. Our results indicated that Xoo strains from different regions exhibited distinctly different expression patterns of putative virulence-relevant genes. Interestingly, 40 and 44 genes involved in chemotaxis and motility exhibited higher transcript alterations in C5 compared with P6 and P2, respectively. Most other genes associated with virulence, including exopolysaccharide (EPS) synthesis, Hrp genes and type III effectors, including Xanthomonas outer protein (Xop) effectors and transcription activator-like (TAL) effectors, were down-regulated in C5 compared with P6 and P2. The data were confirmed by real-time quantitative RT-PCR, tests of bacterial motility, and enzyme activity analysis of EPS and xylanase. These results highlight the complexity of Xoo and offer new avenues for improving our understanding of Xoo-rice interactions and the evolution of Xoo virulence.
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Affiliation(s)
- Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenglin Du
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Liyu Huang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Casiana Vera Cruz
- International Rice Research Institute, Metro Manila, The Philippines
| | - Yongli Zhou
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
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