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Cardoso-Sichieri R, Oliveira LS, Lopes-Caitar VS, Silva DCGD, Lopes IDON, Oliveira MFD, Arias CA, Abdelnoor RV, Marcelino-Guimarães FC. Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused by Xanthomonas citri pv. glycines in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:2484. [PMID: 39273969 PMCID: PMC11397087 DOI: 10.3390/plants13172484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024]
Abstract
Bacterial pustule (BP), caused by Xanthomonas citri pv. glycines, is an important disease that, under favorable conditions, can drastically affect soybean production. We performed a genome-wide association study (GWAS) with a panel containing Brazilian and American cultivars, which were screened qualitatively and quantitatively against two Brazilian X. citri isolates (IBS 333 and IBS 327). The panel was genotyped using a genotyping by sequencing (GBS) approach, and we identified two main new regions in soybeans associated with X. citri resistance on chromosomes 6 (IBS 333) and 18 (IBS 327), different from the traditional rxp gene located on chromosome 17. The region on chromosome 6 was also detected by QTL mapping using a biparental cross between Williams 82 (R) and PI 416937 (S), showing that Williams 82 has another recessive resistance gene besides rxp, which was also detected in nine BP-resistant ancestors of the Brazilian cultivars (including CNS, S-100), based on haplotype analysis. Furthermore, we identified additional SNPs in strong LD (0.8) with peak SNPs by exploring variation available in WGS (whole genome sequencing) data among 31 soybean accessions. In these regions in strong LD, two candidate resistance genes were identified (Glyma.06g311000 and Glyma.18g025100) for chromosomes 6 and 18, respectively. Therefore, our results allowed the identification of new chromosomal regions in soybeans associated with BP disease, which could be useful for marker-assisted selection and will enable a reduction in time and cost for the development of resistant cultivars.
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Affiliation(s)
- Rafaella Cardoso-Sichieri
- Center for Biological Sciences, Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina 86057-970, PR, Brazil
| | - Liliane Santana Oliveira
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Alberto Carazzai Avenue, 1640, Cornélio Procópio 86300-000, PR, Brazil
| | | | | | - Ivani de O N Lopes
- Brazilian Agricultural Research Corporation (Embrapa Soja), Carlos João Strass Road, Warta County 86085-981, PR, Brazil
| | - Marcelo Fernandes de Oliveira
- Brazilian Agricultural Research Corporation (Embrapa Soja), Carlos João Strass Road, Warta County 86085-981, PR, Brazil
| | - Carlos Arrabal Arias
- Brazilian Agricultural Research Corporation (Embrapa Soja), Carlos João Strass Road, Warta County 86085-981, PR, Brazil
| | - Ricardo Vilela Abdelnoor
- Brazilian Agricultural Research Corporation (Embrapa Soja), Carlos João Strass Road, Warta County 86085-981, PR, Brazil
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Calia G, Cestaro A, Schuler H, Janik K, Donati C, Moser M, Bottini S. Definition of the effector landscape across 13 phytoplasma proteomes with LEAPH and EffectorComb. NAR Genom Bioinform 2024; 6:lqae087. [PMID: 39081684 PMCID: PMC11287381 DOI: 10.1093/nargab/lqae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
'Candidatus Phytoplasma' genus, a group of fastidious phloem-restricted bacteria, can infect a wide variety of both ornamental and agro-economically important plants. Phytoplasmas secrete effector proteins responsible for the symptoms associated with the disease. Identifying and characterizing these proteins is of prime importance for expanding our knowledge of the molecular bases of the disease. We faced the challenge of identifying phytoplasma's effectors by developing LEAPH, a machine learning ensemble predictor composed of four models. LEAPH was trained on 479 proteins from 53 phytoplasma species, described by 30 features. LEAPH achieved 97.49% accuracy, 95.26% precision and 98.37% recall, ensuring a low false-positive rate and outperforming available state-of-the-art methods. The application of LEAPH to 13 phytoplasma proteomes yields a comprehensive landscape of 2089 putative pathogenicity proteins. We identified three classes according to different secretion models: 'classical', 'classical-like' and 'non-classical'. Importantly, LEAPH identified 15 out of 17 known experimentally validated effectors belonging to the three classes. Furthermore, to help the selection of novel candidates for biological validation, we applied the Self-Organizing Maps algorithm and developed a Shiny app called EffectorComb. LEAPH and the EffectorComb app can be used to boost the characterization of putative effectors at both computational and experimental levels, and can be employed in other phytopathological models.
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Affiliation(s)
- Giulia Calia
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, 39100 Bolzano, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- INRAE, Institut Sophia Agrobiotech, Université Côte d’Azur, CNRS, 06903 Sophia-Antipolis, France
| | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy
| | - Hannes Schuler
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, 39100 Bolzano, Italy
- Competence Centre for Plant Health, Free University of Bolzano, 39100 Bolzano, Italy
| | - Katrin Janik
- Institute for Plant Health, Molecular Biology and Microbiology, Laimburg Research Centre, 47141 Pfatten-Vadena, Italy
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
| | - Mirko Moser
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
| | - Silvia Bottini
- INRAE, Institut Sophia Agrobiotech, Université Côte d’Azur, CNRS, 06903 Sophia-Antipolis, France
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3
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Carpenter SCD, Bogdanove AJ, Abbot B, Stajich JE, Uehling JK, Lovett B, Kasson MT, Carter ME. Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp. Microb Genom 2024; 10:001261. [PMID: 38860878 PMCID: PMC11261895 DOI: 10.1099/mgen.0.001261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Endofungal Mycetohabitans (formerly Burkholderia) spp. rely on a type III secretion system to deliver mostly unidentified effector proteins when colonizing their host fungus, Rhizopus microsporus. The one known secreted effector family from Mycetohabitans consists of homologues of transcription activator-like (TAL) effectors, which are used by plant pathogenic Xanthomonas and Ralstonia spp. to activate host genes that promote disease. These 'Burkholderia TAL-like (Btl)' proteins bind corresponding specific DNA sequences in a predictable manner, but their genomic target(s) and impact on transcription in the fungus are unknown. Recent phenotyping of Btl mutants of two Mycetohabitans strains revealed that the single Btl in one Mycetohabitans endofungorum strain enhances fungal membrane stress tolerance, while others in a Mycetohabitans rhizoxinica strain promote bacterial colonization of the fungus. The phenotypic diversity underscores the need to assess the sequence diversity and, given that sequence diversity translates to DNA targeting specificity, the functional diversity of Btl proteins. Using a dual approach to maximize capture of Btl protein sequences for our analysis, we sequenced and assembled nine Mycetohabitans spp. genomes using long-read PacBio technology and also mined available short-read Illumina fungal-bacterial metagenomes. We show that btl genes are present across diverse Mycetohabitans strains from Mucoromycota fungal hosts yet vary in sequences and predicted DNA binding specificity. Phylogenetic analysis revealed distinct clades of Btl proteins and suggested that Mycetohabitans might contain more species than previously recognized. Within our data set, Btl proteins were more conserved across M. rhizoxinica strains than across M. endofungorum, but there was also evidence of greater overall strain diversity within the latter clade. Overall, the results suggest that Btl proteins contribute to bacterial-fungal symbioses in myriad ways.
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Affiliation(s)
- Sara C. D. Carpenter
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
| | - Adam J. Bogdanove
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
| | - Bhuwan Abbot
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Jessie K. Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARS, Ithaca, NY 14850, USA
| | - Matt T. Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Morgan E. Carter
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- CIPHER Center, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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4
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Ramprasad E, Rani CVD, Neeraja CN, Padmavathi G, Jagadeeshwar R, Anjali C, Thakur P, Yamini KN, Laha GS, Prasad MS, Alhelaify SS, Aharthy OM, Sayed SM, Mushtaq M. Understanding the nature of blast resistance in combined bacterial leaf blight and blast gene pyramided lines of rice variety tellahamsa. Mol Biol Rep 2024; 51:619. [PMID: 38709339 DOI: 10.1007/s11033-024-09549-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Rice blast and bacterial leaf blight (BLB) are the most limiting factors for rice production in the world which cause yield losses typically ranging from 20 to 30% and can be as high as 50% in some areas of Asia especially India under severe infection conditions. METHODS AND RESULTS An improved line of Tellahamsa, TH-625-491 having two BLB resistance genes (xa13 and Xa21) and two blast resistance genes (Pi54 and Pi1) with 95% Tellahamsa genome was used in the present study. TH-625-491 was validated for all four target genes and was used for backcrossing with Tellahamsa. Seventeen IBC1F1 plants heterozygous for all four target genes, 19 IBC1F2 plants homozygous for four, three and two gene combinations and 19 IBC1F2:3 plants also homozygous for four, three and two gene combinations were observed. Among seventeen IBC1F1 plants, IBC1F1-62 plant recorded highest recurrent parent genome (97.5%) covering 75 polymorphic markers. Out of the total of 920 IBC1F2 plants screened, 19 homozygous plants were homozygous for four, three and two target genes along with bacterial blight resistance. Background analysis was done in all 19 homozygous IBC1F2 plants possessing BLB resistance (possessing xa13, Xa21, Pi54 and Pi1 in different combinations) with five parental polymorphic SSR markers. IBC1F2-62-515 recovered 98.5% recurrent parent genome. The four, three and two gene pyramided lines of Tellahamsa exhibited varying resistance to blast. CONCLUSIONS Results show that there might be presence of antagonistic effect between bacterial blight and blast resistance genes since the lines with Pi54 and Pi1 combination are showing better resistance than the combinations with both bacterial blight and blast resistance genes.
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Affiliation(s)
- E Ramprasad
- Institute of Biotechnology, Professor Jayashanker Telangana State Agriculture University, Hyderabad, 500030, India
| | - Ch V Durga Rani
- Institute of Biotechnology, Professor Jayashanker Telangana State Agriculture University, Hyderabad, 500030, India.
| | - C N Neeraja
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - G Padmavathi
- Department of Genetics and Plant Breeding, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - R Jagadeeshwar
- Institute of Biotechnology, Professor Jayashanker Telangana State Agriculture University, Hyderabad, 500030, India
| | - C Anjali
- Plant Biotechnology Department, Mallareddy University, Hyderabad, 500100, India
| | - Priya Thakur
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh, 173229, India
| | - K N Yamini
- Institute of Biotechnology, Professor Jayashanker Telangana State Agriculture University, Hyderabad, 500030, India
| | - G S Laha
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - M Srinivas Prasad
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Seham Sater Alhelaify
- Department of Biotechnology, Faculty of Science, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
| | - Ohud Muslat Aharthy
- Department of Biotechnology, Faculty of Science, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
| | - Samy M Sayed
- Department of Science and Technology, University College-Ranyah, Taif University, B.O. Box 11099, 21944, Taif, Saudi Arabia
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh, 173229, India.
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5
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Diallo A, Wonni I, Sicard A, Blondin L, Gagnevin L, Vernière C, Szurek B, Hutin M. Genetic Structure and TALome Analysis Highlight a High Level of Diversity in Burkinabe Xanthomonas Oryzae pv. oryzae Populations. RICE (NEW YORK, N.Y.) 2023; 16:33. [PMID: 37523017 PMCID: PMC10390441 DOI: 10.1186/s12284-023-00648-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Bacterial Leaf Blight of rice (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat for food security in many rice growing countries including Burkina Faso, where the disease was first reported in the 1980's. In line with the intensification of rice cultivation in West-Africa, BLB incidence has been rising for the last 15 years. West-African strains of Xoo differ from their Asian counterparts as they (i) are genetically distant, (ii) belong to new races and, (iii) contain reduced repertoires of Transcription Activator Like (TAL) effector genes. In order to investigate the evolutionary dynamics of Xoo populations in Burkina Faso, 177 strains were collected from 2003 to 2018 in three regions where BLB is occurring. Multilocus VNTR Analysis (MLVA-14) targeting 10 polymorphic loci discriminated 24 haplotypes and showed that Xoo populations were structured according to their geographical localization and year of collection. Considering their major role in Xoo pathogenicity, we assessed the TAL effector repertoires of the 177 strains upon RFLP-based profiling. Surprisingly, an important diversity was revealed with up to eight different RFLP patterns. Finally, comparing neutral vs. tal effector gene diversity allowed to suggest scenarios underlying the evolutionary dynamics of Xoo populations in Burkina Faso, which is key to rationally guide the deployment of durably resistant rice varieties against BLB in the country.
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Affiliation(s)
- A Diallo
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - I Wonni
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso.
| | - A Sicard
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Blondin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Gagnevin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - C Vernière
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - B Szurek
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - M Hutin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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6
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Mondal KK, Kulshreshtha A, Handique PJ, Borbora D, Rajrana Y, Verma G, Bhattacharya A, Qamar A, Lakshmi A, Reddy K, Soni M, Ghoshal T, Rashmi ER, Mrutyunjaya S, Kalaivanan NS, Mani C. Rice transcriptome upon infection with Xanthomonas oryzae pv. oryzae relative to its avirulent T3SS-defective strain exposed modulation of many stress responsive genes. 3 Biotech 2022; 12:130. [PMID: 35607392 DOI: 10.1007/s13205-022-03193-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/28/2022] [Indexed: 11/01/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a destructive pathogen that causes bacterial blight disease of rice worldwide. Xoo uses T3SS (type III secretion system) effectors to subvert rice innate immunity. However, the comprehensive knowledge of rice genes involved in T3SS effectors-mediated interaction remains unclear. In this study, the transcriptome profiles of rice infected with a virulent Xoo strain from North-eastern region of India relatives to its avirulent strain (that lacks functional T3SS) were analyzed at early (2-6 hpi) and late (16-24 hpi) hours of infection. Out of total 255 differentially expressed genes (DEGs), during early infection, 62 and 70 genes were upregulated and downregulated, respectively. At late infection, 70 and 53 genes were upregulated and downregulated, respectively. The transcriptomic data identified many differentially expressed resistant genes, transposons, transcription factors, serine/threonine protein kinase, cytochrome P450 and peroxidase genes that are involved in plant defense. Pathway analysis revealed that these DEGs are involved in hormone signaling, plant defense, cellular metabolism, growth and development processes. DEGs associated with plant defense were also validated through quantitative real-time PCR. Our study brings a comprehensive picture of the rice genes that are being differentially expressed during bacterial blight infection. Nevertheless, the DEG-associated pathways would provide sensible targets for developing resistance to bacterial blight. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03193-4.
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Affiliation(s)
- Kalyan K Mondal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Aditya Kulshreshtha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | | | - Yuvika Rajrana
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Geeta Verma
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Aarzoo Qamar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Amrutha Lakshmi
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - KishoreKumar Reddy
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Madhvi Soni
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Thungri Ghoshal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - E R Rashmi
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.,Department of Biotechnology, Gauhati University, Assam, India
| | - S Mrutyunjaya
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - N S Kalaivanan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Chander Mani
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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7
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Hu Z, Tang Z, Zhang Y, Niu L, Yang F, Zhang D, Hu Y. Rice SUT and SWEET Transporters. Int J Mol Sci 2021; 22:11198. [PMID: 34681858 PMCID: PMC8540626 DOI: 10.3390/ijms222011198] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/17/2022] Open
Abstract
Sugar transporters play important or even indispensable roles in sugar translocation among adjacent cells in the plant. They are mainly composed of sucrose-proton symporter SUT family members and SWEET family members. In rice, 5 and 21 members are identified in these transporter families, and some of their physiological functions have been characterized on the basis of gene knockout or knockdown strategies. Existing evidence shows that most SUT members play indispensable roles, while many SWEET members are seemingly not so critical in plant growth and development regarding whether their mutants display an aberrant phenotype or not. Generally, the expressions of SUT and SWEET genes focus on the leaf, stem, and grain that represent the source, transport, and sink organs where carbohydrate production, allocation, and storage take place. Rice SUT and SWEET also play roles in both biotic and abiotic stress responses in addition to plant growth and development. At present, these sugar transporter gene regulation mechanisms are largely unclear. In this review, we compare the expressional profiles of these sugar transporter genes on the basis of chip data and elaborate their research advances. Some suggestions concerning future investigation are also proposed.
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Affiliation(s)
- Zhi Hu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.T.)
| | - Zhenjia Tang
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.T.)
| | - Yanming Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (L.N.); (F.Y.)
| | - Liping Niu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (L.N.); (F.Y.)
| | - Fang Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (L.N.); (F.Y.)
| | - Dechun Zhang
- Bio-Technology Research Center, China Three Gorges University, Yichang 443002, China
| | - Yibing Hu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.T.)
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8
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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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9
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Schreiber KJ, Chau-Ly IJ, Lewis JD. What the Wild Things Do: Mechanisms of Plant Host Manipulation by Bacterial Type III-Secreted Effector Proteins. Microorganisms 2021; 9:1029. [PMID: 34064647 PMCID: PMC8150971 DOI: 10.3390/microorganisms9051029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 01/05/2023] Open
Abstract
Phytopathogenic bacteria possess an arsenal of effector proteins that enable them to subvert host recognition and manipulate the host to promote pathogen fitness. The type III secretion system (T3SS) delivers type III-secreted effector proteins (T3SEs) from bacterial pathogens such as Pseudomonas syringae, Ralstonia solanacearum, and various Xanthomonas species. These T3SEs interact with and modify a range of intracellular host targets to alter their activity and thereby attenuate host immune signaling. Pathogens have evolved T3SEs with diverse biochemical activities, which can be difficult to predict in the absence of structural data. Interestingly, several T3SEs are activated following injection into the host cell. Here, we review T3SEs with documented enzymatic activities, as well as T3SEs that facilitate virulence-promoting processes either indirectly or through non-enzymatic mechanisms. We discuss the mechanisms by which T3SEs are activated in the cell, as well as how T3SEs modify host targets to promote virulence or trigger immunity. These mechanisms may suggest common enzymatic activities and convergent targets that could be manipulated to protect crop plants from infection.
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Affiliation(s)
- Karl J. Schreiber
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
| | - Ilea J. Chau-Ly
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
| | - Jennifer D. Lewis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
- Plant Gene Expression Center, United States Department of Agriculture, University of California, Berkeley, CA 94710, USA
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10
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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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11
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Msami JA, Kawaguchi Y, Ichitani K, Taura S. Linkage analysis of rice bacterial blight resistance gene xa20 in XM6, a mutant line from IR24. BREEDING SCIENCE 2021; 71:144-154. [PMID: 34377062 PMCID: PMC8329881 DOI: 10.1270/jsbbs.20104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/06/2020] [Indexed: 06/13/2023]
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is an important disease constraining rice (Oryza sativa L.) production worldwide. The XM6 line was induced by N-methyl-N-nitrosourea from IR24, an Indica cultivar that is susceptible to Philippine and Japanese Xoo races. XM6 was confirmed to carry a recessive gene named xa20, resistant to six Philippine and five Japanese Xoo races. The chromosomal gene location was found using 10 plants with the shortest lesion length in an F2 population consisting of 298 plants from a susceptible Japonica variety Koshihikari × XM6. Analysis using PCR-based DNA markers covering the whole rice genome indicated the gene as located on the distal region of the long arm of chromosome 3. The IKC3 line carries IR24 genetic background with Koshihikari fragment on chromosome 3 where a resistance gene was thought to be located. The F2 population from IKC3 × XM6 clearly showed a bimodal distribution separating resistant and susceptible plants. Further linkage analysis conducted using this F2 population revealed that xa20 is located within the 0.8 cM region flanked by DNA markers KIC3-33.88 (33.0 Mb) and KIC3-34.06 (33.2 Mb). This study yields important findings for resistance breeding and for the genetic mechanism of Xoo resistance.
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Affiliation(s)
- Jessey Anderson Msami
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yoshiki Kawaguchi
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Katsuyuki Ichitani
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Satoru Taura
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Division of Gene Research, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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12
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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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13
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Teper D, Wang N. Consequences of adaptation of TAL effectors on host susceptibility to Xanthomonas. PLoS Genet 2021; 17:e1009310. [PMID: 33465093 PMCID: PMC7845958 DOI: 10.1371/journal.pgen.1009310] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/29/2021] [Accepted: 12/11/2020] [Indexed: 12/03/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are virulence factors of Xanthomonas that induce the expression of host susceptibility (S) genes by specifically binding to effector binding elements (EBEs) in their promoter regions. The DNA binding specificity of TALEs is dictated by their tandem repeat regions, which are highly variable between different TALEs. Mutation of the EBEs of S genes is being utilized as a key strategy to generate resistant crops against TALE-dependent pathogens. However, TALE adaptations through rearrangement of their repeat regions is a potential obstacle for successful implementation of this strategy. We investigated the consequences of TALE adaptations in the citrus pathogen Xanthomonas citri subsp. citri (Xcc), in which PthA4 is the TALE required for pathogenicity, whereas CsLOB1 is the corresponding susceptibility gene, on host resistance. Seven TALEs, containing two-to-nine mismatching-repeats to the EBEPthA4 that were unable to induce CsLOB1 expression, were introduced into Xcc pthA4:Tn5 and adaptation was simulated by repeated inoculations into and isolations from sweet orange for a duration of 30 cycles. While initially all strains failed to promote disease, symptoms started to appear between 9–28 passages in four TALEs, which originally harbored two-to-five mismatches. Sequence analysis of adapted TALEs identified deletions and mutations within the TALE repeat regions which enhanced putative affinity to the CsLOB1 promoter. Sequence analyses suggest that TALEs adaptations result from recombinations between repeats of the TALEs. Reintroduction of these adapted TALEs into Xcc pthA4:Tn5 restored the ability to induce the expression of CsLOB1, promote disease symptoms and colonize host plants. TALEs harboring seven-to-nine mismatches were unable to adapt to overcome the incompatible interaction. Our study experimentally documented TALE adaptations to incompatible EBE and provided strategic guidance for generation of disease resistant crops against TALE-dependent pathogens. Mutation of the EBEs of susceptibility (S) genes via genome editing and utilization of naturally occurring EBE variants have been used to generate disease resistant plants. However, TALE adaptations may lead to resistance loss, limiting the long-term efficacy of the strategy. We utilized an experimental evolution approach to test TALEs adaptations in the Xanthomonas citri-citrus pathosystem using designer TALEs that cannot recognize the EBE of host targets. We identified adaptive TALE mutations and deletions that occurred during less than 30 cycles of repeated infections, which reconstituted the virulence on the host. Adaptive variants originated from TALEs that harbored a small number of mismatches (≤5) to the EBE, whereas designer TALEs that harbored larger number of mismatches (≥7) to the EBE failed to adapt in the duration of this study. Our study experimentally demonstrates adaptive rearrangements of TALEs during host adaptation and suggests that the potential durability in the resistance of modified crops should be a significant factor to be considered prior to their introduction into the field.
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Affiliation(s)
- Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
- * E-mail:
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14
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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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15
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Carpenter SCD, Mishra P, Ghoshal C, Dash PK, Wang L, Midha S, Laha GS, Lore JS, Kositratana W, Singh NK, Singh K, Patil PB, Oliva R, Patarapuwadol S, Bogdanove AJ, Rai R. An xa5 Resistance Gene-Breaking Indian Strain of the Rice Bacterial Blight Pathogen Xanthomonas oryzae pv. oryzae Is Nearly Identical to a Thai Strain. Front Microbiol 2020; 11:579504. [PMID: 33193207 PMCID: PMC7610140 DOI: 10.3389/fmicb.2020.579504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) constrains production in major rice growing countries of Asia. Xoo injects transcription activator-like effectors (TALEs) that bind to and activate host “susceptibility” (S) genes that are important for disease. The bacterial blight resistance gene xa5, which reduces TALE activity generally, has been widely deployed. However, strains defeating xa5 have been reported in India and recently also in Thailand. We completely sequenced and compared the genomes of one such strain from each country and examined the encoded TALEs. The two genomes are nearly identical, including the TALE genes, and belong to a previously identified, highly clonal lineage. Each strain harbors a TALE known to activate the major S gene SWEET11 strongly enough to be effective even when diminished by xa5. The findings suggest international migration of the xa5-compatible pathotype and highlight the utility of whole genome sequencing and TALE analysis for understanding and responding to breakdown of resistance.
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Affiliation(s)
- Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Prashant Mishra
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Chandrika Ghoshal
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Prasanta K Dash
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Gouri S Laha
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Jagjeet S Lore
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | - Wichai Kositratana
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Nagendra K Singh
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Rhitu Rai
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
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16
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An SQ, Potnis N, Dow M, Vorhölter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol Rev 2020; 44:1-32. [PMID: 31578554 PMCID: PMC8042644 DOI: 10.1093/femsre/fuz024] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/29/2019] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.
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Affiliation(s)
- Shi-Qi An
- National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA
| | - Max Dow
- School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland
| | | | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Yi Li
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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17
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Teper D, Xu J, Li J, Wang N. The immunity of Meiwa kumquat against Xanthomonas citri is associated with a known susceptibility gene induced by a transcription activator-like effector. PLoS Pathog 2020; 16:e1008886. [PMID: 32931525 PMCID: PMC7518600 DOI: 10.1371/journal.ppat.1008886] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/25/2020] [Accepted: 08/14/2020] [Indexed: 12/22/2022] Open
Abstract
Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) is one of the most devastating diseases in citrus. Meiwa kumquat (Fortunella crassifolia) has shown a durable resistance against Xcc. Here, we aimed to characterize the mechanisms responsible for such a durable resistance by characterizing the transcriptional and physiological responses of Meiwa kumquat to Xcc. Inoculation of Meiwa kumquat with Xcc promoted immune responses such as upregulation of PR genes, accumulation of salicylic acid, hypersensitive response (HR)-like cell death and early leaf abscission. Hypertrophy and hyperplasia symptoms, which are known to be caused by Xcc-induction of the canker susceptibility gene LOB1 through the transcription activator-like effector (TALE) PthA4, always appear prior to the development of cell death. Mutation of pthA4 in Xcc abolished the induction of LOB1, canker symptoms, cell death, and leaf abscission and reduced the expression of PR genes in inoculated kumquat leaves without reducing Xcc titers in planta. Transcriptome analysis demonstrated that PthA4 promotes plant biotic and abiotic stress responses and the biosynthesis of abscisic acid. Transcriptional induction of LOB1 homologs in Meiwa kumquat by Xcc pthA4 mutant strains carrying a repertoire of designer TALEs promoted the elicitation of HR-like phenotype and leaf abscission, suggesting that kumquat response to Xcc is associated with upregulation of LOB1. Our study suggests a novel mechanism of plant resistance to Xanthomonas via elicitation of immune responses by upregulation of a host susceptibility gene.
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Affiliation(s)
- Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, United States of America
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, United States of America
| | - Jinyun Li
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, United States of America
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, United States of America
- * E-mail:
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18
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A TAL effector-like protein of an endofungal bacterium increases the stress tolerance and alters the transcriptome of the host. Proc Natl Acad Sci U S A 2020; 117:17122-17129. [PMID: 32632014 PMCID: PMC7382252 DOI: 10.1073/pnas.2003857117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Endosymbiotic bacteria are found in diverse fungi, but little is known about how they communicate with their hosts. Some plant pathogenic bacteria use type III-translocated TAL effectors to control host transcription, and TAL-like proteins are encoded in genomes of the fungal endosymbiotic bacterium Mycetohabitans rhizoxinica. In this paper, we present evidence that these proteins are, like TAL effectors, type III-secreted, nuclear-localizing effectors that perturb host transcription and show that one enhances tolerance of the fungal host to cell membrane stress. Our characterization of an effector in a bacterial–fungal symbiosis opens a new door to molecular understanding of these interkingdom partnerships. Our findings also provide insight into the functional diversity and evolution of the TAL effector protein family. Symbioses of bacteria with fungi have only recently been described and are poorly understood. In the symbiosis of Mycetohabitans (formerly Burkholderia) rhizoxinica with the fungus Rhizopus microsporus, bacterial type III (T3) secretion is known to be essential. Proteins resembling T3-secreted transcription activator-like (TAL) effectors of plant pathogenic bacteria are encoded in the three sequenced Mycetohabitans spp. genomes. TAL effectors nuclear-localize in plants, where they bind and activate genes important in disease. The Burkholderia TAL-like (Btl) proteins bind DNA but lack the N- and C-terminal regions, in which TAL effectors harbor their T3 and nuclear localization signals, and activation domain. We characterized a Btl protein, Btl19-13, and found that, despite the structural differences, it can be T3-secreted and can nuclear-localize. A btl19-13 gene knockout did not prevent the bacterium from infecting the fungus, but the fungus became less tolerant to cell membrane stress. Btl19-13 did not alter transcription in a plant-based reporter assay, but 15 R. microsporus genes were differentially expressed in comparisons both of the fungus infected with the wild-type bacterium vs. the mutant and with the mutant vs. a complemented strain. Southern blotting revealed btl genes in 14 diverse Mycetohabitans isolates. However, banding patterns and available sequences suggest variation, and the btl19-13 phenotype could not be rescued by a btl gene from a different strain. Our findings support the conclusion that Btl proteins are effectors that act on host DNA and play important but varied or possibly host genotype-specific roles in the M. rhizoxinica–R. microsporus symbiosis.
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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: 149] [Impact Index Per Article: 37.3] [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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Read AC, Moscou MJ, Zimin AV, Pertea G, Meyer RS, Purugganan MD, Leach JE, Triplett LR, Salzberg SL, Bogdanove AJ. Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing. PLoS Genet 2020; 16:e1008571. [PMID: 31986137 PMCID: PMC7004385 DOI: 10.1371/journal.pgen.1008571] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 02/06/2020] [Accepted: 12/16/2019] [Indexed: 12/26/2022] Open
Abstract
Long-read sequencing facilitates assembly of complex genomic regions. In plants, loci containing nucleotide-binding, leucine-rich repeat (NLR) disease resistance genes are an important example of such regions. NLR genes constitute one of the largest gene families in plants and are often clustered, evolving via duplication, contraction, and transposition. We recently mapped the Xo1 locus for resistance to bacterial blight and bacterial leaf streak, found in the American heirloom rice variety Carolina Gold Select, to a region that in the Nipponbare reference genome is NLR gene-rich. Here, toward identification of the Xo1 gene, we combined Nanopore and Illumina reads and generated a high-quality Carolina Gold Select genome assembly. We identified 529 complete or partial NLR genes and discovered, relative to Nipponbare, an expansion of NLR genes at the Xo1 locus. One of these has high sequence similarity to the cloned, functionally similar Xa1 gene. Both harbor an integrated zfBED domain, and the repeats within each protein are nearly perfect. Across diverse Oryzeae, we identified two sub-clades of NLR genes with these features, varying in the presence of the zfBED domain and the number of repeats. The Carolina Gold Select genome assembly also uncovered at the Xo1 locus a rice blast resistance gene and a gene encoding a polyphenol oxidase (PPO). PPO activity has been used as a marker for blast resistance at the locus in some varieties; however, the Carolina Gold Select sequence revealed a loss-of-function mutation in the PPO gene that breaks this association. Our results demonstrate that whole genome sequencing combining Nanopore and Illumina reads effectively resolves NLR gene loci. Our identification of an Xo1 candidate is an important step toward mechanistic characterization, including the role(s) of the zfBED domain. Finally, the Carolina Gold Select genome assembly will facilitate identification of other useful traits in this historically important variety. Plants lack adaptive immunity, and instead contain repeat-rich, disease resistance genes that evolve rapidly through duplication, recombination, and transposition. The number, variation, and often clustered arrangement of these genes make them challenging to sequence and catalog. The US heirloom rice variety Carolina Gold Select has resistance to two important bacterial diseases. Toward identifying the responsible gene(s), we combined long- and short-read sequencing technologies to assemble the whole genome and identify the resistance gene repertoire. We previously narrowed the location of the gene(s) to a region on chromosome four. The region in Carolina Gold Select is larger than in the rice reference genome (Nipponbare) and contains twice as many resistance genes. One shares unusual features with a known bacterial disease resistance gene, suggesting that it confers the resistance. Across diverse varieties and related species, we identified two widely-distributed groups of such genes. The results are an important step toward mechanistic characterization and deployment of the bacterial disease resistance. The genome assembly also identified a resistance gene for a fungal disease and predicted a marker phenotype used in breeding for resistance. Thus, the Carolina Gold Select genome assembly can be expected to aid in the identification and deployment of other valuable traits.
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Affiliation(s)
- Andrew C. Read
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
| | - Matthew J. Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
| | - Aleksey V. Zimin
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Geo Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Rachel S. Meyer
- Center for Genomics and Systems Biology, New York University, New York, NY, United States of America
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY, United States of America
- Center for Genomics and Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Lindsay R. Triplett
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Steven L. Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States of America
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, United States of America
| | - Adam J. Bogdanove
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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Salonia F, Ciacciulli A, Poles L, Pappalardo HD, La Malfa S, Licciardello C. New Plant Breeding Techniques in Citrus for the Improvement of Important Agronomic Traits. A Review. FRONTIERS IN PLANT SCIENCE 2020; 11:1234. [PMID: 32922420 PMCID: PMC7456868 DOI: 10.3389/fpls.2020.01234] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/28/2020] [Indexed: 05/18/2023]
Abstract
New plant breeding techniques (NPBTs) aim to overcome traditional breeding limits for fruit tree species, in order to obtain new varieties with improved organoleptic traits and resistance to biotic and abiotic stress, and to maintain fruit quality achieved over centuries by (clonal) selection. Knowledge on the gene(s) controlling a specific trait is essential for the use of NPBTs, such as genome editing and cisgenesis. In the framework of the international scientific community working on fruit tree species, including citrus, NPBTs have mainly been applied to address pathogen threats. Citrus could take advantage of NPBTs because of its complex species biology (seedlessness, apomixis, high heterozygosity, and long juvenility phase) and aptitude for in vitro manipulation. To our knowledge, genome editing in citrus via transgenesis has successful for induced resistance to Citrus bacterial canker in sweet orange and grapefruit using the resistance gene CsLOB1. In the future, NPBTs will also be used to improve fruit traits, making them healthier. The regeneration of plants following the application of NPBTs is a bottleneck, making it necessary to optimize the efficiency of current protocols. The strengths and weaknesses of using explants from young in vitro plantlets, and from mature plants, will be discussed. Other major issues addressed in this review are related to the requirement for marker-free systems and shortening the long juvenility phase. This review aims to summarize methods and approaches available in the literature that are suitable to citrus, focusing on the principles observed before the use of NPBTs.
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Affiliation(s)
- Fabrizio Salonia
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Angelo Ciacciulli
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Lara Poles
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | | | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
- *Correspondence: Stefano La Malfa, ; Concetta Licciardello,
| | - Concetta Licciardello
- CREA - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- *Correspondence: Stefano La Malfa, ; Concetta Licciardello,
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Zafar K, Khan MZ, Amin I, Mukhtar Z, Yasmin S, Arif M, Ejaz K, Mansoor S. Precise CRISPR-Cas9 Mediated Genome Editing in Super Basmati Rice for Resistance Against Bacterial Blight by Targeting the Major Susceptibility Gene. FRONTIERS IN PLANT SCIENCE 2020; 11:575. [PMID: 32595655 PMCID: PMC7304078 DOI: 10.3389/fpls.2020.00575] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/17/2020] [Indexed: 05/12/2023]
Abstract
Basmati rice is famous around the world for its flavor, aroma, and long grain. Its demand is increasing worldwide, especially in Asia. However, its production is threatened by various problems faced in the fields, resulting in major crop losses. One of the major problems is bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo). Xoo hijacks the host machinery by activating the susceptibility genes (OsSWEET family genes), using its endogenous transcription activator like effectors (TALEs). TALEs have effector binding elements (EBEs) in the promoter region of the OsSWEET genes. Out of six well-known TALEs found to have EBEs in Clade III SWEET genes, four are present in OsSWEET14 gene's promoter region. Thus, targeting the promoter of OsSWEET14 is very important for creating broad-spectrum resistance. To engineer resistance against bacterial blight, we established CRISPR-Cas9 mediated genome editing in Super Basmati rice by targeting 4 EBEs present in the promoter of OsSWEET14. We were able to obtain four different Super Basmati lines (SB-E1, SB-E2, SB-E3, and SB-E4) having edited EBEs of three TALEs (AvrXa7, PthXo3, and TalF). The edited lines were then evaluated in triplicate for resistance against bacterial blight by choosing one of the locally isolated virulent Xoo strains with AvrXa7 and infecting Super Basmati. The lines with deletions in EBE of AvrXa7 showed resistance against the Xoo strain. Thus, it was confirmed that edited EBEs provide resistance against their respective TALEs present in Xoo strains. In this study up to 9% editing efficiency was obtained. Our findings showed that CRISPR-Cas9 can be harnessed to generate resistance against bacterial blight in indigenous varieties, against locally prevalent Xoo strains.
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Affiliation(s)
- Kashaf Zafar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
- Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Muhammad Zuhaib Khan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Sumera Yasmin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Arif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Khansa Ejaz
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
- *Correspondence: Shahid Mansoor,
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Carpenter SCD, Kladsuwan L, Han SW, Prathuangwong S, Bogdanove AJ. Complete Genome Sequences of Xanthomonas axonopodis pv. glycines Isolates from the United States and Thailand Reveal Conserved Transcription Activator-Like Effectors. Genome Biol Evol 2019; 11:1380-1384. [PMID: 31028379 PMCID: PMC6505444 DOI: 10.1093/gbe/evz085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2019] [Indexed: 12/20/2022] Open
Abstract
To compare overall genome structure and transcription activator-like effector content, we completely sequenced Xanthomonas axonopodis pv. glycines strain 12-2, isolated in 1992 in Thailand, and strain EB08, isolated in 2008 in the United States (Iowa) using PacBio technology. We reassembled the genome sequence for a second US strain, 8ra, derived from a 1980 Iowa isolate, from existing PacBio reads. Despite geographic and temporal separation, the three genomes are highly syntenous, and their transcription activator-like effector repertoires are highly conserved.
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Affiliation(s)
- Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University
| | - Lawan Kladsuwan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Sang-Wook Han
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Sutruedee Prathuangwong
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University
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24
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Kim YA, Moon H, Park CJ. CRISPR/Cas9-targeted mutagenesis of Os8N3 in rice to confer resistance to Xanthomonas oryzae pv. oryzae. RICE (NEW YORK, N.Y.) 2019; 12:67. [PMID: 31446506 PMCID: PMC6708514 DOI: 10.1186/s12284-019-0325-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/13/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Genome editing tools are important for functional genomics research and biotechnology applications. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9) system for gene knockout has emerged as the most effective genome-editing tool. It has previously been reported that, in rice plants, knockdown of the Os8N3 gene resulted in enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo), while displaying abnormal pollen development. RESULTS The CRISPR/Cas9 system was employed to knockout rice Os8N3, in order to confer enhanced resistance to Xoo. Analysis of the genotypes and edited Os8N3 in T0, T1, T2, and T3 transgenic rice plants showed that the mutations were transmitted to subsequent generations, and homozygous mutants displayed significantly enhanced resistance to Xoo. Stable transmission of CRISPR/Cas9-mediated Os8N3 gene editing without the transferred DNA (T-DNA) was confirmed by segregation in the T1 generation. With respect to many investigated agronomic traits including pollen development, there was no significant difference between homozygous mutants and non-transgenic control plants under greenhouse growth conditions. CONCLUSION Data from this study indicate that the CRISPR/Cas9-mediated Os8N3 edition can be successfully employed for non-transgenic crop improvements.
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Affiliation(s)
- Young-Ah Kim
- Department of Plant Biotechnology, Sejong University, Seoul, 05006 South Korea
| | - Hyeran Moon
- Department of Molecular Biology, Sejong University, Seoul, 05006 South Korea
| | - Chang-Jin Park
- Department of Plant Biotechnology, Sejong University, Seoul, 05006 South Korea
- Department of Molecular Biology, Sejong University, Seoul, 05006 South Korea
- Plant Engineering Research Institute, Sejong University, Seoul, 05006 South Korea
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25
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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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Gautam T, Saripalli G, Gahlaut V, Kumar A, Sharma PK, Balyan HS, Gupta PK. Further studies on sugar transporter (SWEET) genes in wheat (Triticum aestivum L.). Mol Biol Rep 2019; 46:2327-2353. [PMID: 30830588 DOI: 10.1007/s11033-019-04691-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/08/2019] [Indexed: 12/20/2022]
Abstract
SWEET proteins represent one of the largest sugar transporter family in the plant kingdom and play crucial roles in plant development and stress responses. In the present study, a total of 108 TaSWEET genes distributed on all the 21 wheat chromosomes were identified using the latest whole genome sequence (as against 59 genes reported in an earlier report). These 108 genes included 14 of the 17 types reported in Arabidopsis and also included three novel types. Tandem duplications (22) and segmental duplications (5) played a significant role in the expansion of TaSWEET family. A number of cis-elements were also identified in the promoter regions of TaSWEET genes, indicating response of TaSWEET genes during development and also during biotic/abiotic stresses. The TaSWEET proteins carried 4-7 trans-membrane helices (TMHs) showing diversity in structure. Phylogenetic analysis using SWEET proteins of wheat and 8 other species gave four well-known clusters. Expression analysis involving both in silico and in planta indicated relatively higher expression of TaSWEET genes in water/heat sensitive and leaf rust resistant genotypes. The results provided insights into the functional role of TaSWEETs in biotic and abiotic stresses, which may further help in planning strategies to develop high yielding wheat varieties tolerant to environmental stresses.
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Affiliation(s)
- Tinku Gautam
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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Carpenter SCD, Mishra P, Ghoshal C, Dash PK, Wang L, Midha S, Laha GS, Lore JS, Kositratana W, Singh NK, Singh K, Patil PB, Oliva R, Patarapuwadol S, Bogdanove AJ, Rai R. A Strain of an Emerging Indian Xanthomonas oryzae pv. oryzae Pathotype Defeats the Rice Bacterial Blight Resistance Gene xa13 Without Inducing a Clade III SWEET Gene and Is Nearly Identical to a Recent Thai Isolate. Front Microbiol 2018; 9:2703. [PMID: 30483230 PMCID: PMC6243107 DOI: 10.3389/fmicb.2018.02703] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/23/2018] [Indexed: 01/03/2023] Open
Abstract
The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription activator-like effectors (TALEs) that bind and activate host "susceptibility" (S) genes important for disease. Clade III SWEET genes are major S genes for bacterial blight. The resistance genes xa5, which reduces TALE activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been effectively deployed. However, strains that defeat both resistance genes individually were recently reported in India and Thailand. To gain insight into the mechanism(s), we completely sequenced the genome of one such strain from each country and examined the encoded TALEs. Strikingly, the two strains are clones, sharing nearly identical TALE repertoires, including a TALE known to activate SWEET11 strongly enough to be effective even when diminished by xa5. We next investigated SWEET gene induction by the Indian strain. The Indian strain induced no clade III SWEET in plants harboring xa13, indicating a pathogen adaptation that relieves dependence on these genes for susceptibility. The findings open a door to mechanistic understanding of the role SWEET genes play in susceptibility and illustrate the importance of complete genome sequence-based monitoring of Xoo populations in developing varieties with effective disease resistance.
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Affiliation(s)
- Sara C. D. Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Prashant Mishra
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Chandrika Ghoshal
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Prasanta K. Dash
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, Institute of Microbial Technology (CSIR), Chandigarh, India
| | - Gouri S. Laha
- Department of Plant Pathology, Indian Institute of Rice Research (ICAR), Hyderabad, India
| | - Jagjeet S. Lore
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | - Wichai Kositratana
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Nagendra K. Singh
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Kuldeep Singh
- National Bureau of Plant Genetic Resources (ICAR), New Delhi, India
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, Institute of Microbial Technology (CSIR), Chandigarh, India
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Adam J. Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Rhitu Rai
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
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Ma W, Zou L, Zhiyuan JI, Xiameng XU, Zhengyin XU, Yang Y, Alfano JR, Chen G. Xanthomonas oryzae pv. oryzae TALE proteins recruit OsTFIIAγ1 to compensate for the absence of OsTFIIAγ5 in bacterial blight in rice. MOLECULAR PLANT PATHOLOGY 2018; 19:2248-2262. [PMID: 29704467 PMCID: PMC6638009 DOI: 10.1111/mpp.12696] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 05/12/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight (BB) of rice, uses transcription activator-like effectors (TALEs) to interact with the basal transcription factor gamma subunit OsTFIIAγ5 (Xa5) and activates the transcription of host genes. However, how OsTFIIAγ1, the other OsTFIIAγ protein, functions in the presence of TALEs remains unclear. In this study, we show that OsTFIIAγ1 plays a compensatory role in the absence of Xa5. The expression of OsTFIIAγ1, which is activated by TALE PthXo7, increases the expression of host genes targeted by avirulent and virulent TALEs. Defective OsTFIIAγ1 rice lines show reduced expression of the TALE-targeted susceptibility (S) genes, OsSWEET11 and OsSWEET14, which results in increased BB resistance. Selected TALEs (PthXo1, AvrXa7 and AvrXa27) were evaluated for interactions with OsTFIIAγ1, Xa5 and xa5 (naturally occurring mutant form of Xa5) using biomolecular fluorescence complementation (BiFC) and microscale thermophoresis (MST). BiFC and MST demonstrated that the three TALEs bind Xa5 and OsTFIIAγ1 with a stronger affinity than xa5. These results provide insights into the complex roles of OsTFIIAγ1 and OsTFIIAγ5 in TALE-mediated host gene transcription.
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Affiliation(s)
- Wenxiu Ma
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Lifang Zou
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - JI Zhiyuan
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
- Present address:
Present address: National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop ScienceChinese Academy of Agriculture Sciences (CAAS)Beijing 100081China
| | - XU Xiameng
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - XU Zhengyin
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Yangyang Yang
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - James R. Alfano
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- The Center for Plant Science Innovation, University of NebraskaLincolnNE68588‐0660USA
| | - Gongyou Chen
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
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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: 28] [Impact Index Per Article: 4.7] [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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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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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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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: 52] [Impact Index Per Article: 8.7] [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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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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Schandry N, Jacobs JM, Szurek B, Perez‐Quintero AL. A cautionary TALE: how plant breeding may have favoured expanded TALE repertoires in Xanthomonas. MOLECULAR PLANT PATHOLOGY 2018; 19:1297-1301. [PMID: 29723447 PMCID: PMC6638153 DOI: 10.1111/mpp.12670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 05/19/2023]
Affiliation(s)
- Niklas Schandry
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)Vienna 1030Austria
| | - Jonathan M. Jacobs
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCO 80523USA
- Applied Microbiology ‐ PhytopathologyEarth and Life Institute, Université Catholique de LouvainLouvain‐la‐Neuve, 1348Belgium
| | - Boris Szurek
- IRD, Cirad, University of Montpellier, IPMEMontpellier 34000France
| | - Alvaro L. Perez‐Quintero
- IRD, Cirad, University of Montpellier, IPMEMontpellier 34000France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research UniversityParis 75005France
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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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Büttner D. Behind the lines-actions of bacterial type III effector proteins in plant cells. FEMS Microbiol Rev 2018; 40:894-937. [PMID: 28201715 PMCID: PMC5091034 DOI: 10.1093/femsre/fuw026] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/31/2016] [Accepted: 07/03/2016] [Indexed: 01/30/2023] Open
Abstract
Pathogenicity of most Gram-negative plant-pathogenic bacteria depends on the type III secretion (T3S) system, which translocates bacterial effector proteins into plant cells. Type III effectors modulate plant cellular pathways to the benefit of the pathogen and promote bacterial multiplication. One major virulence function of type III effectors is the suppression of plant innate immunity, which is triggered upon recognition of pathogen-derived molecular patterns by plant receptor proteins. Type III effectors also interfere with additional plant cellular processes including proteasome-dependent protein degradation, phytohormone signaling, the formation of the cytoskeleton, vesicle transport and gene expression. This review summarizes our current knowledge on the molecular functions of type III effector proteins with known plant target molecules. Furthermore, plant defense strategies for the detection of effector protein activities or effector-triggered alterations in plant targets are discussed.
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Affiliation(s)
- Daniela Büttner
- Genetics Department, Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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Jeger M, Candresse T, Chatzivassiliou E, Dehnen-Schmutz K, Gilioli G, Grégoire JC, Jaques Miret JA, MacLeod A, Navajas Navarro M, Niere B, Parnell S, Potting R, Rafoss T, Rossi V, Urek G, Van Bruggen A, Van der Werf W, West J, Winter S, Bragard C, Szurek B, Hollo G, Caffier D. Pest categorisation of Xanthomonas oryzae pathovars oryzae and oryzicola. EFSA J 2018; 16:e05109. [PMID: 32625664 PMCID: PMC7009692 DOI: 10.2903/j.efsa.2018.5109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The EFSA Panel on Plant Health performed a pest categorisation for Xanthomonas oryzae pathovars oryzae (Xoo) and oryzicola (Xoc), the causal agents of the bacterial blight and the bacterial leaf streak of rice, respectively. These pathovars are widely distributed in Asia, Africa and Australia. Xoo is also reported in some states of the USA and in some other countries of America. The identity of both pathovars is well established and efficient identification methods are available. The major host is cultivated rice (Oryza sativa), but different Oryza spp. as well as Poaceae weeds are reported as alternative hosts, with some uncertainty concerning the actual host range. Both pathovars are seed associated, despite the fact that seed transmission is still controversial for Xoo. Both pathovars are already regulated in Directives 2000/29/EC, on harmful organisms for plants, and 66/402/EEC, on the marketing of cereal seeds. The main pathway for entry is seed. Should these pathovars enter into EU, they may establish and spread, and they may have an impact on the rice crops, with uncertainties. The knowledge gaps identified are (1) the quantity of EU importation of rice seeds, (2) the risk of introduction through unprocessed rice for consumption, (3) the suitability of the EU growing climate conditions for the bacteria to establish and spread, (4) role of seed transmission (Xoo), (5) the role of weeds in the epidemiology and especially in seed transmission and dispersal, (6) host range of weeds. As none of the pathovars is known to occur in the EU, they do not meet one of the criteria for being considered as Union regulated non-quarantine pests. Nevertheless, both pathovars meet the criteria assessed by EFSA for consideration as Union quarantine pest.
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Cao J, Zhang M, Xiao J, Li X, Yuan M, Wang S. Dominant and Recessive Major R Genes Lead to Different Types of Host Cell Death During Resistance to Xanthomonas oryzae in Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:1711. [PMID: 30519255 PMCID: PMC6258818 DOI: 10.3389/fpls.2018.01711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/02/2018] [Indexed: 05/21/2023]
Abstract
The bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is the most devastating bacterial disease of rice worldwide. A number of dominant major disease resistance (MR) genes and recessive MR genes against Xoo have been cloned and molecularly characterized in the last two decades. However, how these MR genes mediated-resistances occur at the cytological level is largely unknown. Here, by ultrastructural examination of xylem parenchyma cells, we show that resistances to Xoo conferred by dominant MR genes and recessive MR genes resulted in different types of programmed cell death (PCD). Three dominant MR genes Xa1, Xa4, and Xa21 and two recessive MR genes xa5 and xa13 that encode very different proteins were used in this study. We observed that Xa1-, Xa4-, and Xa21-mediated resistances to Xoo were associated mainly with autophagy-like cell death featured by the formation of autophagosome-like bodies in the xylem parenchyma cells. In contrast, the xa5- and xa13-mediated resistances to Xoo were associated mainly with vacuolar-mediated cell death characterized by tonoplast disruption of the xylem parenchyma cells. Application of autophagy inhibitor 3-methyladenine partially compromised Xa1-, Xa4-, and Xa21-mediated resistances, as did Na2HPO4 alkaline solution to xa5- and xa13-mediated resistances. These results suggest that autophagy-like cell death is a feature of the dominant MR gene-mediated resistance to Xoo and vacuolar-mediated cell death is a characteristic of the recessive MR gene-mediated resistance.
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Affiliation(s)
- Jianbo Cao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Public Laboratory of Electron Microscopy, Huazhong Agricultural University, Wuhan, China
| | - Meng Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- *Correspondence: Shiping Wang,
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39
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Zhang J, Huguet ‐Tapia JC, Hu Y, Jones J, Wang N, Liu S, White FF. Homologues of CsLOB1 in citrus function as disease susceptibility genes in citrus canker. MOLECULAR PLANT PATHOLOGY 2017; 18:798-810. [PMID: 27276658 PMCID: PMC6638217 DOI: 10.1111/mpp.12441] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 05/01/2016] [Accepted: 06/05/2016] [Indexed: 05/06/2023]
Abstract
The lateral organ boundary domain (LBD) genes encode a group of plant-specific proteins that function as transcription factors in the regulation of plant growth and development. Citrus sinensis lateral organ boundary 1 (CsLOB1) is a member of the LBD family and functions as a disease susceptibility gene in citrus bacterial canker (CBC). Thirty-four LBD members have been identified from the Citrus sinensis genome. We assessed the potential for additional members of LBD genes in citrus to function as surrogates for CsLOB1 in CBC, and compared host gene expression on induction of different LBD genes. Using custom-designed transcription activator-like (TAL) effectors, two members of the same clade as CsLOB1, named CsLOB2 and CsLOB3, were found to be capable of functioning similarly to CsLOB1 in CBC. RNA sequencing and quantitative reverse transcription-polymerase chain reaction analyses revealed a set of cell wall metabolic genes that are associated with CsLOB1, CsLOB2 and CsLOB3 expression and may represent downstream genes involved in CBC.
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Affiliation(s)
- Junli Zhang
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA 32611
| | | | - Yang Hu
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA 32611
- Present address:
Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina 100101
| | - Jeffrey Jones
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA 32611
| | - Nian Wang
- Citrus Research and Education Center/Department of Microbiology and Cell ScienceUniversity of FloridaLake AlfredFLUSA 33850
| | - Sanzhen Liu
- Department of Plant PathologyKansas State UniversityManhattanKSUSA 66506
| | - Frank F. White
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA 32611
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40
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Cox KL, Meng F, Wilkins KE, Li F, Wang P, Booher NJ, Carpenter SCD, Chen LQ, Zheng H, Gao X, Zheng Y, Fei Z, Yu JZ, Isakeit T, Wheeler T, Frommer WB, He P, Bogdanove AJ, Shan L. TAL effector driven induction of a SWEET gene confers susceptibility to bacterial blight of cotton. Nat Commun 2017; 8:15588. [PMID: 28537271 PMCID: PMC5458083 DOI: 10.1038/ncomms15588] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 04/11/2017] [Indexed: 12/22/2022] Open
Abstract
Transcription activator-like (TAL) effectors from Xanthomonas citri subsp. malvacearum (Xcm) are essential for bacterial blight of cotton (BBC). Here, by combining transcriptome profiling with TAL effector-binding element (EBE) prediction, we show that GhSWEET10, encoding a functional sucrose transporter, is induced by Avrb6, a TAL effector determining Xcm pathogenicity. Activation of GhSWEET10 by designer TAL effectors (dTALEs) restores virulence of Xcm avrb6 deletion strains, whereas silencing of GhSWEET10 compromises cotton susceptibility to infections. A BBC-resistant line carrying an unknown recessive b6 gene bears the same EBE as the susceptible line, but Avrb6-mediated induction of GhSWEET10 is reduced, suggesting a unique mechanism underlying b6-mediated resistance. We show via an extensive survey of GhSWEET transcriptional responsiveness to different Xcm field isolates that additional GhSWEETs may also be involved in BBC. These findings advance our understanding of the disease and resistance in cotton and may facilitate the development cotton with improved resistance to BBC. Transcription activator-like effectors contribute to virulence of the Xanthomonas strain responsible for bacterial blight in cotton. Here Cox et al. show that the Xanthomonas Avrb6 effector induces expression of the cotton SWEET10 sugar transporter and that this induction promotes disease.
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Affiliation(s)
- Kevin L Cox
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
| | - Fanhong Meng
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
| | - Katherine E Wilkins
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Fangjun Li
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
| | - Ping Wang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Li-Qing Chen
- Department of Plant Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Hui Zheng
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Xiquan Gao
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - John Z Yu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, Texas 77845, USA
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
| | - Terry Wheeler
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Texas Agricultural Experiment Station, Lubbock, Texas 79403, USA
| | - Wolf B Frommer
- Carnegie Science, Department of Plant Biology, 260 Panama Street, Stanford, California 94305, USA
| | - Ping He
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Libo Shan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843, USA
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Blanvillain‐Baufumé S, Reschke M, Solé M, Auguy F, Doucoure H, Szurek B, Meynard D, Portefaix M, Cunnac S, Guiderdoni E, Boch J, Koebnik R. Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14-inducing TAL effectors. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:306-317. [PMID: 27539813 PMCID: PMC5316920 DOI: 10.1111/pbi.12613] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 05/04/2023]
Abstract
As a key virulence strategy to cause bacterial leaf blight, Xanthomonas oryzae pv. oryzae (Xoo) injects into the plant cell DNA-binding proteins called transcription activator-like effectors (TALEs) that bind to effector-binding elements (EBEs) in a sequence-specific manner, resulting in host gene induction. TALEs AvrXa7, PthXo3, TalC and Tal5, found in geographically distant Xoo strains, all target OsSWEET14, thus considered as a pivotal TALE target acting as major susceptibility factor during rice-Xoo interactions. Here, we report the generation of an allele library of the OsSWEET14 promoter through stable expression of TALE-nuclease (TALEN) constructs in rice. The susceptibility level of lines carrying mutations in AvrXa7, Tal5 or TalC EBEs was assessed. Plants edited in AvrXa7 or Tal5 EBEs were resistant to bacterial strains relying on the corresponding TALE. Surprisingly, although indels within TalC EBE prevented OsSWEET14 induction in response to BAI3 wild-type bacteria relying on TalC, loss of TalC responsiveness failed to confer resistance to this strain. The TalC EBE mutant line was, however, resistant to a strain expressing an artificial SWEET14-inducing TALE whose EBE was also edited in this line. This work offers the first set of alleles edited in TalC EBE and uncovers a distinct, broader range of activities for TalC compared to AvrXa7 or Tal5. We propose the existence of additional targets for TalC beyond SWEET14, suggesting that TALE-mediated plant susceptibility may result from induction of several, genetically redundant, host susceptibility genes by a single effector.
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Affiliation(s)
- Servane Blanvillain‐Baufumé
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
- Present address: LabEx CeMEBUniversité de MontpellierMontpellierFrance
| | - Maik Reschke
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Montserrat Solé
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Sustainable Agro Solutions S.A.Almacelles (Lleida)Spain
| | - Florence Auguy
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Hinda Doucoure
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Boris Szurek
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Donaldo Meynard
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Murielle Portefaix
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Sébastien Cunnac
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Emmanuel Guiderdoni
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Jens Boch
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Ralf Koebnik
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
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42
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Zuluaga P, Szurek B, Koebnik R, Kroj T, Morel JB. Effector Mimics and Integrated Decoys, the Never-Ending Arms Race between Rice and Xanthomonas oryzae. FRONTIERS IN PLANT SCIENCE 2017; 8:431. [PMID: 28400786 PMCID: PMC5368246 DOI: 10.3389/fpls.2017.00431] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 03/14/2017] [Indexed: 05/19/2023]
Abstract
Plants are constantly challenged by a wide range of pathogens and have therefore evolved an array of mechanisms to defend against them. In response to these defense systems, pathogens have evolved strategies to avoid recognition and suppress plant defenses (Brown and Tellier, 2011). Three recent reports dealing with the resistance of rice to Xanthomonas oryzae have added a new twist to our understanding of this fascinating co-evolutionary arms race (Ji et al., 2016; Read et al., 2016; Triplett et al., 2016). They show that pathogens also develop sophisticated effector mimics to trick recognition.
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Affiliation(s)
- Paola Zuluaga
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet,Montpellier, France
| | - Boris Szurek
- UMR – Interactions Plantes-Microorganismes-Environnement, IRD–Cirad–Université Montpellier, Institut de Recherche pour le Développement,Montpellier, France
| | - Ralf Koebnik
- UMR – Interactions Plantes-Microorganismes-Environnement, IRD–Cirad–Université Montpellier, Institut de Recherche pour le Développement,Montpellier, France
| | - Thomas Kroj
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet,Montpellier, France
| | - Jean-Benoit Morel
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet,Montpellier, France
- *Correspondence: Jean-Benoit Morel,
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43
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Cohn M, Morbitzer R, Lahaye T, Staskawicz BJ. Comparison of gene activation by two TAL effectors from Xanthomonas axonopodis pv. manihotis reveals candidate host susceptibility genes in cassava. MOLECULAR PLANT PATHOLOGY 2016; 17:875-89. [PMID: 26575863 PMCID: PMC6638523 DOI: 10.1111/mpp.12337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/23/2015] [Accepted: 10/13/2015] [Indexed: 05/10/2023]
Abstract
Xanthomonas axonopodis pv. manihotis (Xam) employs transcription activator-like (TAL) effectors to promote bacterial growth and symptom formation during infection of cassava. TAL effectors are secreted via the bacterial type III secretion system into plant cells, where they are directed to the nucleus, bind DNA in plant promoters and activate the expression of downstream genes. The DNA-binding activity of TAL effectors is carried out by a central domain which contains a series of repeat variable diresidues (RVDs) that dictate the sequence of bound nucleotides. TAL14Xam668 promotes virulence in Xam strain Xam668 and has been shown to activate multiple cassava genes. In this study, we used RNA sequencing to identify the full target repertoire of TAL14Xam668 in cassava, which includes over 50 genes. A subset of highly up-regulated genes was tested for activation by TAL14CIO151 from Xam strain CIO151. Although TAL14CIO151 and TAL14Xam668 differ by only a single RVD, they display differential activation of gene targets. TAL14CIO151 complements the TAL14Xam668 mutant defect, implying that shared target genes are important for TAL14Xam668 -mediated disease susceptibility. Complementation with closely related TAL effectors is a novel approach to the narrowing down of biologically relevant susceptibility genes of TAL effectors with multiple targets. This study provides an example of how TAL effector target activation by two strains within a single species of Xanthomonas can be dramatically affected by a small change in RVD-nucleotide affinity at a single site, and reflects the parameters of RVD-nucleotide interaction determined using designer TAL effectors in transient systems.
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Affiliation(s)
- Megan Cohn
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3120, USA
| | - Robert Morbitzer
- Department of General Genetics, Center of Plant Molecular Biology (ZMBP) University of Tübingen, D-72076, Tübingen, Germany
| | - Thomas Lahaye
- Department of General Genetics, Center of Plant Molecular Biology (ZMBP) University of Tübingen, D-72076, Tübingen, Germany
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3120, USA
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44
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Zhang J, Yin Z, White F. TAL effectors and the executor R genes. FRONTIERS IN PLANT SCIENCE 2015; 6:641. [PMID: 26347759 PMCID: PMC4542534 DOI: 10.3389/fpls.2015.00641] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/02/2015] [Indexed: 05/19/2023]
Abstract
Transcription activator-like (TAL) effectors are bacterial type III secretion proteins that function as transcription factors in plants during Xanthomonas/plant interactions, conditioning either host susceptibility and/or host resistance. Three types of TAL effector associated resistance (R) genes have been characterized-recessive, dominant non-transcriptional, and dominant TAL effector-dependent transcriptional based resistance. Here, we discuss the last type of R genes, whose functions are dependent on direct TAL effector binding to discrete effector binding elements in the promoters. Only five of the so-called executor R genes have been cloned, and commonalities are not clear. We have placed the protein products in two groups for conceptual purposes. Group 1 consists solely of the protein from pepper, BS3, which is predicted to have catalytic function on the basis of homology to a large conserved protein family. Group 2 consists of BS4C-R, XA27, XA10, and XA23, all of which are relatively short proteins from pepper or rice with multiple potential transmembrane domains. Group 2 members have low sequence similarity to proteins of unknown function in closely related species. Firm predictions await further experimentation on these interesting new members to the R gene repertoire, which have potential broad application in new strategies for disease resistance.
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Affiliation(s)
- Junli Zhang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
- *Correspondence: Junli Zhang, Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA,
| | - Zhongchao Yin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Frank White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
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Pérez-Quintero AL, Lamy L, Gordon JL, Escalon A, Cunnac S, Szurek B, Gagnevin L. QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically. FRONTIERS IN PLANT SCIENCE 2015; 6:545. [PMID: 26284082 PMCID: PMC4522561 DOI: 10.3389/fpls.2015.00545] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/06/2015] [Indexed: 05/20/2023]
Abstract
Transcription Activator-Like (TAL) effectors from Xanthomonas plant pathogenic bacteria can bind to the promoter region of plant genes and induce their expression. DNA-binding specificity is governed by a central domain made of nearly identical repeats, each determining the recognition of one base pair via two amino acid residues (a.k.a. Repeat Variable Di-residue, or RVD). Knowing how TAL effectors differ from each other within and between strains would be useful to infer functional and evolutionary relationships, but their repetitive nature precludes reliable use of traditional alignment methods. The suite QueTAL was therefore developed to offer tailored tools for comparison of TAL effector genes. The program DisTAL considers each repeat as a unit, transforms a TAL effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. The program FuncTAL is aimed at finding TAL effectors with similar DNA-binding capabilities. It calculates correlations between position weight matrices of potential target DNA sequence predicted from the RVD sequence, and builds trees based on these correlations. The programs accurately represented phylogenetic and functional relationships between TAL effectors using either simulated or literature-curated data. When using the programs on a large set of TAL effector sequences, the DisTAL tree largely reflected the expected species phylogeny. In contrast, FuncTAL showed that TAL effectors with similar binding capabilities can be found between phylogenetically distant taxa. This suite will help users to rapidly analyse any TAL effector genes of interest and compare them to other available TAL genes and should improve our understanding of TAL effectors evolution. It is available at http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi.
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Affiliation(s)
| | - Léo Lamy
- UMR IPME, IRD-CIRAD-Université MontpellierMontpellier, France
| | | | - Aline Escalon
- UMR PVBMT, CIRAD-Université de la RéunionSaint-Pierre, France
| | | | - Boris Szurek
- UMR IPME, IRD-CIRAD-Université MontpellierMontpellier, France
- *Correspondence: Boris Szurek and Lionel Gagnevin, UMR IPME, IRD-CIRAD-UM, 911, Av. Agropolis BP 64501, 34394 Montpellier, France ;
| | - Lionel Gagnevin
- UMR IPME, IRD-CIRAD-Université MontpellierMontpellier, France
- *Correspondence: Boris Szurek and Lionel Gagnevin, UMR IPME, IRD-CIRAD-UM, 911, Av. Agropolis BP 64501, 34394 Montpellier, France ;
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