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Schepler-Luu V, Sciallano C, Stiebner M, Ji C, Boulard G, Diallo A, Auguy F, Char SN, Arra Y, Schenstnyi K, Buchholzer M, Loo EPI, Bilaro AL, Lihepanyama D, Mkuya M, Murori R, Oliva R, Cunnac S, Yang B, Szurek B, Frommer WB. Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains. eLife 2023; 12:e84864. [PMID: 37337668 DOI: 10.7554/elife.84864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.
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Affiliation(s)
- Van Schepler-Luu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Coline Sciallano
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Melissa Stiebner
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Chonghui Ji
- Division of Plant Science and Technology, University of Missouri, Columbia, United States
| | - Gabriel Boulard
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Amadou Diallo
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Florence Auguy
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Si Nian Char
- Division of Plant Science and Technology, University of Missouri, Columbia, United States
| | - Yugander Arra
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kyrylo Schenstnyi
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marcel Buchholzer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eliza P I Loo
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Atugonza L Bilaro
- Tanzania Agricultural Research Institute (TARI)-Uyole Centre, Mbeya, United Republic of Tanzania
| | - David Lihepanyama
- Tanzania Agricultural Research Institute (TARI)-Uyole Centre, Mbeya, United Republic of Tanzania
| | - Mohammed Mkuya
- Eastern and Southern Africa Region, International Rice Research Institute, Nairobi, Kenya
| | - Rosemary Murori
- Africa Regional Office, International Rice Research Institute, Nairobi, Kenya
| | | | - Sebastien Cunnac
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Bing Yang
- Division of Plant Science and Technology, University of Missouri, Columbia, United States
| | - Boris Szurek
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [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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Tekete C, Cunnac S, Doucouré H, Dembele M, Keita I, Sarra S, Dagno K, Koita O, Verdier V. Characterization of New Races of Xanthomonas oryzae pv. oryzae in Mali Informs Resistance Gene Deployment. Phytopathology 2020; 110:267-277. [PMID: 31464159 DOI: 10.1094/phyto-02-19-0070-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae represents a severe threat to rice cultivation in Mali. Characterizing the pathotypic diversity of bacterial populations is key to the management of pathogen-resistant varieties. Forty-one X. oryzae pv. oryzae isolates were collected between 2010 and 2013 in the major rice growing regions in Mali. All isolates were virulent on the susceptible rice variety Azucena; evaluation of the isolates on 12 near isogenic rice lines, each carrying a single resistance gene, identified six new races (A4 to A9) and confirmed race A3 that was previously reported in Mali. Races A5 and A6, isolated in Office du Niger and Sélingué, were the most prevalent races in Mali. Race A9 was the most virulent, circumventing all of the resistance genes tested. Xa3 controlled six of seven races (i.e., 89% of the isolates tested). The expansion of race A9 represents a major risk to rice cultivation and highlights the urgent need to identify a local source of resistance. We selected 14 isolates of X. oryzae pv. oryzae representative of the most prevalent races to evaluate 29 rice varieties grown by farmers in Mali. Six isolates showed a high level of resistance to X. oryzae pv. oryzae and were then screened with a larger collection of isolates. Based on the interactions among the six varieties and the X. oryzae pv. oryzae isolates, we characterized eight different pathotypes (P1 to P8). Two rice varieties, SK20-28 and Gigante, effectively controlled all of the isolates tested. The low association observed among races and pathotypes of X. oryzae pv. oryzae suggests that the resistance observed in the local rice varieties does not simply rely on single known Xa genes. X. oryzae pv. oryzae is pathogenically and geographically diverse. Both the races of X. oryzae pv. oryzae characterized in this study and the identification of sources of resistance in local rice varieties provide useful information to inform the design of effective breeding programs for resistance to bacterial leaf blight in Mali.
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Affiliation(s)
- C Tekete
- Applied Molecular Biology Laboratory, Faculty of Science and Technology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - S Cunnac
- IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - H Doucouré
- Applied Molecular Biology Laboratory, Faculty of Science and Technology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - M Dembele
- Institute of Rural Economy, Regional Center for Agronomic Research, Niono and Bamako, Mali
| | - I Keita
- Applied Molecular Biology Laboratory, Faculty of Science and Technology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - S Sarra
- Institute of Rural Economy, Regional Center for Agronomic Research, Niono and Bamako, Mali
| | - K Dagno
- Institute of Rural Economy, Regional Center for Agronomic Research, Niono and Bamako, Mali
| | - O Koita
- Applied Molecular Biology Laboratory, Faculty of Science and Technology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - V Verdier
- IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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. Front Plant Sci 2017; 8:645. [PMID: 28507553 PMCID: PMC5410622 DOI: 10.3389/fpls.2017.00645] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thébault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 2002; 415:497-502. [PMID: 11823852 DOI: 10.1038/415497a] [Citation(s) in RCA: 608] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors.
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Affiliation(s)
- M Salanoubat
- Genoscope and CNRS UMR-8030, 2 rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
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