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Kong L, Sun J, Zhang W, Zhan Z, Piao Z. Functional analysis of the key BrSWEET genes for sugar transport involved in the Brassica rapa-Plasmodiophora brassicae interaction. Gene 2024; 927:148708. [PMID: 38885818 DOI: 10.1016/j.gene.2024.148708] [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: 03/02/2024] [Revised: 06/02/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Plasmodiophora brassicae, the causative agent of clubroot disease, establishes a long-lasting parasitic relationship with its host by inducing the expression of sugar transporters. Previous studies have indicated that most BrSWEET genes in Chinese cabbage are up-regulated upon infection with P. brassicae. However, the key BrSWEET genes responsive to P. brassicae have not been definitively identified. In this study, we selected five BrSWEET genes and conducted a functional analysis of them. These five BrSWEET genes showed a notable up-regulation in roots after P. brassicae inoculation. Furthermore, these BrSWEET proteins were localized to the plasma membrane. Yeast functional complementation assays confirmed transport activity for glucose, fructose, or sucrose in four BrSWEETs, with the exception of BrSWEET2a. Mutants and silenced plants of BrSWEET1a, -11a, and -12a showed lower clubroot disease severity compared to wild-type plants, while gain-of-function Arabidopsis thaliana plants overexpressing these three BrSWEET genes exhibited significantly higher disease incidence and severity. Our findings suggested that BrSWEET1a, BrSWEET11a, and BrSWEET12a play pivotal roles in P. brassicae-induced gall formation, shedding light on the role of sugar transporters in host-pathogen interactions.
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Affiliation(s)
- Liyan Kong
- Molecular Biology of Vegetable Laboratory, Department of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
| | - Jiadi Sun
- Molecular Biology of Vegetable Laboratory, Department of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
| | - Wenjun Zhang
- Molecular Biology of Vegetable Laboratory, Department of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
| | - Zongxiang Zhan
- Molecular Biology of Vegetable Laboratory, Department of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
| | - Zhongyun Piao
- Molecular Biology of Vegetable Laboratory, Department of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
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2
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Liu L, Li Y, Wang Q, Xu X, Yan J, Wang Y, Wang Y, Shah SMA, Peng Y, Zhu Z, Xu Z, Chen G. Constructed Rice Tracers Identify the Major Virulent Transcription Activator-Like Effectors of the Bacterial Leaf Blight Pathogen. RICE (NEW YORK, N.Y.) 2024; 17:30. [PMID: 38656724 PMCID: PMC11043257 DOI: 10.1186/s12284-024-00704-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) injects major transcription activator-like effectors (TALEs) into plant cells to activate susceptibility (S) genes for promoting bacterial leaf blight in rice. Numerous resistance (R) genes have been used to construct differential cultivars of rice to identify races of Xoo, but the S genes were rarely considered. Different edited lines of rice cv. Kitaake were constructed using CRISPR/Cas9 gene-editing, including single, double and triple edits in the effector-binding elements (EBEs) located in the promoters of rice S genes OsSWEET11a, OsSWEET13 and OsSWEET14. The near-isogenic lines (NILs) were used as tracers to detect major TALEs (PthXo1, PthXo2, PthXo3 and their variants) in 50 Xoo strains. The pathotypes produced on the tracers determined six major TALE types in the 50 Xoo strains. The presence of the major TALEs in Xoo strains was consistent with the expression of S genes in the tracers, and it was also by known genome sequences. The EBE editing had little effect on agronomic traits, which was conducive to balancing yield and resistance. The rice-tracers generated here provide a valuable tool to track major TALEs of Xoo in Asia which then shows what rice cultivars are needed to combat Xoo in the field.
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Affiliation(s)
- Linlin Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying Li
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiameng Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiali Yan
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yijie Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Syed Mashab Ali Shah
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yongzheng Peng
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhangfei Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengyin Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Gongyou Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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3
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Xu Z, Xu X, Li Y, Liu L, Wang Q, Wang Y, Wang Y, Yan J, Cheng G, Zou L, Zhu B, Chen G. Tal6b/AvrXa27A, a hidden TALE targeting the susceptibility gene OsSWEET11a and the resistance gene Xa27 in rice. PLANT COMMUNICATIONS 2024; 5:100721. [PMID: 37735868 PMCID: PMC10873877 DOI: 10.1016/j.xplc.2023.100721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 07/12/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) secretes transcription activator-like effectors (TALEs) to activate rice susceptibility (S) genes, causing bacterial blight (BB), as well as resistance (R) genes, leading to defense against BB. This activation follows a gene-for-gene paradigm that results in an arms race between the TALE of the pathogen and effector-binding elements (EBEs) in the promoters of host genes. In this study, we characterized a novel TALE, designated Tal6b/AvrXa27A, that activates the rice S gene OsSWEET11a and the rice R gene Xa27. Tal6b/AvrXa27A is a member of the AvrXa27/TalAO class and contains 16 repeat variable diresidues (RVDs); one RVD is altered and one is deleted in Tal6b/AvrXa27A compared with AvrXa27, a known avirulence (avr) effector of Xa27. Tal6b/AvrXa27A can transcriptionally activate the expression of Xa27 and OsSWEET11a via EBEs in their corresponding promoters, leading to effector-triggered immunity and susceptibility, respectively. The 16 RVDs in Tal6b/AvrXa27A have no obvious similarity to the 24 RVDs in the effector PthXo1, but EBETal6b and EBEPthXo1 are overlapped in the OsSWEET11a promoter. Tal6b/AvrXa27A is prevalent among Asian Xoo isolates, but PthXo1 has only been reported in the Philippine strain PXO99A. Genome editing of EBETal6b in the OsSWEET11a promoter further confirmed the requirement for OsSWEET11a expression in Tal6b/AvrXa27A-dependent susceptibility to Xoo. Moreover, Tal6b/AvrXa27A resulted in higher transcription of Xa27 than of OsSWEET11a, which led to a strong, rapid resistance response that blocked disease development. These findings suggest that Tal6b/AvrXa27A has a dual function: triggering resistance by activating Xa27 gene expression as an avirulence factor and inducing transcription of the S gene OsSWEET11a, resulting in virulence. Intriguingly, Tal6b/AvrXa27A, but not AvrXa27, can bind to the promoter of OsSWEET11a. The underlying recognition mechanism for this binding remains unclear but appears to deviate from the currently accepted TALE code.
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Affiliation(s)
- Zhengyin Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiameng Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yijie Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiali Yan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guanyun Cheng
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lifang Zou
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Gongyou Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
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Tian D, Teo J, Yin Z. Ectopic Expression of the Executor-Type R Gene Paralog Xa27B in Rice Leads to Spontaneous Lesions and Enhanced Disease Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:143-154. [PMID: 38381127 DOI: 10.1094/mpmi-10-23-0153-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Plant disease resistance (R) gene-mediated effector-triggered immunity (ETI) is usually associated with hypersensitive response (HR) and provides robust and race-specific disease resistance against pathogenic infection. The activation of ETI and HR in plants is strictly regulated, and improper activation will lead to cell death. Xa27 is an executor-type R gene in rice induced by the TAL effector AvrXa27 and confers disease resistance to Xanthomonas oryzae pv. oryzae (Xoo). Here we reported the characterization of a transgenic line with lesion mimic phenotype, designated as Spotted leaf and resistance 1 (Slr1), which was derived from rice transformation with a genomic subclone located 5,125 bp downstream of the Xa27 gene. Slr1 develops spontaneous lesions on its leaves caused by cell death and confers disease resistance to both Xoo and Xanthomonas oryzae pv. oryzicola. Further investigation revealed that the Slr1 phenotype resulted from the ectopic expression of an Xa27 paralog gene, designated as Xa27B, in the inserted DNA fragment at the Slr1 locus driven by a truncated CaMV35Sx2 promoter in reverse orientation. Disease evaluation of IRBB27, IR24, and Xa27B mutants with Xoo strains expressing dTALE-Xa27B confirmed that Xa27B is a functional executor-type R gene. The functional XA27B-GFP protein was localized to the endoplasmic reticulum and apoplast. The identification of Xa27B as a new functional executor-type R gene provides additional genetic resources for studying the mechanism of executor-type R protein-mediated ETI and developing enhanced and broad-spectrum disease resistance to Xoo through promoter engineering. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Dongsheng Tian
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Joanne Teo
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Zhongchao Yin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
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Kalaivanan NS, Ghoshal T, Lakshmi MA, Mondal KK, Kulshreshtha A, Singh KBM, Thakur JK, Supriya P, Bhatnagar S, Mani C. Complete genome resource unravels the close relation of an Indian Xanthomonas oryzae pv. oryzae strain IXOBB0003 with Philippines strain causing bacterial blight of rice. 3 Biotech 2023; 13:187. [PMID: 37193328 PMCID: PMC10182915 DOI: 10.1007/s13205-023-03596-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/29/2023] [Indexed: 05/18/2023] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a pathogen of concern for rice growers as it limits the production potential of rice varieties worldwide. Due to their high genomic plasticity, the pathogen continues to evolve, nullifying the deployed resistance mechanisms. It is pertinent to monitor the evolving Xoo population for the virulent novel stains, and the affordable sequencing technologies made the task feasible with an in-depth understanding of their pathogenesis arsenals. We present the complete genome of a highly virulent Indian Xoo strain IXOBB0003, predominantly found in northwestern parts of India, by employing next-generation sequencing and single-molecule sequencing in real-time technologies. The final genome assembly comprises 4,962,427 bp and has 63.96% GC content. The pan genome analysis reveals that strain IXOBB0003 houses total of 3655 core genes, 1276 accessory genes and 595 unique genes. Comparative analysis of the predicted gene clusters of coding sequences and protein count of strain IXOBB0003 depicts 3687 of almost 90% gene clusters shared by other Asian strains, 17 unique to IXOBB0003 and 139 CDSs of IXOBB0003 are shared with PXO99A. AnnoTALE-based studies revealed 16 TALEs conferred from the whole genome sequence. Prominent TALEs of our strain are found orthologous to TALEs of the Philippines strain PXO99A. The genomic features of Indian Xoo strain IXOBB0003 and in comparison with other Asian strains would certainly contribute significantly while formulating novel strategies for BB management. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03596-x.
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Affiliation(s)
- N. S. Kalaivanan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Thungri Ghoshal
- Amity Institute of Biotechnology, Amity University, Noida, UP 201313 India
| | - M. Amrutha Lakshmi
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Kalyan K. Mondal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Kajol B. M. Singh
- National Institute of Plant Genome Research, New Delhi, 110067 India
| | - Jithendra K. Thakur
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| | - P. Supriya
- ICAR-National Academy of Agricultural Research Management, Hyderabad, 500030 India
| | - Seema Bhatnagar
- Amity Institute of Biotechnology, Amity University, Noida, UP 201313 India
| | - Chandra Mani
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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6
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Teper D, White FF, Wang N. The Dynamic Transcription Activator-Like Effector Family of Xanthomonas. PHYTOPATHOLOGY 2023; 113:651-666. [PMID: 36449529 DOI: 10.1094/phyto-10-22-0365-kd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transcription activator-like effectors (TALEs) are bacterial proteins that are injected into the eukaryotic nucleus to act as transcriptional factors and function as key virulence factors of the phytopathogen Xanthomonas. TALEs are translocated into plant host cells via the type III secretion system and induce the expression of host susceptibility (S) genes to facilitate disease. The unique modular DNA binding domains of TALEs comprise an array of nearly identical direct repeats that enable binding to DNA targets based on the recognition of a single nucleotide target per repeat. The very nature of TALE structure and function permits the proliferation of TALE genes and evolutionary adaptations in the host to counter TALE function, making the TALE-host interaction the most dynamic story in effector biology. The TALE genes appear to be a relatively young effector gene family, with a presence in all virulent members of some species and absent in others. Genome sequencing has revealed many TALE genes throughout the xanthomonads, and relatively few have been associated with a cognate S gene. Several species, including Xanthomonas oryzae pv. oryzae and X. citri pv. citri, have near absolute requirement for TALE gene function, while the genes appear to be just now entering the disease interactions with new fitness contributions to the pathogens of tomato and pepper among others. Deciphering the simple and effective DNA binding mechanism also has led to the development of DNA manipulation tools in fields of gene editing and transgenic research. In the three decades since their discovery, TALE research remains at the forefront of the study of bacterial evolution, plant-pathogen interactions, and synthetic biology. We also discuss critical questions that remain to be addressed regarding TALEs.
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Affiliation(s)
- Doron Teper
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Frank F White
- Department of Plant Pathology, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, U.S.A
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Tehrani N, Mitra RM. Plant pathogens and symbionts target the plant nucleus. Curr Opin Microbiol 2023; 72:102284. [PMID: 36868049 DOI: 10.1016/j.mib.2023.102284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 03/05/2023]
Abstract
In plant-microbe interactions, symbionts and pathogens live within plants and attempt to avoid triggering plant defense responses. In order to do so, these microbes have evolved multiple mechanisms that target components of the plant cell nucleus. Rhizobia-induced symbiotic signaling requires the function of specific legume nucleoporins within the nuclear pore complex. Symbiont and pathogen effectors harbor nuclear localization sequences that facilitate movement across nuclear pores, allowing these proteins to target transcription factors that function in defense. Oomycete pathogens introduce proteins that interact with plant pre-mRNA splicing components in order to alter host splicing of defense-related transcripts. Together, these functions indicate that the nucleus is an active site of symbiotic and pathogenic functioning in plant-microbe interactions.
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Effector-Dependent and -Independent Molecular Mechanisms of Soybean-Microbe Interaction. Int J Mol Sci 2022; 23:ijms232214184. [PMID: 36430663 PMCID: PMC9695568 DOI: 10.3390/ijms232214184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Soybean is a pivotal staple crop worldwide, supplying the main food and feed plant proteins in some countries. In addition to interacting with mutualistic microbes, soybean also needs to protect itself against pathogens. However, to grow inside plant tissues, plant defense mechanisms ranging from passive barriers to induced defense reactions have to be overcome. Pathogenic but also symbiotic micro-organisms effectors can be delivered into the host cell by secretion systems and can interfere with the immunity system and disrupt cellular processes. This review summarizes the latest advances in our understanding of the interaction between secreted effectors and soybean feedback mechanism and uncovers the conserved and special signaling pathway induced by pathogenic soybean cyst nematode, Pseudomonas, Xanthomonas as well as by symbiotic rhizobium.
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Doucouré H, Auguy F, Blanvillain-Baufumé S, Fabre S, Gabriel M, Thomas E, Dambreville F, Sciallano C, Szurek B, Koita O, Verdier V, Cunnac S. The Rice ILI2 Locus Is a Bidirectional Target of the African Xanthomonas oryzae pv. oryzae Major Transcription Activator-like Effector TalC but Does Not Contribute to Disease Susceptibility. Int J Mol Sci 2022; 23:ijms23105559. [PMID: 35628368 PMCID: PMC9142087 DOI: 10.3390/ijms23105559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/16/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription activator-like effectors (TALEs) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed effector binding elements (EBEs). Xoo major TALEs universally target susceptibility genes of the SWEET transporter family. TALE-unresponsive alleles of clade III OsSWEET susceptibility gene promoter created with genome editing confer broad resistance on Asian Xoo strains. African Xoo strains rely primarily on the major TALE TalC, which targets OsSWEET14. Although the virulence of a talC mutant strain is severely impaired, abrogating OsSWEET14 induction with genome editing does not confer equivalent resistance on African Xoo. To address this contradiction, we postulated the existence of a TalC target susceptibility gene redundant with OsSWEET14. Bioinformatics analysis identified a rice locus named ATAC composed of the INCREASED LEAF INCLINATION 2 (ILI2) gene and a putative lncRNA that are shown to be bidirectionally upregulated in a TalC-dependent fashion. Gain-of-function approaches with designer TALEs inducing ATAC sequences did not complement the virulence of a Xoo strain defective for SWEET gene activation. While editing the TalC EBE at the ATAC loci compromised TalC-mediated induction, multiplex edited lines with mutations at the OsSWEET14 and ATAC loci remained essentially susceptible to African Xoo strains. Overall, this work indicates that ATAC is a probable TalC off-target locus but nonetheless documents the first example of divergent transcription activation by a native TALE during infection.
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Affiliation(s)
- Hinda Doucouré
- LBMA, Faculté des Sciences et Techniques, University des Sciences Techniques et Technologiques, Bamako E 3206, Mali; (H.D.); (O.K.)
| | - Florence Auguy
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Servane Blanvillain-Baufumé
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Sandrine Fabre
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Marc Gabriel
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Emilie Thomas
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Fleur Dambreville
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Coline Sciallano
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Boris Szurek
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Ousmane Koita
- LBMA, Faculté des Sciences et Techniques, University des Sciences Techniques et Technologiques, Bamako E 3206, Mali; (H.D.); (O.K.)
| | - Valérie Verdier
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
| | - Sébastien Cunnac
- PHIM Plant Health Institute, University Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; (F.A.); (S.B.-B.); (S.F.); (M.G.); (E.T.); (F.D.); (C.S.); (B.S.); (V.V.)
- Correspondence:
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10
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Zhang B, Han X, Yuan W, Zhang H. TALEs as double-edged swords in plant-pathogen interactions: Progress, challenges, and perspectives. PLANT COMMUNICATIONS 2022; 3:100318. [PMID: 35576155 PMCID: PMC9251431 DOI: 10.1016/j.xplc.2022.100318] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/08/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Xanthomonas species colonize many host plants and cause huge losses worldwide. Transcription activator-like effectors (TALEs) are secreted by Xanthomonas and translocated into host cells to manipulate the expression of target genes, especially by Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, which cause bacterial blight and bacterial leaf streak, respectively, in rice. In this review, we summarize the progress of studies on the interaction between Xanthomonas and hosts, covering both rice and other plants. TALEs are not only key factors that make plants susceptible but are also essential components of plant resistance. Characterization of TALEs and TALE-like proteins has improved our understanding of TALE evolution and promoted the development of gene editing tools. In addition, the interactions between TALEs and hosts have also provided strategies and possibilities for genetic engineering in crop improvement.
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Affiliation(s)
- Biaoming Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaoyuan Han
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wenya Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Haitao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
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11
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Wu LB, Eom JS, Isoda R, Li C, Char SN, Luo D, Schepler-Luu V, Nakamura M, Yang B, Frommer WB. OsSWEET11b, a potential sixth leaf blight susceptibility gene involved in sugar transport-dependent male fertility. THE NEW PHYTOLOGIST 2022; 234:975-989. [PMID: 35211968 DOI: 10.1111/nph.18054] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
SWEETs play important roles in intercellular sugar transport. Induction of SWEET sugar transporters by Transcription Activator-Like effectors (TALe) of Xanthomonas ssp. is key for virulence in rice, cassava and cotton. We identified OsSWEET11b with roles in male fertility and potential bacterial blight (BB) susceptibility in rice. While single ossweet11a or 11b mutants were fertile, double mutants were sterile. As clade III SWEETs can transport gibberellin (GA), a key hormone for spikelet fertility, sterility and BB susceptibility might be explained by GA transport deficiencies. However, in contrast with the Arabidopsis homologues, OsSWEET11b did not mediate detectable GA transport. Fertility and susceptibility therefore are likely to depend on sucrose transport activity. Ectopic induction of OsSWEET11b by designer TALe enabled TALe-free Xanthomonas oryzae pv. oryzae (Xoo) to cause disease, identifying OsSWEET11b as a potential BB susceptibility gene and demonstrating that the induction of host sucrose uniporter activity is key to virulence of Xoo. Notably, only three of six clade III SWEETs are targeted by known Xoo strains from Asia and Africa. The identification of OsSWEET11b is relevant for fertility and for protecting rice against emerging Xoo strains that target OsSWEET11b.
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Affiliation(s)
- Lin-Bo Wu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding I, Justus-Liebig University Giessen, Giessen, 35392, Germany
| | - Joon-Seob Eom
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Reika Isoda
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Chenhao Li
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Si Nian Char
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Dangping Luo
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Van Schepler-Luu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Masayoshi Nakamura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Bing Yang
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
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12
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Chen X, Li Q, Wang J, Zhang Y, Tang L, Huang S, Mo J, Guo T. Genome Resource of a Hypervirulent Strain C9-3 of Xanthomonas oryzae pv. oryzae Causing Bacterial Blight of Rice. PLANT DISEASE 2022; 106:741-744. [PMID: 34598657 DOI: 10.1094/pdis-07-21-1565-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Xanthomonas oryzae pv. oryzae is the causal agent of bacterial blight, one of the most devastating diseases of rice. Here, a hypervirulent strain, C9-3, defeating Xa1, Xa10, xa13, and Xa23 resistance genes, was used to extract genomic DNA for single molecule real-time (SMRT) sequencing. After assembly, the genome consists of a single-circular chromosome with the size of 4,924,298 bp with G+C content of 63.7% and contains 4,715 genes. Annotation and analysis of the TALE genes using a suite of applications named AnnoTALE suggested that 17 transcription activator-like effectors, including 15 typical TALEs and 2 iTALEs/truncTALEs, were encoded in the genome. The approach and genome resource will contribute to the discovery of new virulence effectors and understanding on rice-X. oryzae pv. oryzae interactions.
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Affiliation(s)
- Xiaolin Chen
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Qili Li
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Jinkai Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Lihua Tang
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Suiping Huang
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Jianyou Mo
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Tangxun Guo
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
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13
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Ji J, Yang L, Fang Z, Zhang Y, Zhuang M, Lv H, Wang Y. Plant SWEET Family of Sugar Transporters: Structure, Evolution and Biological Functions. Biomolecules 2022; 12:biom12020205. [PMID: 35204707 PMCID: PMC8961523 DOI: 10.3390/biom12020205] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/20/2022] Open
Abstract
The SWEET (sugars will eventually be exported transporter) family was identified as a new class of sugar transporters that function as bidirectional uniporters/facilitators and facilitate the diffusion of sugars across cell membranes along a concentration gradient. SWEETs are found widely in plants and play central roles in many biochemical processes, including the phloem loading of sugar for long-distance transport, pollen nutrition, nectar secretion, seed filling, fruit development, plant–pathogen interactions and responses to abiotic stress. This review focuses on advances of the plant SWEETs, including details about their discovery, characteristics of protein structure, evolution and physiological functions. In addition, we discuss the applications of SWEET in plant breeding. This review provides more in-depth and comprehensive information to help elucidate the molecular basis of the function of SWEETs in plants.
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Affiliation(s)
- Jialei Ji
- Correspondence: ; Tel.: +86-10-82108756
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14
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Haq F, Xu X, Ma W, Shah SMA, Liu L, Zhu B, Zou L, Chen G. A Xanthomonas transcription activator-like effector is trapped in nonhost plants for immunity. PLANT COMMUNICATIONS 2022; 3:100249. [PMID: 35059629 PMCID: PMC8760140 DOI: 10.1016/j.xplc.2021.100249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/29/2021] [Accepted: 10/13/2021] [Indexed: 05/10/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight in rice, delivers transcription activator-like effector (TALE) proteins into host cells to activate susceptibility or resistance (R) genes that promote disease or immunity, respectively. Nonhost plants serve as potential reservoirs of R genes; consequently, nonhost R genes may trap TALEs to trigger an immune response. In this study, we screened 17 Xoo TALEs for their ability to induce a hypersensitive response (HR) in the nonhost plant Nicotiana benthamiana (Nb); only AvrXa10 elicited an HR when transiently expressed in Nb. The HR generated by AvrXa10 required both the central repeat region and the activation domain, suggesting a specific interaction between AvrXa10 and a potential R-like gene in nonhost plants. Evans blue staining and ion leakage measurements confirmed that the AvrXa10-triggered HR was a form of cell death, and the transient expression of AvrXa10 in Nb induced immune responses. Genes targeted by AvrXa10 in the Nb genome were identified by transcriptome profiling and prediction of effector binding sites. Using several approaches (in vivo reporter assays, electrophoretic mobility-shift assays, targeted designer TALEs, and on-spot gene silencing), we confirmed that AvrXa10 targets NbZnFP1, a C2H2-type zinc finger protein that resides in the nucleus. Functional analysis indicated that overexpression of NbZnFP1 and its rice orthologs triggered cell death in rice protoplasts. An NbZnFP1 ortholog was also identified in tomato and was specifically activated by AvrXa10. These results demonstrate that NbZnFP1 is a nonhost R gene that traps AvrXa10 to promote plant immunity in Nb.
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Affiliation(s)
- Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Wenxiu Ma
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Linlin Liu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Bo Zhu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
- Corresponding author
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15
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Becker S, Mücke S, Grau J, Boch J. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2387-2400. [PMID: 35150566 PMCID: PMC8887545 DOI: 10.1093/nar/gkac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are bacterial proteins with a programmable DNA-binding domain, which turned them into exceptional tools for biotechnology. TALEs contain a central array of consecutive 34 amino acid long repeats to bind DNA in a simple one-repeat-to-one-nucleotide manner. However, a few naturally occurring aberrant repeat variants break this strict binding mechanism, allowing for the recognition of an additional sequence with a −1 nucleotide frameshift. The limits and implications of this extended TALE binding mode are largely unexplored. Here, we analyse the complete diversity of natural and artificially engineered aberrant repeats for their impact on the DNA binding of TALEs. Surprisingly, TALEs with several aberrant repeats can loop out multiple repeats simultaneously without losing DNA-binding capacity. We also characterized members of the only natural TALE class harbouring two aberrant repeats and confirmed that their target is the major virulence factor OsSWEET13 from rice. In an aberrant TALE repeat, the position and nature of the amino acid sequence strongly influence its function. We explored the tolerance of TALE repeats towards alterations further and demonstrate that inserts as large as GFP can be tolerated without disrupting DNA binding. This illustrates the extraordinary DNA-binding capacity of TALEs and opens new uses in biotechnology.
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Affiliation(s)
- Sebastian Becker
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Stefanie Mücke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jens Boch
- To whom correspondence should be addressed. Tel: +49 511 762 4082; Fax: +49 511 762 4088;
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16
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Deb S, Madhavan VN, Gokulan CG, Patel HK, Sonti RV. Arms and ammunitions: effectors at the interface of rice and it's pathogens and pests. RICE (NEW YORK, N.Y.) 2021; 14:94. [PMID: 34792681 PMCID: PMC8602583 DOI: 10.1186/s12284-021-00534-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
The plant immune system has evolved to resist attack by pathogens and pests. However, successful phytopathogens deliver effector proteins into plant cells where they hijack the host cellular machinery to suppress the plant immune responses and promote infection. This manipulation of the host cellular pathways is done by the pathogen using various enzymatic activities, protein- DNA or protein- protein interactions. Rice is one the major economically important crops and its yield is affected by several pathogens and pests. In this review, we summarize the various effectors at the plant- pathogen/ pest interface for the major pathogens and pests of rice, specifically, on the mode of action and target genes of the effector proteins. We then compare this across the major rice pathogens and pests in a bid to understand probable conserved pathways which are under attack from pathogens and pests in rice. This analysis highlights conserved patterns of effector action, as well as unique host pathways targeted by the pathogens and pests.
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Affiliation(s)
- Sohini Deb
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007 India
- Present Address: Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | | | - C. G. Gokulan
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007 India
| | - Hitendra K. Patel
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007 India
| | - Ramesh V. Sonti
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007 India
- Present Address: Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507 India
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17
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Anjali A, Fatima U, Senthil-Kumar M. The ins and outs of SWEETs in plants: Current understanding of the basics and their prospects in crop improvement. J Biosci 2021. [DOI: 10.1007/s12038-021-00227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Pan-Genome Analysis of Effectors in Korean Strains of the Soybean Pathogen Xanthomonas citri pv. glycines. Microorganisms 2021; 9:microorganisms9102065. [PMID: 34683386 PMCID: PMC8538872 DOI: 10.3390/microorganisms9102065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Xanthomonas citri pv. glycines is a major pathogen of soybean in Korea. Here, we analyzed pathogenicity genes based on a comparative genome analysis of five Korean strains and one strain from the United States, 8ra. Whereas all six strains had nearly identical profiles of carbohydrate-active enzymes, they varied in diversity and number of candidate type III secretion system effector (T3SE) genes. The five Korean strains were similar in their effectors, but differed from the 8ra strain. Across the six strains, transcription activator-like effectors (TALEs) showed diverse repeat sizes and at least six forms of the repeat variable di-residue (RVD) sequences, with differences not correlated with the origin of the strains. However, a phylogenetic tree based on the alignment of RVD sequences showed two distinct clusters with 17.5 repeats, suggesting that two distinct 17.5 RVD clusters have evolved, potentially to adapt Xcg to growth on distinct soybean cultivars. The predicted effector binding elements of the TALEs fell into six groups and were strongly overlapping in sequence, suggesting evolving target specificity of the binding domains in soybean cultivars. Our findings reveal the variability and adaptability of T3SEs in the Xcg strains and enhance our understanding of Xcg pathogenicity in soybean.
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19
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Gupta PK, Balyan HS, Gautam T. SWEET genes and TAL effectors for disease resistance in plants: Present status and future prospects. MOLECULAR PLANT PATHOLOGY 2021; 22:1014-1026. [PMID: 34076324 PMCID: PMC8295518 DOI: 10.1111/mpp.13075] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/13/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
SWEET genes encode sugar transporter proteins and often function as susceptibility (S) genes. Consequently, the recessive alleles of these SWEET genes provide resistance. This review summarizes the available literature on the molecular basis of the role of SWEET genes (as S genes) in the host and corresponding transcription activator-like effectors (TALEs) secreted by the pathogen. The review has four major sections, which follow a brief introduction: The first part gives some details about the occurrence and evolution of SWEET genes in approximately 30 plant species; the second part gives some details about systems where (a) SWEET genes with and without TALEs and (b) TALEs without SWEET genes cause different diseases; the third part summarizes the available information about TALEs along with interfering/truncated TALEs secreted by the pathogens; this section also summarizes the available information on effector-binding elements (EBEs) available in the promoters of either the SWEET genes or the Executor R genes; the code that is used for binding of TALEs to EBEs is also described in this section; the fourth part gives some details about the available approaches that are being used or can be used in the future for exploiting SWEET genes for developing disease-resistant cultivars. The review concludes with a section giving conclusions and future possibilities of using SWEET genes for developing disease-resistant cultivars using different approaches, including conventional breeding and genome editing.
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Affiliation(s)
| | | | - Tinku Gautam
- Department of Genetics and Plant BreedingCCS UniversityMeerutIndia
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20
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Chen X, Liu P, Mei L, He X, Chen L, Liu H, Shen S, Ji Z, Zheng X, Zhang Y, Gao Z, Zeng D, Qian Q, Ma B. Xa7, a new executor R gene that confers durable and broad-spectrum resistance to bacterial blight disease in rice. PLANT COMMUNICATIONS 2021; 2:100143. [PMID: 34027390 PMCID: PMC8132130 DOI: 10.1016/j.xplc.2021.100143] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/02/2021] [Accepted: 01/07/2021] [Indexed: 05/03/2023]
Abstract
Bacterial blight (BB) is a globally devastating rice disease caused by Xanthomonas oryzae pv. oryzae (Xoo). The use of disease resistance (R) genes in rice breeding is an effective and economical strategy for the control of this disease. Nevertheless, a majority of R genes lack durable resistance for long-term use under global warming conditions. Here, we report the isolation of a novel executor R gene, Xa7, that confers extremely durable, broad-spectrum, and heat-tolerant resistance to Xoo. The expression of Xa7 was induced by incompatible Xoo strains that secreted the transcription activator-like effector (TALE) AvrXa7 or PthXo3, which recognized effector binding elements (EBEs) in the Xa7 promoter. Furthermore, Xa7 induction was faster and stronger under high temperatures. Overexpression of Xa7 or co-transformation of Xa7 with avrXa7 triggered a hypersensitive response in plants. Constitutive expression of Xa7 activated a defense response in the absence of Xoo but inhibited the growth of transgenic rice plants. In addition, analysis of over 3000 rice varieties showed that the Xa7 locus was found primarily in the indica and aus subgroups. A variation consisting of an 11-bp insertion and a base substitution (G to T) was found in EBEAvrXa7 in the tested varieties, resulting in a loss of Xa7 BB resistance. Through a decade of effort, we have identified an important BB resistance gene and characterized its distinctive interaction with Xoo strains; these findings will greatly facilitate research on the molecular mechanism of Xa7-mediated resistance and promote the use of this valuable gene in breeding.
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Affiliation(s)
- Xifeng Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Pengcheng Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Le Mei
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoling He
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Long Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Hui Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Shurong Shen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhandong Ji
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xixi Zheng
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yuchen Zhang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhenyu Gao
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Dali Zeng
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Qian Qian
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Bojun Ma
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Corresponding author
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21
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Luo D, Huguet-Tapia JC, Raborn RT, White FF, Brendel VP, Yang B. The Xa7 resistance gene guards the rice susceptibility gene SWEET14 against exploitation by the bacterial blight pathogen. PLANT COMMUNICATIONS 2021; 2:100164. [PMID: 34027391 PMCID: PMC8132128 DOI: 10.1016/j.xplc.2021.100164] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 05/03/2023]
Abstract
Many plant disease resistance (R) genes function specifically in reaction to the presence of cognate effectors from a pathogen. Xanthomonas oryzae pathovar oryzae (Xoo) uses transcription activator-like effectors (TALes) to target specific rice genes for expression, thereby promoting host susceptibility to bacterial blight. Here, we report the molecular characterization of Xa7, the cognate R gene to the TALes AvrXa7 and PthXo3, which target the rice major susceptibility gene SWEET14. Xa7 was mapped to a unique 74-kb region. Gene expression analysis of the region revealed a candidate gene that contained a putative AvrXa7 effector binding element (EBE) in its promoter and encoded a 113-amino-acid peptide of unknown function. Genome editing at the Xa7 locus rendered the plants susceptible to avrXa7-carrying Xoo strains. Both AvrXa7 and PthXo3 activated a GUS reporter gene fused with the EBE-containing Xa7 promoter in Nicotiana benthamiana. The EBE of Xa7 is a close mimic of the EBE of SWEET14 for TALe-induced disease susceptibility. Ectopic expression of Xa7 triggers cell death in N. benthamiana. Xa7 is prevalent in indica rice accessions from 3000 rice genomes. Xa7 appears to be an adaptation that protects against pathogen exploitation of SWEET14 and disease susceptibility.
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Affiliation(s)
- Dangping Luo
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jose C. Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - R. Taylor Raborn
- Department of Biology, Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
- Current address: Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Volker P. Brendel
- Department of Biology, Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Corresponding author
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Veley KM, Okwuonu I, Jensen G, Yoder M, Taylor NJ, Meyers BC, Bart RS. Gene tagging via CRISPR-mediated homology-directed repair in cassava. G3 (BETHESDA, MD.) 2021; 11:jkab028. [PMID: 33855431 PMCID: PMC8049417 DOI: 10.1093/g3journal/jkab028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/21/2021] [Indexed: 12/21/2022]
Abstract
Research on a few model plant-pathogen systems has benefitted from years of tool and resource development. This is not the case for the vast majority of economically and nutritionally important plants, creating a crop improvement bottleneck. Cassava bacterial blight (CBB), caused by Xanthomonas axonopodis pv. manihotis (Xam), is an important disease in all regions where cassava (Manihot esculenta Crantz) is grown. Here, we describe the development of cassava that can be used to visualize one of the initial steps of CBB infection in vivo. Using CRISPR-mediated homology-directed repair (HDR), we generated plants containing scarless insertion of GFP at the 3' end of CBB susceptibility (S) gene MeSWEET10a. Activation of MeSWEET10a-GFP by the transcription activator-like (TAL) effector TAL20 was subsequently visualized at transcriptional and translational levels. To our knowledge, this is the first such demonstration of HDR via gene editing in cassava.
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Affiliation(s)
- Kira M Veley
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Ihuoma Okwuonu
- Biotechnology Research Division, National Root Crops Research Institute, Umudike, Abia State, Nigeria
| | - Greg Jensen
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Marisa Yoder
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Nigel J Taylor
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
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Moon H, Pandey A, Yoon H, Choi S, Jeon H, Prokchorchik M, Jung G, Witek K, Valls M, McCann HC, Kim M, Jones JDG, Segonzac C, Sohn KH. Identification of RipAZ1 as an avirulence determinant of Ralstonia solanacearum in Solanum americanum. MOLECULAR PLANT PATHOLOGY 2021; 22:317-333. [PMID: 33389783 PMCID: PMC7865085 DOI: 10.1111/mpp.13030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 05/08/2023]
Abstract
Ralstonia solanacearum causes bacterial wilt disease in many plant species. Type III-secreted effectors (T3Es) play crucial roles in bacterial pathogenesis. However, some T3Es are recognized by corresponding disease resistance proteins and activate plant immunity. In this study, we identified the R. solanacearum T3E protein RipAZ1 (Ralstonia injected protein AZ1) as an avirulence determinant in the black nightshade species Solanum americanum. Based on the S. americanum accession-specific avirulence phenotype of R. solanacearum strain Pe_26, 12 candidate avirulence T3Es were selected for further analysis. Among these candidates, only RipAZ1 induced a cell death response when transiently expressed in a bacterial wilt-resistant S. americanum accession. Furthermore, loss of ripAZ1 in the avirulent R. solanacearum strain Pe_26 resulted in acquired virulence. Our analysis of the natural sequence and functional variation of RipAZ1 demonstrated that the naturally occurring C-terminal truncation results in loss of RipAZ1-triggered cell death. We also show that the 213 amino acid central region of RipAZ1 is sufficient to induce cell death in S. americanum. Finally, we show that RipAZ1 may activate defence in host cell cytoplasm. Taken together, our data indicate that the nucleocytoplasmic T3E RipAZ1 confers R. solanacearum avirulence in S. americanum. Few avirulence genes are known in vascular bacterial phytopathogens and ripAZ1 is the first one in R. solanacearum that is recognized in black nightshades. This work thus opens the way for the identification of disease resistance genes responsible for the specific recognition of RipAZ1, which can be a source of resistance against the devastating bacterial wilt disease.
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Affiliation(s)
- Hayoung Moon
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Ankita Pandey
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Hayeon Yoon
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Sera Choi
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Hyelim Jeon
- Department of Agriculture, Forestry and BioresourcesSeoul National UniversitySeoulRepublic of Korea
- Plant Immunity Research CenterSeoul National UniversitySeoulRepublic of Korea
| | - Maxim Prokchorchik
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Gayoung Jung
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Kamil Witek
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Marc Valls
- Department of GeneticsUniversity of BarcelonaBarcelonaSpain
- Centre for Research in Agricultural Genomics (CSIC‐IRTA‐UAB‐UB)BellaterraSpain
| | - Honour C. McCann
- New Zealand Institute of Advanced StudiesMassey UniversityAucklandNew Zealand
- Max Planck Institute for Developmental BiologyTübingenGermany
| | - Min‐Sung Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
- Division of Integrative Biosciences and BiotechnologyPohang University of Science and TechnologyRepublic of Korea
| | | | - Cécile Segonzac
- Department of Agriculture, Forestry and BioresourcesSeoul National UniversitySeoulRepublic of Korea
- Plant Immunity Research CenterSeoul National UniversitySeoulRepublic of Korea
- Department of Plant Science, Plant Genomics and Breeding InstituteAgricultural Life Science Research InstituteSeoul National UniversitySeoulRepublic of Korea
| | - Kee Hoon Sohn
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and TechnologyPohangRepublic of Korea
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24
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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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25
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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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26
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Xu Z, Wang S, Liu L, Yang Y, Zhu B, Zou L, Chen G. Genome Resource of a Hypervirulent Strain LN4 of Xanthomonas oryzae pv. oryzae Causing Bacterial Blight of Rice. PLANT DISEASE 2020; 104:2764-2767. [PMID: 32897843 DOI: 10.1094/pdis-12-19-2724-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Xanthomonas oryzae pv. oryzae is the causative agent of bacterial blight of rice and causes severe harvest loss and challenges to a stable food supply globally. In this study, a hypervirulent strain, LN4, compatible in rice varieties carrying Xa3, Xa4, xa13, and xa25 resistance genes, was used to generate DNA for nanopore sequencing. After assembly, the genome comprises a single chromosome of 5,012,583 bp, consisting of a total of 6,700 predicted coding sequences. Seventeen transcription activator-like effectors (TALEs) were encoded in the genome, of which two (Tal7 and Tal6c) were major TALEs. The approach and genome data provide information for the discovery of new virulence effectors and understanding of the virulence mechanism of TALEs in rice.
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Affiliation(s)
- Zhengyin Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sai Wang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Liu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yangyang Yang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Zhu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
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27
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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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28
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 DOI: 10.21203/rs.3.rs-17010/v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. RESULTS We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. CONCLUSIONS This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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29
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 PMCID: PMC7437933 DOI: 10.1186/s12864-020-06972-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. Results We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. Conclusions This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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30
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Xue J, Lu Z, Liu W, Wang S, Lu D, Wang X, He X. The genetic arms race between plant and Xanthomonas: lessons learned from TALE biology. SCIENCE CHINA-LIFE SCIENCES 2020; 64:51-65. [PMID: 32661897 DOI: 10.1007/s11427-020-1699-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/29/2020] [Indexed: 10/23/2022]
Abstract
The pathogenic bacterial genus Xanthomonas infects a wide variety of host plants and causes devastating diseases in many crops. Transcription activator-like effectors (TALEs) are important virulence factors secreted by Xanthomonas with the ability to directly bind to the promoters of target genes in plant hosts and activate their expression, which often facilitates the proliferation of pathogens. Understanding how plants cope with TALEs will provide mechanistic insights into crop breeding for Xanthomonas defense. Over the past 30 years, numerous studies have revealed the modes of action of TALEs in plant cells and plant defense strategies to overcome TALE attack. Based on these findings, new technologies were adopted for disease management to optimize crop production. In this article, we will review the most recent advances in the evolutionary arms race between plant resistance and TALEs from Xanthomonas, with a specific focus on TALE applications in the development of novel breeding strategies for durable and broad-spectrum resistance.
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Affiliation(s)
- Jiao Xue
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Dongbai Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China.
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31
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Haq F, Xie S, Huang K, Shah SMA, Ma W, Cai L, Xu X, Xu Z, Wang S, Zou L, Zhu B, Chen G. Identification of a virulence tal gene in the cotton pathogen, Xanthomonas citri pv. malvacearum strain Xss-V 2-18. BMC Microbiol 2020; 20:91. [PMID: 32293266 PMCID: PMC7160923 DOI: 10.1186/s12866-020-01783-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/05/2020] [Indexed: 01/22/2023] Open
Abstract
Background Bacterial blight of cotton (BBC), which is caused by the bacterium Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease in cotton. Transcription activator-like effectors (TALEs), encoded by tal-genes, play critical roles in the pathogenesis of xanthomonads. Characterized strains of cotton pathogenic Xcm harbor 8–12 different tal genes and only one of them is functionally decoded. Further identification of novel tal genes in Xcm strains with virulence contributions are prerequisite to decipher the Xcm-cotton interactions. Results In this study, we identified six tal genes in Xss-V2–18, a highly-virulent strain of Xcm from China, and assessed their role in BBC. RFLP-based Southern hybridization assays indicated that Xss-V2–18 harbors the six tal genes on a plasmid. The plasmid-encoded tal genes were isolated by cloning BamHI fragments and screening clones by colony hybridization. The tal genes were sequenced by inserting a Tn5 transposon in the DNA encoding the central repeat region (CRR) of each tal gene. Xcm TALome evolutionary relationship based on TALEs CRR revealed relatedness of Xss-V2–18 to MSCT1 and MS14003 from the United States. However, Tal2 of Xss-V2–18 differs at two repeat variable diresidues (RVDs) from Tal6 and Tal26 in MSCT1 and MS14003, respectively, inferred functional dissimilarity. The suicide vector pKMS1 was then used to construct tal deletion mutants in Xcm Xss-V2–18. The mutants were evaluated for pathogenicity in cotton based on symptomology and growth in planta. Four mutants showed attenuated virulence and all contained mutations in tal2. One tal2 mutant designated M2 was further investigated in complementation assays. When tal2 was introduced into Xcm M2 and expressed in trans, the mutant was complemented for both symptoms and growth in planta, thus indicating that tal2 functions as a virulence factor in Xcm Xss-V2–18. Conclusions Overall, the results demonstrated that Tal2 is a major pathogenicity factor in Xcm strain Xss-V2–18 that contributes significantly in BBC. This study provides a foundation for future efforts aimed at identifying susceptibility genes in cotton that are targeted by Tal2.
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Affiliation(s)
- Fazal Haq
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiwang Xie
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China
| | - Kunxuan Huang
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenxiu Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lulu Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiameng Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengyin Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sai Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China
| | - Lifang Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bo Zhu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China. .,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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32
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Dossa GS, Quibod I, Atienza-Grande G, Oliva R, Maiss E, Vera Cruz C, Wydra K. Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight. Sci Rep 2020; 10:683. [PMID: 31959799 PMCID: PMC6971257 DOI: 10.1038/s41598-020-57499-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/21/2019] [Indexed: 01/03/2023] Open
Abstract
Rice bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) implies substantial yield loss to rice. In times of climate change, increasing temperatures are observed and further acceleration is expected worldwide. Increasing temperature often turns into inhibition of host plant defense to pathogens. Recently, a reduced resistance in rice IRBB4 carrying Xa4, but an increase in resistance in IRBB7 carrying Xa7 resistance by increasing temperature has been reported. Influence of high temperature on both R genes (Xa4+Xa7) combined in IRBB67 was analyzed under growth chamber conditions and transcriptomic analysis performed. The pyramided line IRBB67 showed no differences in lesion length between both temperature regimes, demonstrating that non-effectiveness of Xa4 at high temperature did not affect IRBB67 resistance. Moreover, Xa4 complements Xa7 resistance with no Xoo spread in planta beyond the symptomatic area under both temperature regimes in IRBB67. Time course transcriptomic analysis revealed that temperature enhanced IRBB67 resistance to combined heat and Xoo. Our findings highlight altered cellular compartments and point at a role of the cell wall involved in Xoo resistance and heat stress tolerance in both susceptible (IR24) and the resistant (IRBB67) NILs. Interestingly, up-regulation of trehalose-6-phosphatase gene and low affinity cation transporter in IRBB67 suggest that IRBB67 maintained a certain homeostasis under high temperature which may have enhanced its resistance. The interplay of both heat stress and Xoo responses as determined by up-regulated and down-regulated genes demonstrates how resistant plants cope with combined biotic and abiotic stresses.
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Affiliation(s)
- Gerbert Sylvestre Dossa
- International Rice Research Institute, Los Baños, Philippines.
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany.
- Food and Agriculture Organization, Sub Regional Office for Central Africa, PO. Box 2643, Libreville, Gabon.
| | - Ian Quibod
- International Rice Research Institute, Los Baños, Philippines
| | - Genelou Atienza-Grande
- International Rice Research Institute, Los Baños, Philippines
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Ricardo Oliva
- International Rice Research Institute, Los Baños, Philippines
| | - Edgar Maiss
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
| | | | - Kerstin Wydra
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
- Plant Production and Climate Change, Erfurt University of Applied Sciences, Erfurt, Germany
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33
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Kumar A, Kumar R, Sengupta D, Das SN, Pandey MK, Bohra A, Sharma NK, Sinha P, Sk H, Ghazi IA, Laha GS, Sundaram RM. Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice- Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:1152. [PMID: 32849710 PMCID: PMC7417518 DOI: 10.3389/fpls.2020.01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant's defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.
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Affiliation(s)
- Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
| | - Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Debashree Sengupta
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Subha Narayan Das
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Manish K. Pandey
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Abhishek Bohra
- ICAR-Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Naveen K. Sharma
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Hajira Sk
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Gouri Sankar Laha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Meenakshi Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
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34
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Xu Z, Xu X, Gong Q, Li Z, Li Y, Wang S, Yang Y, Ma W, Liu L, Zhu B, Zou L, Chen G. Engineering Broad-Spectrum Bacterial Blight Resistance by Simultaneously Disrupting Variable TALE-Binding Elements of Multiple Susceptibility Genes in Rice. MOLECULAR PLANT 2019; 12:1434-1446. [PMID: 31493565 DOI: 10.1016/j.molp.2019.08.006] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/01/2019] [Accepted: 08/11/2019] [Indexed: 05/04/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight of rice, employs the transcription activator-like effectors (TALEs) to induce the expression of the OsSWEET family of putative sugar transporter genes, which function in conferring disease susceptibility (S) in rice plants. To engineer broad-spectrum bacterial blight resistance, we used CRISPR/Cas9-mediated gene editing to disrupt the TALE-binding elements (EBEs) of two S genes, OsSWEET11 and OsSWEET14, in rice cv. Kitaake, which harbors the recessive resistance allele of Xa25/OsSWEET13. The engineered rice line MS14K exhibited broad-spectrum resistance to most Xoo strains with a few exceptions, suggesting that the compatible strains may contain new TALEs. We identified two PthXo2-like TALEs, Tal5LN18 and Tal7PXO61, as major virulence factors in the compatible Xoo strains LN18 and PXO61, respectively, and found that Xoo encodes at least five types of PthXo2-like effectors. Given that PthXo2/PthXo2.1 target OsSWEET13 for transcriptional activation, the genomes of 3000 rice varieties were analyzed for EBE variationsin the OsSWEET13 promoter, and 10 Xa25-like haplotypes were identified. We found that Tal5LN18 and Tal7PXO61 bind slightly different EBE sequences in the OsSWEET13 promoter to activate its expression. CRISPR/Cas9 technology was then used to generate InDels in the EBE of the OsSWEET13 promoter in MS14K to creat a new germplasm with three edited OsSWEET EBEs and broad-spectrum resistance against all Xoo strains tested. Collectively, our findings illustrate how to disarm TALE-S co-evolved loci to generate broad-spectrum resistance through the loss of effector-triggered susceptibility in plants.
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Affiliation(s)
- Zhengyin Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Gong
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ziyang Li
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Li
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sai Wang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yangyang Yang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenxiu Ma
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Longyu Liu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Zhu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
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35
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Oliva R, Ji C, Atienza-Grande G, Huguet-Tapia JC, Perez-Quintero A, Li T, Eom JS, Li C, Nguyen H, Liu B, Auguy F, Sciallano C, Luu VT, Dossa GS, Cunnac S, Schmidt SM, Slamet-Loedin IH, Vera Cruz C, Szurek B, Frommer WB, White FF, Yang B. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat Biotechnol 2019; 37:1344-1350. [PMID: 31659337 PMCID: PMC6831514 DOI: 10.1038/s41587-019-0267-z] [Citation(s) in RCA: 305] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/28/2019] [Indexed: 02/01/2023]
Abstract
Bacterial blight of rice is an important disease in Asia and Africa. The pathogen, Xanthomonas oryzae pv. oryzae (Xoo), secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genes SWEET11, SWEET13 and SWEET14, the expression of which is required for disease susceptibility. We used CRISPR-Cas9-mediated genome editing to introduce mutations in all three SWEET gene promoters. Editing was further informed by sequence analyses of TALe genes in 63 Xoo strains, which revealed multiple TALe variants for SWEET13 alleles. Mutations were also created in SWEET14, which is also targeted by two TALes from an African Xoo lineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-edited SWEET promoters endow rice lines with robust, broad-spectrum resistance.
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Affiliation(s)
- Ricardo Oliva
- International Rice Research Institute, Metro Manila, Philippines.
| | - Chonghui Ji
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Genelou Atienza-Grande
- International Rice Research Institute, Metro Manila, Philippines
- College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños, Philippines
| | | | - Alvaro Perez-Quintero
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Ting Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Joon-Seob Eom
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Chenhao Li
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Hanna Nguyen
- International Rice Research Institute, Metro Manila, Philippines
| | - Bo Liu
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Florence Auguy
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | | | - Van T Luu
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | | | - Sarah M Schmidt
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | | | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany.
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, Japan.
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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36
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Eom JS, Luo D, Atienza-Grande G, Yang J, Ji C, Thi Luu V, Huguet-Tapia JC, Char SN, Liu B, Nguyen H, Schmidt SM, Szurek B, Vera Cruz C, White FF, Oliva R, Yang B, Frommer WB. Diagnostic kit for rice blight resistance. Nat Biotechnol 2019; 37:1372-1379. [PMID: 31659338 PMCID: PMC6831515 DOI: 10.1038/s41587-019-0268-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
Blight-resistant rice lines are the most effective solution for bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo). Key resistance mechanisms involve SWEET genes as susceptibility factors. Bacterial transcription activator-like (TAL) effectors bind to effector-binding elements (EBEs) in SWEET gene promoters and induce SWEET genes. EBE variants that cannot be recognized by TAL effectors abrogate induction, causing resistance. Here we describe a diagnostic kit to enable analysis of bacterial blight in the field and identification of suitable resistant lines. Specifically, we include a SWEET promoter database, RT–PCR primers for detecting SWEET induction, engineered reporter rice lines to visualize SWEET protein accumulation and knock-out rice lines to identify virulence mechanisms in bacterial isolates. We also developed CRISPR–Cas9 genome-edited Kitaake rice to evaluate the efficacy of EBE mutations in resistance, software to predict the optimal resistance gene set for a specific geographic region, and two resistant ‘mega’ rice lines that will empower farmers to plant lines that are most likely to resist rice blight. Strategic deployment of blight-resistant rice lines is enabled by a molecular diagnostic kit.
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Affiliation(s)
- Joon-Seob Eom
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dangping Luo
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Genelou Atienza-Grande
- International Rice Research Institute, Metro Manila, Philippines.,College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Jungil Yang
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Chonghui Ji
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Van Thi Luu
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Si Nian Char
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Bo Liu
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Hanna Nguyen
- International Rice Research Institute, Metro Manila, Philippines
| | - Sarah Maria Schmidt
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | | | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Ricardo Oliva
- International Rice Research Institute, Metro Manila, Philippines
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA. .,Donald Danforth Plant Science Center, St. Louis, MO, USA.
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany. .,Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, Japan.
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37
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Li C, Ji C, Huguet‐Tapia JC, White FF, Dong H, Yang B. An efficient method to clone TAL effector genes from Xanthomonas oryzae using Gibson assembly. MOLECULAR PLANT PATHOLOGY 2019; 20:1453-1462. [PMID: 31414714 PMCID: PMC6792135 DOI: 10.1111/mpp.12820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transcription Activator-Like effectors (TALes) represent the largest family of type III effectors among pathogenic bacteria and play a critical role in the process of infection. Strains of Xanthomonas oryzae pv. oryzae (Xoo) and some strains of other Xanthomonas pathogens contain large numbers of TALe genes. Previous techniques to clone individual or a complement of TALe genes through conventional strategies are inefficient and time-consuming due to multiple genes (up to 29 copies) in a given genome, and technically challenging due to the repetitive sequences (up to 33 nearly identical 102-nucleotide repeats) of individual TALe genes. Thus, only a limited number of TALe genes have been molecularly cloned and characterized, and the functions of most TALe genes remain unknown. Here, we present an easy and efficient cloning technique to clone TALe genes selectively through in vitro homologous recombination and single-strand annealing, and demonstrate the feasibility of this approach with four different Xoo strains. Based on the Gibson assembly strategy, two complementary vectors with scaffolds that can preferentially capture all TALe genes from a pool of genomic fragments were designed. Both vector systems enabled cloning of a full complement of TALe genes from each of four Xoo strains and functional analysis of individual TALes in rice in approximately 1 month compared to 3 months by previously used methods. The results demonstrate a robust tool to advance TALe biology and a potential for broad usage of this approach to clone multiple copies of highly competitive DNA elements in any genome of interest.
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Affiliation(s)
- Chenhao Li
- Department of Plant PathologyNanjing Agricultural UniversityNanjing210095Jiangsu ProvidenceP.R. China
- Division of Plant SciencesUniversity of MissouriColumbiaMO65211USA
| | - Chonghui Ji
- Division of Plant SciencesUniversity of MissouriColumbiaMO65211USA
| | | | - Frank F. White
- Department of Plant PathologyUniversity of FloridaGainesvilleFL32611USA
| | - Hansong Dong
- Department of Plant PathologyNanjing Agricultural UniversityNanjing210095Jiangsu ProvidenceP.R. China
| | - Bing Yang
- Division of Plant SciencesUniversity of MissouriColumbiaMO65211USA
- Donald Danforth Plant Science CenterSt. LouisMO63132USA
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38
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Yin K, Qiu JL. Genome editing for plant disease resistance: applications and perspectives. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180322. [PMID: 30967029 PMCID: PMC6367152 DOI: 10.1098/rstb.2018.0322] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Abstract
Diseases severely affect crop yield and quality, thereby threatening global food security. Genetic improvement of plant disease resistance is essential for sustainable agriculture. Genome editing has been revolutionizing plant biology and biotechnology by enabling precise, targeted genome modifications. Editing provides new methods for genetic improvement of plant disease resistance and accelerates resistance breeding. Here, we first summarize the challenges for breeding resistant crops. Next, we focus on applications of genome editing technology in generating plants with resistance to bacterial, fungal and viral diseases. Finally, we discuss the potential of genome editing for breeding crops that present novel disease resistance in the future. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.
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Affiliation(s)
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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39
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Mücke S, Reschke M, Erkes A, Schwietzer CA, Becker S, Streubel J, Morgan RD, Wilson GG, Grau J, Boch J. Transcriptional Reprogramming of Rice Cells by Xanthomonas oryzae TALEs. FRONTIERS IN PLANT SCIENCE 2019; 10:162. [PMID: 30858855 PMCID: PMC6397873 DOI: 10.3389/fpls.2019.00162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/29/2019] [Indexed: 05/12/2023]
Abstract
Rice-pathogenic Xanthomonas oryzae bacteria cause severe harvest loss and challenge a stable food supply. The pathogen virulence relies strongly on bacterial TALE (transcription activator-like effector) proteins that function as transcriptional activators inside the plant cell. To understand the plant targets of TALEs, we determined the genome sequences of the Indian X. oryzae pv. oryzae (Xoo) type strain ICMP 3125T and the strain PXO142 from the Philippines. Their complete TALE repertoire was analyzed and genome-wide TALE targets in rice were characterized. Integrating computational target predictions and rice transcriptomics data, we were able to verify 12 specifically induced target rice genes. The TALEs of the Xoo strains were reconstructed and expressed in a TALE-free Xoo strain to attribute specific induced genes to individual TALEs. Using reporter assays, we could show that individual TALEs act directly on their target promoters. In particular, we show that TALE classes assigned by AnnoTALE reflect common target genes, and that TALE classes of Xoo and the related pathogen X. oryzae pv. oryzicola share more common target genes than previously believed. Taken together, we establish a detailed picture of TALE-induced plant processes that significantly expands our understanding of X. oryzae virulence strategies and will facilitate the development of novel resistances to overcome this important rice disease.
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Affiliation(s)
- Stefanie Mücke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Claudia-Alice Schwietzer
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Sebastian Becker
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Jana Streubel
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | | | | | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
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40
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Chien CC, Chou MY, Chen CY, Shih MC. Analysis of genetic diversity of Xanthomonas oryzae pv. oryzae populations in Taiwan. Sci Rep 2019; 9:316. [PMID: 30670790 PMCID: PMC6342995 DOI: 10.1038/s41598-018-36575-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/25/2018] [Indexed: 01/22/2023] Open
Abstract
Rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major rice disease. In Taiwan, the tropical indica type of Oryza sativa originally grown in this area is mix-cultivated with the temperate japonica type of O. sativa, and this might have led to adaptive changes of both rice host and Xoo isolates. In order to better understand how Xoo adapts to this unique environment, we collected and analyzed fifty-one Xoo isolates in Taiwan. Three different genetic marker systems consistently identified five groups. Among these groups, two of them had unique sequences in the last acquired ten spacers in the clustered regularly interspaced short palindromic repeats (CRISPR) region, and the other two had sequences that were similar to the Japanese isolate MAFF311018 and the Philippines isolate PXO563, respectively. The genomes of two Taiwanese isolates with unique CRISPR sequence features, XF89b and XM9, were further completely sequenced. Comparison of the genome sequences suggested that XF89b is phylogenetically close to MAFF311018, and XM9 is close to PXO563. Here, documentation of the diversity of groups of Xoo in Taiwan provides evidence of the populations from different sources and hitherto missing information regarding distribution of Xoo populations in East Asia.
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Affiliation(s)
- Chih-Cheng Chien
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Mei-Yi Chou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chun-Yi Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Che Shih
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.
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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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Barnes SN, Wram CL, Mitchum MG, Baum TJ. The plant-parasitic cyst nematode effector GLAND4 is a DNA-binding protein. MOLECULAR PLANT PATHOLOGY 2018; 19:2263-2276. [PMID: 29719112 PMCID: PMC6637993 DOI: 10.1111/mpp.12697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/23/2018] [Accepted: 04/30/2018] [Indexed: 05/24/2023]
Abstract
Cyst nematodes are plant pathogens that infect a wide range of economically important crops. One parasitic mechanism employed by cyst nematodes is the production and in planta delivery of effector proteins to modify plant cells and suppress defences to favour parasitism. This study focuses on GLAND4, an effector of Heterodera glycines and H. schachtii, the soybean and sugar beet cyst nematodes, respectively. We show that GLAND4 is recognized by the plant cellular machinery and is transported to the plant nucleus, an organelle for which little is known about plant nematode effector functions. We show that GLAND4 has DNA-binding ability and represses reporter gene expression in a plant transcriptional assay. One DNA fragment that binds to GLAND4 is localized in an Arabidopsis chromosomal region associated with the promoters of two lipid transfer protein genes (LTP). These LTPs have known defence functions and are down-regulated in the nematode feeding site. When expressed in Arabidopsis, the presence of GLAND4 causes the down-regulation of the two LTP genes in question, which is also associated with increased susceptibility to the plant-pathogenic bacterium Pseudomonas syringae. Furthermore, overexpression of one of the LTP genes reduces plant susceptibility to H. schachtii and P. syringae, confirming that LTP repression probably suppresses plant defences. This study makes GLAND4 one of a small subset of characterized plant nematode nuclear effectors and identifies GLAND4 as the first DNA-binding, plant-parasitic nematode effector.
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Affiliation(s)
- Stacey N. Barnes
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
| | - Catherine L. Wram
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
- Present address:
Department of Botany and Plant PathologyOregon State UniversityCorvallisOR 97330USA
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMO 65211USA
| | - Thomas J. Baum
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
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Gao L, Fang Z, Zhou J, Li L, Lu L, Li L, Li T, Chen L, Zhang W, Zhai W, Peng H. Transcriptional insights into the pyramided resistance to rice bacterial blight. Sci Rep 2018; 8:12358. [PMID: 30120263 PMCID: PMC6098014 DOI: 10.1038/s41598-018-29899-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 07/16/2018] [Indexed: 11/30/2022] Open
Abstract
The pyramiding of resistance (R) genes provides broad-spectrum and durable resistance to plant diseases. However, the genetic basis for bacterial blight (BB) resistance remains unclear. The BB R gene pyramided line IRBB54, which expresses xa5 and Xa21, possessed a higher level of resistance than both single R gene lines. Large-scale genotyping of genetic markers in this study revealed similar genetic backgrounds among the near-isogenic lines (NILs), suggesting that resistance in the resistant NILs was mainly conferred by the individual R genes or the interaction between them. Transcriptome analysis demonstrated that more than 50% of the differentially expressed genes (DEGs), and more than 70% of the differentially expressed functions, were shared between IRBB54 and IRBB5 or IRBB21. Most of the DEGs in the resistant NILs were downregulated and are predicted to function in cellular and biological process. The DEGs common among the resistant NILs mainly showed non-additive expression patterns and enrichment in stress-related pathways. The differential expression of agronomic trait-controlled genes in the resistant NILs, especially in IRBB54, indicated the existence of potential side-effects resulting from gene pyramiding. Our findings contribute to the understanding of R gene pyramiding, as well as its effects on targeted and non-targeted trait(s).
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Affiliation(s)
- Lifen Gao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Long Lu
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Lili Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Tiantian Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Lihong Chen
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China.
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Wen A, Jayawardana M, Fiedler J, Sapkota S, Shi G, Peng Z, Liu S, White FF, Bogdanove AJ, Li X, Liu Z. Genetic mapping of a major gene in triticale conferring resistance to bacterial leaf streak. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:649-658. [PMID: 29218377 DOI: 10.1007/s00122-017-3026-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/21/2017] [Indexed: 06/07/2023]
Abstract
A major gene conferring resistance to bacterial leaf streak was mapped to chromosome 5R in triticale. Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa (Xtu), is an important disease of wheat and triticale around the world. Although resistance to BLS is limited in wheat, several triticale accessions have high levels of resistance. To characterize the genetic basis of this resistance, we developed triticale mapping populations using a resistant accession (Siskiyou) and two susceptible accessions (UC38 and Villax St. Jose). Bulked segregant analysis in an F2 population derived from the cross of Siskiyou × UC38 led to the identification of a simple sequence repeat (SSR) marker (XSCM138) on chromosome 5R that co-segregated with the resistance gene. The cross of Siskiyou × Villax St. Jose was advanced into an F2:5 recombinant inbred line population and evaluated for BLS reaction. Genetic linkage maps on this population were assembled with markers generated using genotyping-by-sequencing as well as several SSR markers previously identified on 5R. Quantitative trait locus (QTL) mapping revealed a single major QTL on chromosome 5R, underlined by the same SSR marker as in the Siskiyou × UC38 population. The F1 hybrids of the two crosses were highly resistant to BLS, indicating that resistance is largely dominant. This work will facilitate introgression of this rye-derived BLS resistance gene into the wheat genome by molecular marker-mediated chromosome engineering.
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Affiliation(s)
- Aimin Wen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Malini Jayawardana
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Jason Fiedler
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Suraj Sapkota
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA.
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Li R, Wang S, Sun R, He X, Liu Y, Song C. Xanthomonas oryzae pv. oryzae type III effector PthXo3JXOV suppresses innate immunity, induces susceptibility and binds to multiple targets in rice. FEMS Microbiol Lett 2018. [DOI: 10.1093/femsle/fny037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Rongmei Li
- College of Plant Protection/Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- College of Plant Protection/Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Ronghua Sun
- College of Plant Protection/Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiang He
- College of Plant Protection/Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongting Liu
- College of Plant Protection/Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Congfeng Song
- College of Plant Protection/Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
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Ma L, Wang Q, Yuan M, Zou T, Yin P, Wang S. Xanthomonas TAL effectors hijack host basal transcription factor IIA α and γ subunits for invasion. Biochem Biophys Res Commun 2018; 496:608-613. [PMID: 29331375 DOI: 10.1016/j.bbrc.2018.01.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 12/20/2022]
Abstract
The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria, which infect a broad range of crops and wild plant species, cause symptoms with leaf blights, streaks, spots, stripes, necrosis, wilt, cankers and gummosis on leaves, stems and fruits in a wide variety of plants via injecting their effector proteins into the host cell during infection. Among these virulent effectors, transcription activator-like effectors (TALEs) interact with the γ subunit of host transcription factor IIA (TFIIAγ) to activate the transcription of host disease susceptibility genes. Functional TFIIA is a ternary complex comprising α, β and γ subunits. However, whether TALEs recruit TFIIAα, TFIIAβ, or both remains unknown. The underlying molecular mechanisms by which TALEs mediate host susceptibility gene activation require full elucidation. Here, we show that TALEs interact with the α+γ binary subcomplex but not the α+β+γ ternary complex of rice TFIIA (holo-OsTFIIA). The transcription factor binding (TFB) regions of TALEs, which are highly conserved in Xanthomonas species, have a dominant role in these interactions. Furthermore, the interaction between TALEs and the α+γ complex exhibits robust DNA binding activity in vitro. These results collectively demonstrate that TALE-carrying pathogens hijack the host basal transcription factors TFIIAα and TFIIAγ, but not TFIIAβ, to enhance host susceptibility during pathogen infection. The uncovered mechanism widens new insights on host-microbe interaction and provide an applicable strategy to breed high-resistance crop varieties.
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Affiliation(s)
- Ling Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Zou
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Falahi Charkhabi N, Booher NJ, Peng Z, Wang L, Rahimian H, Shams-Bakhsh M, Liu Z, Liu S, White FF, Bogdanove AJ. Complete Genome Sequencing and Targeted Mutagenesis Reveal Virulence Contributions of Tal2 and Tal4b of Xanthomonas translucens pv. undulosa ICMP11055 in Bacterial Leaf Streak of Wheat. Front Microbiol 2017; 8:1488. [PMID: 28848509 PMCID: PMC5554336 DOI: 10.3389/fmicb.2017.01488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022] Open
Abstract
Bacterial leaf streak caused by Xanthomonas translucens pv. undulosa (Xtu) is an important disease of wheat (Triticum aestivum) and barley (Hordeum vulgare) worldwide. Transcription activator-like effectors (TALEs) play determinative roles in many of the plant diseases caused by the different species and pathovars of Xanthomonas, but their role in this disease has not been characterized. ICMP11055 is a highly virulent Xtu strain from Iran. The aim of this study was to better understand genetic diversity of Xtu and to assess the role of TALEs in bacterial leaf streak of wheat by comparing the genome of this strain to the recently completely sequenced genome of a U.S. Xtu strain, and to several other draft X. translucens genomes, and by carrying out mutational analyses of the TALE (tal) genes the Iranian strain might harbor. The ICMP11055 genome, including its repeat-rich tal genes, was completely sequenced using single molecule, real-time technology (Pacific Biosciences). It consists of a single circular chromosome of 4,561,583 bp, containing 3,953 genes. Whole genome alignment with the genome of the United States Xtu strain XT4699 showed two major re-arrangements, nine genomic regions unique to ICMP11055, and one region unique to XT4699. ICMP110055 harbors 26 non-TALE type III effector genes and seven tal genes, compared to 25 and eight for XT4699. The tal genes occur singly or in pairs across five scattered loci. Four are identical to tal genes in XT4699. In addition to common repeat-variable diresidues (RVDs), the tal genes of ICMP11055, like those of XT4699, encode several RVDs rarely observed in Xanthomonas, including KG, NF, Y∗, YD, and YK. Insertion and deletion mutagenesis of ICMP11055 tal genes followed by genetic complementation analysis in wheat cv. Chinese Spring revealed that Tal2 and Tal4b of ICMP11055 each contribute individually to the extent of disease caused by this strain. A largely conserved ortholog of tal2 is present in XT4699, but for tal4b, only a gene with partial, fragmented RVD sequence similarity can be found. Our results lay the foundation for identification of important host genes activated by Xtu TALEs as targets for the development of disease resistant varieties.
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Affiliation(s)
- Nargues Falahi Charkhabi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States.,Department of Plant Pathology, Tarbiat Modares UniversityTehran, Iran
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Zhao Peng
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States.,Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Heshmat Rahimian
- Department of Plant Protection, Sari Agricultural Science and Natural Resources UniversitySari, Iran
| | | | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, FargoND, United States
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States
| | - Frank F White
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States.,Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
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48
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A Transcription Activator-Like Effector Tal7 of Xanthomonas oryzae pv. oryzicola Activates Rice Gene Os09g29100 to Suppress Rice Immunity. Sci Rep 2017; 7:5089. [PMID: 28698641 PMCID: PMC5505973 DOI: 10.1038/s41598-017-04800-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/23/2017] [Indexed: 11/09/2022] Open
Abstract
Xanthomonas oryzae pv. oryzicola (Xoc) and X. oryzae pv. oryzae (Xoo) cause bacterial leaf streak (BLS) and bacterial leaf blight (BLB) in rice, respectively. Unlike Xoo, endogenous avirulence-resistance (avr-R) gene interactions have not been identified in the Xoc-rice pathosystem; however, both pathogens possess transcription activator-like effectors (TALEs) that are known to modulate R or S genes in rice. The transfer of individual tal genes from Xoc RS105 (hypervirulent) into Xoc YNB0-17 (hypovirulent) led to the identification of tal7, which suppressed avrXa7-Xa7 mediated defense in rice containing an Xa7 R gene. Mobility shift and microscale thermophoresis assays showed that Tal7 bound two EBE sites in the promoters of two rice genes, Os09g29100 and Os12g42970, which encode predicted Cyclin-D4-1 and GATA zinc finger family protein, respectively. Assays using designer TALEs and a TALE-free strain of Xoo revealed that Os09g29100 was the biologically relevant target of Tal7. Tal7 activates the expression of rice gene Os09g29100 that suppresses avrXa7-Xa7 mediated defense in Rice. TALEN editing of the Tal7-binding site in the Os09g29100 gene promoter further enhanced resistance to the pathogen Xoc RS105. The suppression of effector-trigger immunity (ETI) is a phenomenon that may contribute to the scarcity of BLS resistant cultivars.
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Wang J, Tian D, Gu K, Yang X, Wang L, Zeng X, Yin Z. Induction of Xa10-like Genes in Rice Cultivar Nipponbare Confers Disease Resistance to Rice Bacterial Blight. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:466-477. [PMID: 28304228 DOI: 10.1094/mpmi-11-16-0229-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzae, is one of the most destructive bacterial diseases throughout the major rice-growing regions in the world. The rice disease resistance (R) gene Xa10 confers race-specific disease resistance to X. oryzae pv. oryzae strains that deliver the corresponding transcription activator-like (TAL) effector AvrXa10. Upon bacterial infection, AvrXa10 binds specifically to the effector binding element in the promoter of the R gene and activates its expression. Xa10 encodes an executor R protein that triggers hypersensitive response and activates disease resistance. 'Nipponbare' rice carries two Xa10-like genes in its genome, of which one is the susceptible allele of the Xa23 gene, a Xa10-like TAL effector-dependent executor R gene isolated recently from 'CBB23' rice. However, the function of the two Xa10-like genes in disease resistance to X. oryzae pv. oryzae strains has not been investigated. Here, we designated the two Xa10-like genes as Xa10-Ni and Xa23-Ni and characterized their function for disease resistance to rice bacterial blight. Both Xa10-Ni and Xa23-Ni provided disease resistance to X. oryzae pv. oryzae strains that deliver the matching artificially designed TAL effectors (dTALE). Transgenic rice plants containing Xa10-Ni and Xa23-Ni under the Xa10 promoter provided specific disease resistance to X. oryzae pv. oryzae strains that deliver AvrXa10. Xa10-Ni and Xa23-Ni knock-out mutants abolished dTALE-dependent disease resistance to X. oryzae pv. oryzae. Heterologous expression of Xa10-Ni and Xa23-Ni in Nicotiana benthamiana triggered cell death. The 19-amino-acid residues at the N-terminal regions of XA10 or XA10-Ni are dispensable for their function in inducing cell death in N. benthamiana and the C-terminal regions of XA10, XA10-Ni, and XA23-Ni are interchangeable among each other without affecting their function. Like XA10, both XA10-Ni and XA23-Ni locate to the endoplasmic reticulum (ER) membrane, show self-interaction, and induce ER Ca2+ depletion in leaf cells of N. benthamiana. The results indicate that Xa10-Ni and Xa23-Ni in Nipponbare encode functional executor R proteins, which induce cell death in both monocotyledonous and dicotyledonous plants and have the potential of being engineered to provide broad-spectrum disease resistance to plant-pathogenic Xanthomonas spp.
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Affiliation(s)
- Jun Wang
- 1 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore; and
- 2 Department of Biological Sciences, 14 Science Drive, National University of Singapore, Singapore 117543, Republic of Singapore
| | - Dongsheng Tian
- 1 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore; and
| | - Keyu Gu
- 1 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore; and
| | - Xiaobei Yang
- 1 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore; and
| | - Lanlan Wang
- 1 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore; and
| | - Xuan Zeng
- 1 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore; and
| | - Zhongchao Yin
- 1 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore; and
- 2 Department of Biological Sciences, 14 Science Drive, National University of Singapore, Singapore 117543, Republic of Singapore
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Hummel AW, Wilkins KE, Wang L, Cernadas RA, Bogdanove AJ. A transcription activator-like effector from Xanthomonas oryzae pv. oryzicola elicits dose-dependent resistance in rice. MOLECULAR PLANT PATHOLOGY 2017; 18:55-66. [PMID: 26821568 PMCID: PMC6638286 DOI: 10.1111/mpp.12377] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/24/2016] [Accepted: 01/27/2016] [Indexed: 05/15/2023]
Abstract
Xanthomonas spp. reduce crop yields and quality worldwide. During infection of their plant hosts, many strains secrete transcription activator-like (TAL) effectors, which enter the host cell nucleus and activate specific corresponding host genes at effector binding elements (EBEs) in the promoter. TAL effectors may contribute to disease by activating the expression of susceptibility genes or trigger resistance associated with the hypersensitive reaction (HR) by activating an executor resistance (R) gene. The rice bacterial leaf streak pathogen X. oryzae pv. oryzicola (Xoc) is known to suppress host resistance, and no host R gene has been identified against it, despite considerable effort. To further investigate Xoc suppression of host resistance, we conducted a screen of effectors from BLS256 and identified Tal2a as an HR elicitor in rice when delivered heterologously by a strain of the closely related rice bacterial blight pathogen X. oryzae pv. oryzae (Xoo) or by the soybean pathogen X. axonopodis pv. glycines. The HR required the Tal2a activation domain, suggesting an executor R gene. Tal2a activity was differentially distributed among geographically diverse Xoc isolates, being largely conserved among Asian isolates. We identified four genes induced by Tal2a in next-generation RNA sequencing experiments and confirmed them using quantitative real-time reverse transcription-polymerase chain reaction (qPCR). However, neither individual nor collective activation of these genes by designer TAL effectors resulted in HR. A tal2a knockout mutant of BLS256 showed virulence comparable with the wild-type, but plasmid-based overexpression of tal2a at different levels in the wild-type reduced virulence in a directly corresponding way. Overall, the results reveal that host resistance suppression by Xoc plays a critical role in pathogenesis. Further, the dose-dependent avirulence activity of Tal2a and the apparent lack of a single canonical target that accounts for HR point to a novel, activation domain-dependent mode of action, which might involve, for example, a non-coding gene or a specific pattern of activation across multiple targets.
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Affiliation(s)
- Aaron W. Hummel
- Department of Plant Pathology and MicrobiologyIowa State University 351 Bessey HallAmesIA50011USA
- Present address:
KWS SAAT SE, Gateway Research Center1005 N. Warson Rd.St. LouisMO63132USA
| | - Katherine E. Wilkins
- Plant Pathology and Plant–Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthacaNY14853USA
- Graduate Field of Computational Biology, Cornell UniversityIthacaNY14853USA
| | - Li Wang
- Plant Pathology and Plant–Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthacaNY14853USA
| | - R. Andres Cernadas
- Plant Pathology and Plant–Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthacaNY14853USA
- Present address:
Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453 – C1417DSEBuenos AiresArgentina
| | - Adam J. Bogdanove
- Department of Plant Pathology and MicrobiologyIowa State University 351 Bessey HallAmesIA50011USA
- Plant Pathology and Plant–Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthacaNY14853USA
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