151
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Li N, ma X, Short DPG, Li T, Zhou L, Gui Y, Kong Z, Zhang D, Zhang W, Li J, Subbarao KV, Chen J, Dai X. The island cotton NBS-LRR gene GbaNA1 confers resistance to the non-race 1 Verticillium dahliae isolate Vd991. MOLECULAR PLANT PATHOLOGY 2018; 19:1466-1479. [PMID: 29052967 PMCID: PMC6638185 DOI: 10.1111/mpp.12630] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/06/2017] [Accepted: 10/14/2017] [Indexed: 05/21/2023]
Abstract
Wilt caused by Verticillium dahliae significantly reduces cotton yields, as host resistance in commercially cultivated Gossypium species is lacking. Understanding the molecular basis of disease resistance in non-commercial Gossypium species could galvanize the development of Verticillium wilt resistance in cultivated species. Nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins play a central role in plant defence against pathogens. In this study, we focused on the relationship between a locus enriched with eight NBS-LRR genes and Verticillium wilt resistance in G. barbadense. Independent virus-induced gene silencing of each of the eight NBS-LRR genes in G. barbadense cultivar Hai 7124 revealed that silencing of GbaNA1 alone compromised the resistance of G. barbadense to V. dahliae isolate Vd991. In cultivar Hai 7124, GbaNA1 could be induced by V. dahliae isolate Vd991 and by ethylene, jasmonic acid and salicylic acid. Nuclear protein localization of GbaNA1 was demonstrated by transient expression. Sequencing of the GbaNA1 orthologue in nine G. hirsutum accessions revealed that all carried a non-functional allele, caused by a premature peptide truncation. In addition, all 10 G. barbadense and nine G. hirsutum accessions tested carried a full-length (∼1140 amino acids) homologue of the V. dahliae race 1 resistance gene Gbve1, although some sequence polymorphisms were observed. Verticillium dahliae Vd991 is a non-race 1 isolate that lacks the Ave1 gene. Thus, the resistance imparted by GbaNA1 appears to be mediated by a mechanism distinct from recognition of the fungal effector Ave1.
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Affiliation(s)
- Nan‐Yang Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Xue‐Feng ma
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dylan P. G. Short
- Department of Plant PathologyUniversity of CaliforniaDavisCA 95616USA
| | - Ting‐Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Yue‐Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Zhi‐Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dan‐Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Wen‐Qi Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Jun‐Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | | | - Jie‐Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Xiao‐Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
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152
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Zhang L, Wang M, Li N, Wang H, Qiu P, Pei L, Xu Z, Wang T, Gao E, Liu J, Liu S, Hu Q, Miao Y, Lindsey K, Tu L, Zhu L, Zhang X. Long noncoding RNAs involve in resistance to Verticillium dahliae, a fungal disease in cotton. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1172-1185. [PMID: 29149461 PMCID: PMC5978870 DOI: 10.1111/pbi.12861] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/13/2017] [Accepted: 11/01/2017] [Indexed: 05/20/2023]
Abstract
Long noncoding RNAs (lncRNAs) have several known functions in plant development, but their possible roles in responding to plant disease remain largely unresolved. In this study, we described a comprehensive disease-responding lncRNA profiles in defence against a cotton fungal disease Verticillium dahliae. We further revealed the conserved and specific characters of disease-responding process between two cotton species. Conservatively for two cotton species, we found the expression dominance of induced lncRNAs in the Dt subgenome, indicating a biased induction pattern in the co-existing subgenomes of allotetraploid cotton. Comparative analysis of lncRNA expression and their proposed functions in resistant Gossypium barbadense cv. '7124' versus susceptible Gossypium hirsutum cv. 'YZ1' revealed their distinct disease response mechanisms. Species-specific (LS) lncRNAs containing more SNPs displayed a fiercer inducing level postinfection than the species-conserved (core) lncRNAs. Gene Ontology enrichment of LS lncRNAs and core lncRNAs indicates distinct roles in the process of biotic stimulus. Further functional analysis showed that two core lncRNAs, GhlncNAT-ANX2- and GhlncNAT-RLP7-silenced seedlings, displayed an enhanced resistance towards V. dahliae and Botrytis cinerea, possibly associated with the increased expression of LOX1 and LOX2. This study represents the first characterization of lncRNAs involved in resistance to fungal disease and provides new clues to elucidate cotton disease response mechanism.
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Affiliation(s)
- Lin Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Nannan Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Honglei Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Ping Qiu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Liuling Pei
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zheng Xu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Tianyi Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Erlin Gao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Junxia Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Shiming Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Qin Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yuhuan Miao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Keith Lindsey
- Integrative Cell Biology LaboratorySchool of Biological and Biomedical SciencesDurham UniversityDurhamUK
| | - Lili Tu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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153
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Zaynab M, Fatima M, Abbas S, Umair M, Sharif Y, Raza MA. Long non-coding RNAs as molecular players in plant defense against pathogens. Microb Pathog 2018; 121:277-282. [PMID: 29859899 DOI: 10.1016/j.micpath.2018.05.050] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) has significant role in of gene expression and silencing pathways for several biological processes in eukaryotes. lncRNAs has been reported as key player in remodeling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Host lncRNAs are reckoned as compulsory elements of plant defense. In response to pathogen attack, plants protect themselves with the help of lncRNAs -dependent immune systems in which lncRNAs regulate pathogen-associated molecular patterns (PAMPs) and other effectors. Role of lncRNAs in plant microbe interaction has been studied extensively but regulations of several lncRNAs still need extensive research. In this study we discussed and provide as overview the topical advancements and findings relevant to pathogen attack and plant defense mediated by lncRNAs. It is hoped that lncRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.
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Affiliation(s)
- Madiha Zaynab
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China.
| | - Mahpara Fatima
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Safdar Abbas
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Muhammad Umair
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
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154
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Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725-2741. [PMID: 29729657 PMCID: PMC6032900 DOI: 10.1111/mec.14711] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX‐based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host‐driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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155
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Qin J, Wang K, Sun L, Xing H, Wang S, Li L, Chen S, Guo HS, Zhang J. The plant-specific transcription factors CBP60g and SARD1 are targeted by a Verticillium secretory protein VdSCP41 to modulate immunity. eLife 2018; 7:34902. [PMID: 29757140 PMCID: PMC5993538 DOI: 10.7554/elife.34902] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/11/2018] [Indexed: 11/13/2022] Open
Abstract
The vascular pathogen Verticillium dahliae infects the roots of plants to cause Verticillium wilt. The molecular mechanisms underlying V. dahliae virulence and host resistance remain elusive. Here, we demonstrate that a secretory protein, VdSCP41, functions as an intracellular effector that promotes V. dahliae virulence. The Arabidopsis master immune regulators CBP60g and SARD1 and cotton GhCBP60b are targeted by VdSCP41. VdSCP41 binds the C-terminal portion of CBP60g to inhibit its transcription factor activity. Further analyses reveal a transcription activation domain within CBP60g that is required for VdSCP41 targeting. Mutations in both CBP60g and SARD1 compromise Arabidopsis resistance against V. dahliae and partially impair VdSCP41-mediated virulence. Moreover, virus-induced silencing of GhCBP60b compromises cotton resistance to V. dahliae. This work uncovers a virulence strategy in which the V. dahliae secretory protein VdSCP41 directly targets plant transcription factors to inhibit immunity, and reveals CBP60g, SARD1 and GhCBP60b as crucial components governing V. dahliae resistance. Like animals, plants have an immune system to protect themselves from disease. When a plant detects a disease-causing microbe, proteins that serve as master regulators of its immune system activate defense-related genes. Yet some microbes can overcome these defenses and successfully infect plants. Verticillium dahliae is a fungus, found in soil, that infects the roots of many plants – including cotton, tomatoes and potatoes. Infection by this fungus causes the leaves to curl and discolor, and the plant to wilt. The V. dahliae fungus releases, or secretes, nearly 800 proteins during an infection. Yet it remains unknown if and how any of these proteins help the fungus to infect plants. A better understanding of how V. dahliae impairs plant immunity to infect its hosts could give insights into ways to improve plant resistance against this fungus. Now, Qin et al. show that a secreted protein called VdSCP41 promotes V. dahliae infection in both cotton and Arabidopsis plants. Further experiments showed that after leaving the fungus, VdSCP41 enters into the plant’s own cells. Protein-protein interaction and biochemical studies then indicated VdSCP41 associates with a master immune regulator in Arabidopsis called CBP60g. This interaction interferes with CBP60g’s ability to activate the defense-related genes. Now that this role for VdSCP41 has been confirmed, the next step would be to see if targeting it would make plants more resistant to this fungus. One approach would be to genetically engineer plants so that they can specifically shut down, or ‘silence’, the fungal gene that encodes for this protein. Further experiments are required to see whether using this technique – known as host-induced gene silencing (or HIGS for short) – against VdSCP41would enhance plant resistance to V. dahliae. If it does prove effective, this approach may eventually reduce the need for chemical pesticides to protect crop plants.
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Affiliation(s)
- Jun Qin
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kailun Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lifan Sun
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haiying Xing
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sheng Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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156
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Feng Z, Tian J, Han L, Geng Y, Sun J, Kong Z. The Myosin5-mediated actomyosin motility system is required for Verticillium
pathogenesis of cotton. Environ Microbiol 2018; 20:1607-1621. [DOI: 10.1111/1462-2920.14101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/05/2018] [Accepted: 03/11/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Zhidi Feng
- The Key Laboratory of Oasis Eco-Agriculture; College of Agriculture, Shihezi University; Shihezi Xinjiang 832000 China
- State Key Laboratory of Plant Genomic; Institute of Microbiology, Chinese Academy of Sciences; Beijing 100101 China
| | - Juan Tian
- State Key Laboratory of Plant Genomic; Institute of Microbiology, Chinese Academy of Sciences; Beijing 100101 China
| | - Libo Han
- State Key Laboratory of Plant Genomic; Institute of Microbiology, Chinese Academy of Sciences; Beijing 100101 China
| | - Yuan Geng
- State Key Laboratory of Plant Genomic; Institute of Microbiology, Chinese Academy of Sciences; Beijing 100101 China
| | - Jie Sun
- The Key Laboratory of Oasis Eco-Agriculture; College of Agriculture, Shihezi University; Shihezi Xinjiang 832000 China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomic; Institute of Microbiology, Chinese Academy of Sciences; Beijing 100101 China
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157
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Ficarra FA, Grandellis C, Garavaglia BS, Gottig N, Ottado J. Bacterial and plant natriuretic peptides improve plant defence responses against pathogens. MOLECULAR PLANT PATHOLOGY 2018; 19:801-811. [PMID: 28401640 PMCID: PMC6638127 DOI: 10.1111/mpp.12560] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/08/2017] [Accepted: 04/05/2017] [Indexed: 05/23/2023]
Abstract
Plant natriuretic peptides (PNPs) have been implicated in the regulation of ions and water homeostasis, and their participation in the plant immune response has also been proposed. Xanthomonas citri ssp. citri contains a gene encoding a PNP-like protein (XacPNP) which has no homologues in other bacteria. XacPNP mimics its Arabidopsis thaliana homologue AtPNP-A by modifying host responses to create favourable conditions for pathogen survival. However, the ability of XacPNP to induce plant defence responses has not been investigated. In order to study further the role of XacPNP in vivo, A. thaliana lines over-expressing XacPNP, lines over-expressing AtPNP-A and AtPNP-A-deficient plants were generated. Plants over-expressing XacPNP or AtPNP-A showed larger stomatal aperture and were more resistant to saline or oxidative stress than were PNP-deficient lines. In order to study further the role of PNP in biotic stress responses, A. thaliana leaves were infiltrated with pure recombinant XacPNP, and showed enhanced expression of genes related to the defence response and a higher resistance to pathogen infections. Moreover, AtPNP-A expression increased in A. thaliana on Pseudomonas syringae pv. tomato (Pst) infection. This evidence led us to analyse the responses of the transgenic plants to pathogens. Plants over-expressing XacPNP or AtPNP-A were more resistant to Pst infection than control plants, whereas PNP-deficient plants were more susceptible and showed a stronger hypersensitive response when challenged with non-host bacteria. Therefore, XacPNP, acquired by horizontal gene transfer, is able to mimic PNP functions, even with an increase in plant defence responses.
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Affiliation(s)
- Florencia A. Ficarra
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de Rosario (UNR), Ocampo y Esmeralda2000, RosarioArgentina
| | - Carolina Grandellis
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de Rosario (UNR), Ocampo y Esmeralda2000, RosarioArgentina
| | - Betiana S. Garavaglia
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de Rosario (UNR), Ocampo y Esmeralda2000, RosarioArgentina
| | - Natalia Gottig
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de Rosario (UNR), Ocampo y Esmeralda2000, RosarioArgentina
| | - Jorgelina Ottado
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR‐CONICET) and Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de Rosario (UNR), Ocampo y Esmeralda2000, RosarioArgentina
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158
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Hartmann FE, Rodríguez de la Vega RC, Brandenburg JT, Carpentier F, Giraud T. Gene Presence-Absence Polymorphism in Castrating Anther-Smut Fungi: Recent Gene Gains and Phylogeographic Structure. Genome Biol Evol 2018; 10:1298-1314. [PMID: 29722826 PMCID: PMC5967549 DOI: 10.1093/gbe/evy089] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Gene presence-absence polymorphisms segregating within species are a significant source of genetic variation but have been little investigated to date in natural populations. In plant pathogens, the gain or loss of genes encoding proteins interacting directly with the host, such as secreted proteins, probably plays an important role in coevolution and local adaptation. We investigated gene presence-absence polymorphism in populations of two closely related species of castrating anther-smut fungi, Microbotryum lychnidis-dioicae (MvSl) and M. silenes-dioicae (MvSd), from across Europe, on the basis of Illumina genome sequencing data and high-quality genome references. We observed presence-absence polymorphism for 186 autosomal genes (2% of all genes) in MvSl, and only 51 autosomal genes in MvSd. Distinct genes displayed presence-absence polymorphism in the two species. Genes displaying presence-absence polymorphism were frequently located in subtelomeric and centromeric regions and close to repetitive elements, and comparison with outgroups indicated that most were present in a single species, being recently acquired through duplications in multiple-gene families. Gene presence-absence polymorphism in MvSl showed a phylogeographic structure corresponding to clusters detected based on SNPs. In addition, gene absence alleles were rare within species and skewed toward low-frequency variants. These findings are consistent with a deleterious or neutral effect for most gene presence-absence polymorphism. Some of the observed gene loss and gain events may however be adaptive, as suggested by the putative functions of the corresponding encoded proteins (e.g., secreted proteins) or their localization within previously identified selective sweeps. The adaptive roles in plant and anther-smut fungi interactions of candidate genes however need to be experimentally tested in future studies.
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Affiliation(s)
- Fanny E Hartmann
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Jean-Tristan Brandenburg
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Fantin Carpentier
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Tatiana Giraud
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
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159
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Zhang W, Gui Y, Short DPG, Li T, Zhang D, Zhou L, Liu C, Bao Y, Subbarao KV, Chen J, Dai X. Verticillium dahliae transcription factor VdFTF1 regulates the expression of multiple secreted virulence factors and is required for full virulence in cotton. MOLECULAR PLANT PATHOLOGY 2018; 19:841-857. [PMID: 28520093 PMCID: PMC6638078 DOI: 10.1111/mpp.12569] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/11/2017] [Accepted: 05/13/2017] [Indexed: 05/05/2023]
Abstract
Fungal transcription factors (TFs) implicated in the regulation of virulence gene expression have been identified in a number of plant pathogens. In Verticillium dahliae, despite its agricultural importance, few regulators of transcription have been characterized. In this study, a T-DNA insertion mutant with significantly reduced virulence towards cotton was identified. The T-DNA was traced to VdFTF1, a gene encoding a TF containing a Fungal_trans domain. Transient expression in onion epidermal cells indicated that VdFTF1 is localized to the nucleus. The VdFTF1-deletion strains displayed normal vegetative growth, mycelial pigmentation and conidial morphology, but exhibited significantly reduced virulence on cotton, suggesting that VdFTF1 is required exclusively for pathogenesis. Comparisons of global transcription patterns of wild-type and VdFTF1-deletion strains indicated that VdFTF1 affected the expression of 802 genes, 233 of which were associated with catalytic processes. These genes encoded 69 potentially secreted proteins, 43 of which contained a carbohydrate enzyme domain known to participate in pathogenesis during infection of cotton. Targeted gene deletion of one VdFTF1-regulated gene resulted in significantly impaired vascular colonization, as measured by quantitative polymerase chain reaction, as well as aggressiveness and symptom severity in cotton. In conclusion, VdFTF1, which encodes a TF containing a Fungal_trans domain, regulates the gene expression of plant cell wall degradation enzymes in V. dahliae, which are required for full virulence on cotton.
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Affiliation(s)
- Wen‐Qi Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Yue‐Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dylan P. G. Short
- Department of Plant PathologyUniversity of CaliforniaDavisCA 95616USA
| | - Ting‐Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dan‐Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Chun Liu
- BGI‐ShenzhenShenzhenGuangdong 518083China
| | - Yu‐Ming Bao
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | | | - Jie‐Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Xiao‐Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
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160
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Hartmann FE, Croll D. Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen. Mol Biol Evol 2018; 34:2808-2822. [PMID: 28981698 PMCID: PMC5850472 DOI: 10.1093/molbev/msx208] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species. Our analyses of gene gains and losses segregating in populations showed that gene copy number variation arose preferentially in subtelomeres and in proximity to transposable elements. Recently lost genes were enriched in virulence factors and secondary metabolite gene clusters. In contrast, recently gained genes encoded mostly secreted protein lacking a conserved domain. We analyzed the frequency spectrum at loci segregating a gene presence–absence polymorphism in four worldwide populations. Recent gene losses showed a significant excess in low-frequency variants compared with genome-wide single nucleotide polymorphism, which is indicative of strong negative selection against gene losses. Recent gene gains were either under weak negative selection or neutral. We found evidence for strong divergent selection among populations at individual loci segregating a gene presence–absence polymorphism. Hence, gene gains and losses likely contributed to local adaptation. Our study shows that microbial eukaryotes harbor extensive copy number variation within populations and that functional differences among recently gained and lost genes led to distinct evolutionary trajectories.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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161
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Martín-Sanz A, Rueda S, García-Carneros AB, González-Fernández S, Miranda-Fuentes P, Castuera-Santacruz S, Molinero-Ruiz L. Genetics, Host Range, and Molecular and Pathogenic Characterization of Verticillium dahliae From Sunflower Reveal Two Differentiated Groups in Europe. FRONTIERS IN PLANT SCIENCE 2018; 9:288. [PMID: 29593756 PMCID: PMC5855324 DOI: 10.3389/fpls.2018.00288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/19/2018] [Indexed: 05/13/2023]
Abstract
Verticillium wilt and leaf mottle of sunflower, caused by the fungus Verticillium dahliae (Vd) has become a major constraint to sunflower oil production in temperate European countries. Information about Vd from sunflower is very scarce despite genetics, molecular traits and pathogenic abilities of fungal strains affecting many other crops being widely known. Understanding and characterizing the diversity of Vd populations in those countries where sunflowers are frequent and severely affected by the fungus are essential for efficient breeding for resistance. In this study, we have analyzed genetic, molecular and pathogenic traits of Vd isolates affecting sunflower in European countries. When their genetics was investigated, almost all the isolates from France, Italy, Spain, Argentina, and Ukraine were assigned to vegetative compatibility group (VCG) 2B. In Bulgaria, Turkey, Romania, and Ukraine, some isolates were assigned to VCG6, but some others could not be assigned to any VCG. Genotyping markers used for Vd affecting crops other than sunflower showed that all the isolates were molecularly identified as race 2 and that markers of defoliating (D) and non-defoliating (ND) pathotypes distinguished two well-differentiated clusters, one (E) grouping those isolates from Eastern Europe and the other (W) all those from the Western Europe and Argentina. All the isolates in cluster W were VCG2B, while the isolates in cluster E belonged to an unknown VCG or to VCG6. When the host range was investigated in the greenhouse, the fungus was highly pathogenic to artichoke, showing the importance of farming alternatives in the management of Verticillium attacks. Sunflower genotypes were inoculated with a selection of isolates in two experiments. Two groups were identified, one including the isolates from Western Europe, Argentina, and Ukraine, and the other including isolates from Bulgaria, Romania, and Turkey. Three pathogenic races were differentiated: V1, V2-EE (Eastern Europe) and V2-WE (Western Europe). Similarly, three differentials are proposed for race identification: HA 458 (universal susceptible), HA 89 (resistant to V2-EE, susceptible to V2-WE) and INRA2603 (susceptible to V2-EE, resistant to V2-WE). The diversity found in Vd affecting sunflower must be taken into account in the search for resistance to the pathogen for European environments of sunflower production.
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Affiliation(s)
| | - Sandra Rueda
- Pioneer Hi-Bred International, Inc., La Rinconada, Spain
| | - Ana B. García-Carneros
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
| | - Sara González-Fernández
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
| | - Pedro Miranda-Fuentes
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
| | - Sandra Castuera-Santacruz
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
| | - Leire Molinero-Ruiz
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
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162
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Reem NT, Chen HY, Hur M, Zhao X, Wurtele ES, Li X, Li L, Zabotina O. Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations. PLANT MOLECULAR BIOLOGY 2018; 96:509-529. [PMID: 29502299 DOI: 10.1007/s11103-018-0714-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/25/2018] [Indexed: 06/08/2023]
Abstract
This research provides new insights into plant response to cell wall perturbations through correlation of transcriptome and metabolome datasets obtained from transgenic plants expressing cell wall-modifying enzymes. Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.
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Affiliation(s)
- Nathan T Reem
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, USA
| | - Han-Yi Chen
- Plants for Human Health Institute, North Carolina State University, Kannapolis, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, USA
| | - Manhoi Hur
- Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, USA
| | - Xuefeng Zhao
- Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, USA
- Information Technology, College of Liberal Arts and Sciences, Iowa State University, Ames, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, USA
| | - Xu Li
- Plants for Human Health Institute, North Carolina State University, Kannapolis, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, USA
| | - Ling Li
- Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, USA
- Department of Biological Sciences, Mississippi State University, Starkville, USA
| | - Olga Zabotina
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, USA.
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163
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Fouché S, Plissonneau C, Croll D. The birth and death of effectors in rapidly evolving filamentous pathogen genomes. Curr Opin Microbiol 2018; 46:34-42. [PMID: 29455143 DOI: 10.1016/j.mib.2018.01.020] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/15/2018] [Accepted: 01/31/2018] [Indexed: 11/19/2022]
Abstract
Plant pathogenic fungi and oomycetes are major risks to food security due to their evolutionary success in overcoming plant defences. Pathogens produce effectors to interfere with host defences and metabolism. These effectors are often encoded in rapidly evolving compartments of the genome. We review how effector genes emerged and were lost in pathogen genomes drawing on the links between effector evolution and chromosomal rearrangements. Some new effectors entered pathogen genomes via horizontal transfer or introgression. However, new effector functions also arose through gene duplication or from previously non-coding sequences. The evolutionary success of an effector is tightly linked to its transcriptional regulation during host colonization. Some effectors converged on an epigenetic control of expression imposed by genomic defences against transposable elements. Transposable elements were also drivers of effector diversification and loss that led to mosaics in effector presence-absence variation. Such effector mosaics within species was the foundation for rapid pathogen adaptation.
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Affiliation(s)
- Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Bretignières, BP 01, Thiverval-Grignon F-78850, France
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland.
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164
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Fan R, Cockerton HM, Armitage AD, Bates H, Cascant-Lopez E, Antanaviciute L, Xu X, Hu X, Harrison RJ. Vegetative compatibility groups partition variation in the virulence of Verticillium dahliae on strawberry. PLoS One 2018; 13:e0191824. [PMID: 29451893 PMCID: PMC5815587 DOI: 10.1371/journal.pone.0191824] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/11/2018] [Indexed: 01/07/2023] Open
Abstract
Verticillium dahliae infection of strawberry (Fragaria x ananassa) is a major cause of disease-induced wilting in soil-grown strawberries across the world. To understand what components of the pathogen are affecting disease expression, the presence of the known effector VdAve1 was screened in a sample of Verticillium dahliae isolates. Isolates from strawberry were found to contain VdAve1 and were divided into two major clades, based upon their vegetative compatibility groups (VCG); no UK strawberry isolates contained VdAve1. VC clade was strongly related to their virulence levels. VdAve1-containing isolates pathogenic on strawberry were found in both clades, in contrast to some recently published findings. On strawberry, VdAve1-containing isolates had significantly higher virulence during early infection, which diminished in significance as the infection progressed. Transformation of a virulent non-VdAve1 containing isolate, with VdAve1 was found neither to increase nor decrease virulence when inoculated on a susceptible strawberry cultivar. There are therefore virulence factors that are epistatic to VdAve1 and potentially multiple independent routes to high virulence on strawberry in V. dahliae lineages. Genome sequencing a subset of isolates across the two VCGs revealed that isolates were differentiated at the whole genome level and contained multiple changes in putative effector content, indicating that different clonal VCGs may have evolved different strategies for infecting strawberry, leading to different virulence levels in pathogenicity tests. It is therefore important to consider both clonal lineage and effector complement as the adaptive potential of each lineage will differ, even if they contain the same race determining effector.
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Affiliation(s)
- Rong Fan
- NIAB-EMR, East Malling, Kent, United Kingdom
- State Key Laboratory of Crop Stress Biology for Arid Areas, Department of Plant Pathology, College of Plant Protection, Northwest A&F University, Yangling, China
| | | | | | - Helen Bates
- NIAB-EMR, East Malling, Kent, United Kingdom
| | | | - Laima Antanaviciute
- NIAB-EMR, East Malling, Kent, United Kingdom
- University of Reading, Reading, United Kingdom
| | - Xiangming Xu
- NIAB-EMR, East Malling, Kent, United Kingdom
- State Key Laboratory of Crop Stress Biology for Arid Areas, Department of Plant Pathology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Department of Plant Pathology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Richard J. Harrison
- NIAB-EMR, East Malling, Kent, United Kingdom
- University of Reading, Reading, United Kingdom
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165
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Wang Y, Xu Y, Sun Y, Wang H, Qi J, Wan B, Ye W, Lin Y, Shao Y, Dong S, Tyler BM, Wang Y. Leucine-rich repeat receptor-like gene screen reveals that Nicotiana RXEG1 regulates glycoside hydrolase 12 MAMP detection. Nat Commun 2018; 9:594. [PMID: 29426870 PMCID: PMC5807360 DOI: 10.1038/s41467-018-03010-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 01/12/2018] [Indexed: 12/30/2022] Open
Abstract
Activation of innate immunity by membrane-localized receptors is conserved across eukaryotes. Plant genomes contain hundreds of such receptor-like genes and those encoding proteins with an extracellular leucine-rich repeat (LRR) domain represent the largest family. Here, we develop a high-throughput approach to study LRR receptor-like genes on a genome-wide scale. In total, 257 tobacco rattle virus-based constructs are generated to target 386 of the 403 identified LRR receptor-like genes in Nicotiana benthamiana for silencing. Using this toolkit, we identify the LRR receptor-like protein Response to XEG1 (RXEG1) that specifically recognizes the glycoside hydrolase 12 protein XEG1. RXEG1 associates with XEG1 via the LRR domain in the apoplast and forms a complex with the LRR receptor-like kinases BAK1 and SOBIR1 to transduce the XEG1-induced defense signal. Thus, this genome-wide silencing assay is demonstrated to be an efficient toolkit to pinpoint new immune receptors, which will contribute to developing durable disease resistance.
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Affiliation(s)
- Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Yuanpeng Xu
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Yujing Sun
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Huibin Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Jiaming Qi
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Bowen Wan
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Yachun Lin
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Yuanyuan Shao
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China.
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China.
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166
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Hua C, Zhao JH, Guo HS. Trans-Kingdom RNA Silencing in Plant-Fungal Pathogen Interactions. MOLECULAR PLANT 2018; 11:235-244. [PMID: 29229568 DOI: 10.1016/j.molp.2017.12.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/31/2017] [Accepted: 12/01/2017] [Indexed: 05/02/2023]
Abstract
Fungal pathogens represent a major group of plant invaders that are the causative agents of many notorious plant diseases. Large quantities of RNAs, especially small RNAs involved in gene silencing, have been found to transmit bidirectionally between fungal pathogens and their hosts. Although host-induced gene silencing (HIGS) technology has been developed and applied to protect crops from fungal infections, the mechanisms of RNA transmission, especially small RNAs regulating trans-kingdom RNA silencing in plant immunity, are largely unknown. In this review, we summarize and discuss recent important findings regarding trans-kingdom sRNAs and RNA silencing in plant-fungal pathogen interactions compared with the well-known RNAi mechanisms in plants and fungi. We focus on the interactions between plant and fungal pathogens with broad hosts, represented by the vascular pathogen Verticillium dahliae and non-vascular pathogen Botrytis cinerea, and discuss the known instances of natural RNAi transmission between fungal pathogens and host plants. Given that HIGS has been developed and recently applied in controlling Verticillium wilt diseases, we propose an ideal research system exploiting plant vasculature-Verticillium interaction to further study trans-kingdom RNA silencing.
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Affiliation(s)
- Chenlei Hua
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China; College of Life Science, University of the Chinese Academy of Sciences, 100049 Beijing, China.
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167
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Song Y, Liu L, Wang Y, Valkenburg D, Zhang X, Zhu L, Thomma BPHJ. Transfer of tomato immune receptor Ve1 confers Ave1-dependent Verticillium resistance in tobacco and cotton. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:638-648. [PMID: 28796297 PMCID: PMC5787823 DOI: 10.1111/pbi.12804] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/14/2017] [Accepted: 08/02/2017] [Indexed: 05/24/2023]
Abstract
Verticillium wilts caused by soilborne fungal species of the Verticillium genus are economically important plant diseases that affect a wide range of host plants and are notoriously difficult to combat. Perception of pathogen(-induced) ligands by plant immune receptors is a key component of plant innate immunity. In tomato, race-specific resistance to Verticillium wilt is governed by the cell surface-localized immune receptor Ve1 through recognition of the effector protein Ave1 that is secreted by race 1 strains of Verticillium spp. It was previously demonstrated that transgenic expression of tomato Ve1 in the model plant Arabidopsis thaliana leads to Verticillium wilt resistance. Here, we investigated whether tomato Ve1 can confer Verticillium resistance when expressed in the crop species tobacco (Nicotiana tabcum) and cotton (Gossypium hirsutum). We show that transgenic tobacco and cotton plants constitutively expressing tomato Ve1 exhibit enhanced resistance against Verticillium wilt in an Ave1-dependent manner. Thus, we demonstrate that the functionality of tomato Ve1 in Verticillium wilt resistance through recognition of the Verticillium effector Ave1 is retained after transfer to tobacco and cotton, implying that the Ve1-mediated immune signalling pathway is evolutionary conserved across these plant species. Moreover, our results suggest that transfer of tomato Ve1 across sexually incompatible plant species can be exploited in breeding programmes to engineer Verticillium wilt resistance.
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Affiliation(s)
- Yin Song
- Laboratory of PhytopathologyWageningen UniversityWageningenThe Netherlands
| | - Linlin Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yidong Wang
- Laboratory of PhytopathologyWageningen UniversityWageningenThe Netherlands
| | | | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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168
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Kourelis J, van der Hoorn RAL. Defended to the Nines: 25 Years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function. THE PLANT CELL 2018; 30:285-299. [PMID: 29382771 PMCID: PMC5868693 DOI: 10.1105/tpc.17.00579] [Citation(s) in RCA: 443] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/14/2017] [Accepted: 01/29/2018] [Indexed: 05/18/2023]
Abstract
Plants have many, highly variable resistance (R) gene loci, which provide resistance to a variety of pathogens. The first R gene to be cloned, maize (Zea mays) Hm1, was published over 25 years ago, and since then, many different R genes have been identified and isolated. The encoded proteins have provided clues to the diverse molecular mechanisms underlying immunity. Here, we present a meta-analysis of 314 cloned R genes. The majority of R genes encode cell surface or intracellular receptors, and we distinguish nine molecular mechanisms by which R proteins can elevate or trigger disease resistance: direct (1) or indirect (2) perception of pathogen-derived molecules on the cell surface by receptor-like proteins and receptor-like kinases; direct (3) or indirect (4) intracellular detection of pathogen-derived molecules by nucleotide binding, leucine-rich repeat receptors, or detection through integrated domains (5); perception of transcription activator-like effectors through activation of executor genes (6); and active (7), passive (8), or host reprogramming-mediated (9) loss of susceptibility. Although the molecular mechanisms underlying the functions of R genes are only understood for a small proportion of known R genes, a clearer understanding of mechanisms is emerging and will be crucial for rational engineering and deployment of novel R genes.
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Affiliation(s)
- Jiorgos Kourelis
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
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169
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Yang Y, Chen T, Ling X, Ma Z. Gbvdr6, a Gene Encoding a Receptor-Like Protein of Cotton ( Gossypium barbadense), Confers Resistance to Verticillium Wilt in Arabidopsis and Upland Cotton. FRONTIERS IN PLANT SCIENCE 2018; 8:2272. [PMID: 29387078 PMCID: PMC5776133 DOI: 10.3389/fpls.2017.02272] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 12/29/2017] [Indexed: 05/23/2023]
Abstract
Verticillium wilt is a soil-borne disease that can cause devastating losses in cotton production. Because there is no effective chemical means to combat the disease, the only effective way to control Verticillium wilt is through genetic improvement. Therefore, the identification of additional disease-resistance genes will benefit efforts toward the genetic improvement of cotton resistance to Verticillium wilt. Based on screening of a BAC library with a partial Ve homologous fragment and expression analysis, a V. dahliae-induced gene, Gbvdr6, was isolated and cloned from the Verticillium wilt-resistant cotton G. barbadense cultivar Hai7124. The gene was located in the gene cluster containing Gbve1 and Gbvdr5 and adjacent to the Verticillium wilt-resistance QTL hotspot. Gbvdr6 was induced by Verticillium dahliae Kleb and by the plant hormones salicylic acid (SA), methyl jasmonate (MeJA) and ethephon (ETH) but not by abscisic acid (ABA). Gbvdr6 was localized to the plasma membrane. Overexpression of Gbvdr6 in Arabidopsis and cotton enhanced resistance to V. dahliae. Moreover, the JA/ET signaling pathway-related genes PR3, PDF 1.2, ERF1 and the SA-related genes PR1 and PR2 were constitutively expressed in transgenic plants. Gbvdr6-overexpressing Arabidopsis was less sensitive than the wild-type plant to MeJA. Furthermore, the accumulation of reactive oxygen species and callose was triggered at early time points after V. dahliae infection. These results suggest that Gbvdr6 confers resistance to V. dahliae through regulation of the JA/ET and SA signaling pathways.
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Affiliation(s)
- Yuwen Yang
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xitie Ling
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhengqiang Ma
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Center, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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170
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Shi-Kunne X, Faino L, van den Berg GCM, Thomma BPHJ, Seidl MF. Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss. Environ Microbiol 2018; 20:1362-1373. [PMID: 29282842 DOI: 10.1111/1462-2920.14037] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 01/09/2023]
Abstract
The fungal genus Verticillium contains ten species, some of which are notorious plant pathogens causing vascular wilt diseases in host plants, while others are known as saprophytes and opportunistic plant pathogens. Whereas the genome of V. dahliae, the most notorious plant pathogen of the genus, has been well characterized, evolution and speciation of other members of the genus received little attention thus far. Here, we sequenced the genomes of the nine haploid Verticillium spp. to study evolutionary trajectories of their divergence from a last common ancestor. Frequent occurrence of chromosomal rearrangement and gene family loss was identified. In addition to ∼11 000 genes that are shared at least between two species, only 200-600 species-specific genes occur. Intriguingly, these species-specific genes show different features than the shared genes.
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Affiliation(s)
- Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
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171
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Li NY, Zhou L, Zhang DD, Klosterman SJ, Li TG, Gui YJ, Kong ZQ, Ma XF, Short DPG, Zhang WQ, Li JJ, Subbarao KV, Chen JY, Dai XF. Heterologous Expression of the Cotton NBS-LRR Gene GbaNA1 Enhances Verticillium Wilt Resistance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:119. [PMID: 29467784 PMCID: PMC5808209 DOI: 10.3389/fpls.2018.00119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/22/2018] [Indexed: 05/06/2023]
Abstract
Verticillium wilt caused by Verticillium dahliae results in severe losses in cotton, and is economically the most destructive disease of this crop. Improving genetic resistance is the cleanest and least expensive option to manage Verticillium wilt. Previously, we identified the island cotton NBS-LRR-encoding gene GbaNA1 that confers resistance to the highly virulent V. dahliae isolate Vd991. In this study, we expressed cotton GbaNA1 in the heterologous system of Arabidopsis thaliana and investigated the defense response mediated by GbaNA1 following inoculations with V. dahliae. Heterologous expression of GbaNA1 conferred Verticillium wilt resistance in A. thaliana. Moreover, overexpression of GbaNA1 enabled recovery of the resistance phenotype of A. thaliana mutants that had lost the function of GbaNA1 ortholog gene. Investigations of the defense response in A. thaliana showed that the reactive oxygen species (ROS) production and the expression of genes associated with the ethylene signaling pathway were enhanced significantly following overexpression of GbaNA1. Intriguingly, overexpression of the GbaNA1 ortholog from Gossypium hirsutum (GhNA1) in A. thaliana did not induce the defense response of ROS production due to the premature termination of GhNA1, which lacks the encoded NB-ARC and LRR motifs. GbaNA1 therefore confers Verticillium wilt resistance in A. thaliana by the activation of ROS production and ethylene signaling. These results demonstrate the functional conservation of the NBS-LRR-encoding GbaNA1 in a heterologous system, and the mechanism of this resistance, both of which may prove valuable in incorporating GbaNA1-mediated resistance into other plant species.
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Affiliation(s)
- Nan-Yang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Steven J. Klosterman
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA, United States
| | - Ting-Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Yue-Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Zhi-Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Xue-Feng Ma
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Dylan P. G. Short
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Wen-Qi Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Jun-Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Krishna V. Subbarao
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- *Correspondence: Xiao-Feng Dai, Jie-Yin Chen, Krishna V. Subbarao,
| | - Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
- *Correspondence: Xiao-Feng Dai, Jie-Yin Chen, Krishna V. Subbarao,
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
- *Correspondence: Xiao-Feng Dai, Jie-Yin Chen, Krishna V. Subbarao,
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172
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Xiao W, He H, Tong Y, Cai M, Shi Y, Liu B, Wang J, Qin Y, Lai S. Transcriptome analysis of Trichophyton mentagrophytes–induced rabbit (Oryctolagus cuniculus) dermatophytosis. Microb Pathog 2018; 114:350-356. [DOI: 10.1016/j.micpath.2017.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/01/2017] [Accepted: 12/06/2017] [Indexed: 12/28/2022]
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173
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Song Y, Thomma BPHJ. Host-induced gene silencing compromises Verticillium wilt in tomato and Arabidopsis. MOLECULAR PLANT PATHOLOGY 2018; 19:77-89. [PMID: 27749994 PMCID: PMC6638114 DOI: 10.1111/mpp.12500] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 05/03/2023]
Abstract
Verticillium wilt, caused by soil-borne fungi of the genus Verticillium, is an economically important disease that affects a wide range of host plants. Unfortunately, host resistance against Verticillium wilts is not available for many plant species, and the disease is notoriously difficult to combat. Host-induced gene silencing (HIGS) is an RNA interference (RNAi)-based process in which small RNAs are produced by the host plant to target parasite transcripts. HIGS has emerged as a promising strategy for the improvement of plant resistance against pathogens by silencing genes that are essential for these pathogens. Here, we assessed whether HIGS can be utilized to suppress Verticillium wilt disease by silencing three previously identified virulence genes of V. dahliae (encoding Ave1, Sge1 and NLP1) through the host plants tomato and Arabidopsis. In transient assays, tomato plants were agroinfiltrated with Tobacco rattle virus (TRV) constructs to target V. dahliae transcripts. Subsequent V. dahliae inoculation revealed the suppression of Verticillium wilt disease on treatment with only one of the three TRV constructs. Next, expression of RNAi constructs targeting transcripts of the same three V. dahliae virulence genes was pursued in stable transgenic Arabidopsis thaliana plants. In this host, V. dahliae inoculation revealed reduced Verticillium wilt disease in two of the three targets. Thus, our study suggests that, depending on the target gene chosen, HIGS against V. dahliae is operational in tomato and A. thaliana plants and may be exploited to engineer resistance in Verticillium wilt-susceptible crops.
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Affiliation(s)
- Yin Song
- Laboratory of PhytopathologyWageningen University, Droevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen University, Droevendaalsesteeg 1Wageningen6708 PBthe Netherlands
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174
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Zhao J, Liu J, Xu J, Zhao L, Wu Q, Xiao S. Quantitative Trait Locus Mapping and Candidate Gene Analysis for Verticillium Wilt Resistance Using Gossypium barbadense Chromosomal Segment Introgressed Line. FRONTIERS IN PLANT SCIENCE 2018; 9:682. [PMID: 29899750 PMCID: PMC5988901 DOI: 10.3389/fpls.2018.00682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/03/2018] [Indexed: 05/08/2023]
Abstract
Verticillium wilt (VW) is a soil-borne fungal disease that is caused by Verticillium dahliae Kleb and seriously damages cotton production annually in China. To date, many efforts have been made to improve the resistance of upland cotton against VW, but little progress has been achieved because of a lack of resistant upland cotton to VW. G. barbadense is known to carry high resistance to VW; however, it is difficult to transfer the resistance trait from G. barbadense to upland cotton because of linkage drag and distortion in the interspecific hybrid. In this study, a chromosomal segment introgression line (CSIL), SuVR043, containing a single and homozygous chromosome segment of G. barbadense cv. H7124 D04 (Chr 22), was created and used to construct an F2 population for mapping of VW resistance quantitative trait loci (QTLs) in the greenhouse. Two major resistance QTLs against nondefoliating V. dahliae isolate Bp2, called qVW-Bp2-1 and qVW-Bp2-2, which were flanked by the markers cgr6409-ZHX37 and ZHX57-ZHX70 and explained an average of 16.38 and 22.36% of the observed phenotypic variation, respectively, were detected in three independent replicate experiments. The genetic distances from cgr6409 to ZHX37 and from ZHX57 to ZHX70 were 2.4 and 0.8 cM, respectively. By analyzing the genome sequence of the qVW-Bp2-1 and qVW-Bp2-2 regions, we determined that the accurate physical distances from cgr6409 to ZHX37 and from ZHX57 to ZHX70 in the G. barbadense genome are 254 and 140 kb, and that those spans 36 and 20 putative genes, respectively. The results of the expression analysis showed significant differences in the expression profiles of GbCYP450, GbTMEM214, and GbRLK among G. barbadense cv. H7124, CSIL SuVR043 and G. hirsutum acc. Sumian 8 at different times after inoculation with V. dahliae isolate Bp2. Virus-induced gene silencing (VIGS) analysis showed that silencing of GbCYP450 and GbTMEM214 decreased H7124 and CSIL SuVR043 resistance to VW. These results form a solid foundation for fine mapping and cloning of resistance genes in the substituted segment and will provide valuable assistance in future efforts to breed for VW resistance.
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Affiliation(s)
- Jun Zhao
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jianguang Liu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jianwen Xu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Liang Zhao
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qiaojuan Wu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Songhua Xiao
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- *Correspondence: Songhua Xiao
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175
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Leyva-Pérez MDLO, Jiménez-Ruiz J, Gómez-Lama Cabanás C, Valverde-Corredor A, Barroso JB, Luque F, Mercado-Blanco J. Tolerance of olive (Olea europaea) cv Frantoio to Verticillium dahliae relies on both basal and pathogen-induced differential transcriptomic responses. THE NEW PHYTOLOGIST 2018; 217:671-686. [PMID: 29023762 DOI: 10.1111/nph.14833] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/26/2017] [Indexed: 05/20/2023]
Abstract
Verticillium wilt of olive (VWO) is one of the most serious biotic constraints for this tree crop. Our knowledge of the genetics of the tolerance/resistance to this disease is very limited. Here we show that tolerance of the cv Frantoio relies on both basal and early pathogen-induced differential transcriptomic responses. A comparative transcriptomic analysis (RNA-seq) was conducted in root tissues of cvs Frantoio (VWO-tolerant) and Picual (VWO-susceptible). RNA samples originated from roots of inoculated olive plants during the early infection stages by Verticillium dahliae (highly virulent, defoliating pathotype). A huge number of differentially expressed genes (DEGs) were found between 'Frantoio' and 'Picual' (27 312 unigenes) in the absence of the pathogen. Upon infection with V. dahliae, 'Picual' and 'Frantoio' plants responded differently too. In the early infection stages, four clusters of DEGs could be identified according to their time-course expression patterns. Among others, a pathogenesis-related protein of the Bet v I family and a dirigent-like protein involved in lignification, and several BAK1, NHL1, reactive oxygen species stress response and BAM unigenes showed noticeable differences between cultivars. Tolerance of 'Frantoio' plants to VWO is a consequence of a complex and multifaceted process which involves many plant traits.
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Affiliation(s)
- María de la O Leyva-Pérez
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of Jaén, Jaén, 23071, Spain
| | - Jaime Jiménez-Ruiz
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of Jaén, Jaén, 23071, Spain
| | - Carmen Gómez-Lama Cabanás
- Department of Crop Protection, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Campus 'Alameda del Obispo', Avenida Menéndez Pidal s/n, Apartado, Córdoba, 14004, Spain
| | - Antonio Valverde-Corredor
- Department of Crop Protection, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Campus 'Alameda del Obispo', Avenida Menéndez Pidal s/n, Apartado, Córdoba, 14004, Spain
| | - Juan B Barroso
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of Jaén, Jaén, 23071, Spain
| | - Francisco Luque
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of Jaén, Jaén, 23071, Spain
| | - Jesús Mercado-Blanco
- Department of Crop Protection, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Campus 'Alameda del Obispo', Avenida Menéndez Pidal s/n, Apartado, Córdoba, 14004, Spain
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176
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Li X, Pei Y, Sun Y, Liu N, Wang P, Liu D, Ge X, Li F, Hou Y. A Cotton Cyclin-Dependent Kinase E Confers Resistance to Verticillium dahliae Mediated by Jasmonate-Responsive Pathway. FRONTIERS IN PLANT SCIENCE 2018; 9:642. [PMID: 29881391 PMCID: PMC5976743 DOI: 10.3389/fpls.2018.00642] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/26/2018] [Indexed: 05/20/2023]
Abstract
Many subunits of the Mediator transcriptional co-activator complex are multifunctional proteins that regulate plant immunity in Arabidopsis. Cotton cyclin-dependent kinase E (GhCDKE), which is a subunit of the cotton (Gossypium hirsutum) Mediator complex, has been annotated, but the biological functions of this gene associated with regulating disease resistance have not been characterized. Here, we cloned GhCDKE from cotton and confirmed that GhCDKE belonged to the E-type CDK family in the phylogenetic tree, and, as in other eukaryotes, we found that GhCDKE interacted with C-type cyclin (GhCycC) by yeast two-hybrid and luciferase complementation imaging assays. Expression of GhCDKE in cotton was induced by Verticillium dahliae infection and MeJA treatment, and silencing of GhCDKE expression in cotton led to enhanced susceptibility to V. dahliae, while overexpression of GhCDKE in Arabidopsis thaliana enhanced resistance to this pathogen. Transgenic expression assay demonstrated that the transcriptional activity of GhPDF1.2pro:LUC in GhCDKE-silenced cotton was dramatically inhibited. In addition, the expression of jasmonic acid (JA)-regulated pathogen-responsive genes was dramatically upregulated in GhCDKE-overexpressed plants after inoculation with V. dahliae, and the roots of GhCDKE-overexpressed A. thaliana were more susceptible to JA treatment. These results indicated that GhCDKE regulates resistance against V. dahliae and that this resistance is mediated by JA response pathway.
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Affiliation(s)
- Xiancai Li
- College of Science, China Agricultural University, Beijing, China
| | - Yakun Pei
- College of Science, China Agricultural University, Beijing, China
| | - Yun Sun
- College of Science, China Agricultural University, Beijing, China
| | - Nana Liu
- College of Science, China Agricultural University, Beijing, China
| | - Ping Wang
- College of Science, China Agricultural University, Beijing, China
| | - Di Liu
- College of Science, China Agricultural University, Beijing, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Fuguang Li, Yuxia Hou,
| | - Yuxia Hou
- College of Science, China Agricultural University, Beijing, China
- *Correspondence: Fuguang Li, Yuxia Hou,
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177
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Wang Y, Wang Y. Trick or Treat: Microbial Pathogens Evolved Apoplastic Effectors Modulating Plant Susceptibility to Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:6-12. [PMID: 29090656 DOI: 10.1094/mpmi-07-17-0177-fi] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The apoplastic space between the plant cell wall and the plasma membrane constitutes a major battleground for plant-pathogen interactions. To survive in harsh conditions in the plant apoplast, pathogens must cope with various immune responses. During infection, plant pathogens secrete an arsenal of effector proteins into the apoplast milieu, some of which are detected by the plant surveillance system and, thus, activate plant innate immunity. Effectors that evade plant perception act in modulating plant apoplast immunity to favor successful pathogen infection. The concerted actions of apoplastic effectors often determine the outcomes of plant-pathogen interactions. In this review, we summarize current advances on the understanding of apoplastic effectors and highlight the strategies employed by pathogens to counter host apoplastic defense.
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Affiliation(s)
- Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, 210095, China
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178
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Castroverde CD, Xu X, Nazar RN, Robb J. Biotic factors that induce the tomato Ve1 R-gene. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:61-69. [PMID: 29223343 DOI: 10.1016/j.plantsci.2017.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/11/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
In tomato, Verticillium resistance is determined by the Ve gene locus encoding two leucine-rich repeat-receptor-like proteins (Ve1, Ve2). The resistance function usually is attributed to Ve1 alone, with two known alleles: Ve1, encoding a resistance protein, and ve1, with a premature stop codon encoding a truncated product. We have examined further Ve-gene expression in resistant and susceptible near-isolines of Verticillium-infected Craigella tomatoes, using both quantitative RT-PCR and an alternative RFLP assay. Ve1 is induced differentially in resistant and susceptible plants, while Ve2 is constitutively expressed throughout disease development. Contrary to their putative role in Verticillium resistance, these profiles were observed even with compatible Verticillium interactions, some bacterial pathogens, and transgenic tomato plants expressing the fungal Ave1 effector. This suggests broader roles in disease and/or stress. To determine the contribution of plant hormones, abscisic acid, methyl jasmonate, naphthaleneacetic acid or salicylic acid were infused independently via the tomato root and effects on Ve1 induction were confirmed using biosynthesis mutants. While all the hormones modulated Ve1-gene induction, abscisic acid and salicylic acid were not required while jasmonic acid appears to play a more direct role.
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Affiliation(s)
| | - Xin Xu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ross N Nazar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jane Robb
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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179
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Hind SR, Hoki JS, Baccile JA, Boyle PC, Schroeder FC, Martin GB. Detecting the interaction of peptide ligands with plant membrane receptors. ACTA ACUST UNITED AC 2017; 2:240-269. [PMID: 29098191 DOI: 10.1002/cppb.20053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The field of plant receptor biology has rapidly expanded in recent years, however the demonstration of direct interaction between receptor-ligand pairs remains a challenge. Click chemistry has revolutionized small molecule research but lacks popularity in plant research. Here we describe a method that tests for the direct physical interaction of a candidate receptor protein and a peptide ligand. This protocol describes the generation of the ligand probe, transient expression of a receptor protein, enrichment of membrane-bound receptors, photo-crosslinking and click chemistry-mediated reporter addition, and detection of the receptor-ligand complex. Copper-based click chemistry confers several advantages, including the versatility to use almost any azide-containing reporter molecule for detection or visualization of the complex and addition of the reporter molecule after receptor-ligand binding which reduces the need for bulky ligand modifications that could interfere with the interaction.
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Affiliation(s)
| | - Jason S Hoki
- Boyce Thompson Institute, Ithaca, New York.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Joshua A Baccile
- Boyce Thompson Institute, Ithaca, New York.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | | | - Frank C Schroeder
- Boyce Thompson Institute, Ithaca, New York.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Gregory B Martin
- Boyce Thompson Institute, Ithaca, New York.,School of Integrative Plant Science, Cornell University, Ithaca, New York
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180
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Puri KD, Gurung S, Short DPG, Atallah ZK, Sandoya G, Davis RM, Hayes RJ, Subbarao KV. Short-Term Host Selection Pressure Has Little Effect on the Evolution of a Monoclonal Population of Verticillium dahliae Race 1. PHYTOPATHOLOGY 2017; 107:1417-1425. [PMID: 28653580 DOI: 10.1094/phyto-02-17-0071-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding pathogen evolution over time is vital for plant breeding and deployment of host resistance. In the context of a soilborne pathogen, the potential of host-directed evolution of a Verticillium dahliae race 1 isolate and genotypic variation of V. dahliae associated with two major hosts (lettuce and tomato) were determined. In total, 427 isolates were recovered over 6 years from a resistance screening nursery infested with a single V. dahliae race 1 isolate. In a separate study, an additional 206 isolates representing 163 and 43 isolates from commercial lettuce and tomato fields, respectively, were collected. Analyses of isolates recovered from the screening nursery over 6 years revealed no changes in the race and mating type composition but did uncover seven simple sequence repeat (SSR) variant genotypes. No significant genotypic variation in V. dahliae was observed between or within fields of either lettuce or tomato but pathogen populations were significantly differentiated between these two hosts. Replicated virulence assays of variant SSR genotypes on lettuce differential cultivars suggested no significant difference in virulence from the wild-type race 1 isolate introduced into the field. This suggests that deployed race 1 host resistance will be robust against the widespread race 1 populations in lettuce-growing regions at least for 6 years unless novel pathogen genotypes or races are introduced into the system.
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Affiliation(s)
- Krishna D Puri
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Suraj Gurung
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Dylan P G Short
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Z K Atallah
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - German Sandoya
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - R Michael Davis
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Ryan J Hayes
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
| | - Krishna V Subbarao
- First, third, sixth, and eighth authors: Department of Plant Pathology, University of California, Davis; second author: Sakata Seed America, Salinas, CA; fourth author: Hartnell College, Salinas, CA 93905; fifth author: Department of Horticultural Science, Everglades Research and Education Center, University of Florida, Belle Glade; and seventh author: United States Department of Agriculture-Agricultural Research Service, Salinas, CA
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181
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Gehring C, Turek IS. Cyclic Nucleotide Monophosphates and Their Cyclases in Plant Signaling. FRONTIERS IN PLANT SCIENCE 2017; 8:1704. [PMID: 29046682 PMCID: PMC5632652 DOI: 10.3389/fpls.2017.01704] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/19/2017] [Indexed: 05/19/2023]
Abstract
The cyclic nucleotide monophosphates (cNMPs), and notably 3',5'-cyclic guanosine monophosphate (cGMP) and 3',5'-cyclic adenosine monophosphate (cAMP) are now accepted as key signaling molecules in many processes in plants including growth and differentiation, photosynthesis, and biotic and abiotic defense. At the single molecule level, we are now beginning to understand how cNMPs modify specific target molecules such as cyclic nucleotide-gated channels, while at the systems level, a recent study of the Arabidopsis cNMP interactome has identified novel target molecules with specific cNMP-binding domains. A major advance came with the discovery and characterization of a steadily increasing number of guanylate cyclases (GCs) and adenylate cyclases (ACs). Several of the GCs are receptor kinases and include the brassinosteroid receptor, the phytosulfokine receptor, the Pep receptor, the plant natriuretic peptide receptor as well as a nitric oxide sensor. We foresee that in the near future many more molecular mechanisms and biological roles of GCs and ACs and their catalytic products will be discovered and further establish cNMPs as a key component of plant responses to the environment.
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Affiliation(s)
- Chris Gehring
- Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Ilona S. Turek
- Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Leibniz Institute of Plant Biochemistry, Halle, Germany
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182
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Gervais J, Plissonneau C, Linglin J, Meyer M, Labadie K, Cruaud C, Fudal I, Rouxel T, Balesdent M. Different waves of effector genes with contrasted genomic location are expressed by Leptosphaeria maculans during cotyledon and stem colonization of oilseed rape. MOLECULAR PLANT PATHOLOGY 2017; 18:1113-1126. [PMID: 27474899 PMCID: PMC6638281 DOI: 10.1111/mpp.12464] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Leptosphaeria maculans, the causal agent of stem canker disease, colonizes oilseed rape (Brassica napus) in two stages: a short and early colonization stage corresponding to cotyledon or leaf colonization, and a late colonization stage during which the fungus colonizes systemically and symptomlessly the plant during several months before stem canker appears. To date, the determinants of the late colonization stage are poorly understood; L. maculans may either successfully escape plant defences, leading to stem canker development, or the plant may develop an 'adult-stage' resistance reducing canker incidence. To obtain an insight into these determinants, we performed an RNA-sequencing (RNA-seq) pilot project comparing fungal gene expression in infected cotyledons and in symptomless or necrotic stems. Despite the low fraction of fungal material in infected stems, sufficient fungal transcripts were detected and a large number of fungal genes were expressed, thus validating the feasibility of the approach. Our analysis showed that all avirulence genes previously identified are under-expressed during stem colonization compared with cotyledon colonization. A validation RNA-seq experiment was then performed to investigate the expression of candidate effector genes during systemic colonization. Three hundred and seven 'late' effector candidates, under-expressed in the early colonization stage and over-expressed in the infected stems, were identified. Finally, our analysis revealed a link between the regulation of expression of effectors and their genomic location: the 'late' effector candidates, putatively involved in systemic colonization, are located in gene-rich genomic regions, whereas the 'early' effector genes, over-expressed in the early colonization stage, are located in gene-poor regions of the genome.
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Affiliation(s)
- Julie Gervais
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Clémence Plissonneau
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Juliette Linglin
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Michel Meyer
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Karine Labadie
- CEA‐Institut de Génomique, GENOSCOPECentre National de SéquençageEvry CedexFrance
| | - Corinne Cruaud
- CEA‐Institut de Génomique, GENOSCOPECentre National de SéquençageEvry CedexFrance
| | - Isabelle Fudal
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
| | - Marie‐Hélène Balesdent
- UMR BIOGER, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, BP 01Thiverval‐GrignonF‐78850France
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183
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Progar V, Jakše J, Štajner N, Radišek S, Javornik B, Berne S. Comparative transcriptional analysis of hop responses to infection with Verticillium nonalfalfae. PLANT CELL REPORTS 2017; 36:1599-1613. [PMID: 28698905 PMCID: PMC5602066 DOI: 10.1007/s00299-017-2177-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/04/2017] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Dynamic transcriptome profiling revealed excessive, yet ineffective, immune response to V. nonalfalfae infection in susceptible hop, global gene downregulation in shoots of resistant hop and only a few infection-associated genes in roots. Hop (Humulus lupulus L.) production is hampered by Verticillium wilt, a disease predominantly caused by the soil-borne fungus Verticillium nonalfalfae. Only a few hop cultivars exhibit resistance towards it and mechanisms of this resistance have not been discovered. In this study, we compared global transcriptional responses in roots and shoots of resistant and susceptible hop plants infected by a lethal strain of V. nonalfalfae. Time-series differential gene expression profiles between infected and mock inoculated plants were determined and subjected to network-based analysis of functional enrichment. In the resistant hop cultivar, a remarkably low number of genes were differentially expressed in roots in response to V. nonalfalfae infection, while the majority of differentially expressed genes were down-regulated in shoots. The most significantly affected genes were related to cutin biosynthesis, cell wall biogenesis, lateral root development and terpenoid biosynthesis. On the other hand, susceptible hop exhibited a strong defence response in shoots and roots, including increased expression of genes associated with plant responses, such as innate immunity, wounding, jasmonic acid pathway and chitinase activity. Strong induction of defence-associated genes in susceptible hop and a low number of infection-responsive genes in the roots of resistant hop are consistent with previous findings, confirming the pattern of excessive response of the susceptible cultivar, which ultimately fails to protect the plant from V. nonalfalfae. This research offers a multifaceted overview of transcriptional responses of susceptible and resistant hop cultivars to V. nonalfalfae infection and represents a valuable resource in the study of this plant-pathogen interaction.
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Affiliation(s)
- Vasja Progar
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sebastjan Radišek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, Žalec, Slovenia
| | - Branka Javornik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sabina Berne
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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184
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Seidl MF, Thomma BPHJ. Transposable Elements Direct The Coevolution between Plants and Microbes. Trends Genet 2017; 33:842-851. [PMID: 28800915 DOI: 10.1016/j.tig.2017.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/24/2017] [Accepted: 07/14/2017] [Indexed: 12/31/2022]
Abstract
Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as 'selfish' genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host-microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a 'two-speed' genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.
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Affiliation(s)
- Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
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185
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Möller M, Stukenbrock EH. Evolution and genome architecture in fungal plant pathogens. Nat Rev Microbiol 2017; 15:756-771. [DOI: 10.1038/nrmicro.2017.76] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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186
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Yu X, Feng B, He P, Shan L. From Chaos to Harmony: Responses and Signaling upon Microbial Pattern Recognition. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:109-137. [PMID: 28525309 PMCID: PMC6240913 DOI: 10.1146/annurev-phyto-080516-035649] [Citation(s) in RCA: 301] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pathogen- or microbe-associated molecular patterns (PAMPs/MAMPs) are detected as nonself by host pattern recognition receptors (PRRs) and activate pattern-triggered immunity (PTI). Microbial invasions often trigger the production of host-derived endogenous signals referred to as danger- or damage-associated molecular patterns (DAMPs), which are also perceived by PRRs to modulate PTI responses. Collectively, PTI contributes to host defense against infections by a broad range of pathogens. Remarkable progress has been made toward demonstrating the cellular and physiological responses upon pattern recognition, elucidating the molecular, biochemical, and genetic mechanisms of PRR activation, and dissecting the complex signaling networks that orchestrate PTI responses. In this review, we present an update on the current understanding of how plants recognize and respond to nonself patterns, a process from which the seemingly chaotic responses form into a harmonic defense.
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Affiliation(s)
- Xiao Yu
- Department of Plant Pathology and Microbiology and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843;
| | - Baomin Feng
- Department of Biochemistry and Biophysics and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843
| | - Ping He
- Department of Biochemistry and Biophysics and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843
| | - Libo Shan
- Department of Plant Pathology and Microbiology and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843;
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187
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Boutrot F, Zipfel C. Function, Discovery, and Exploitation of Plant Pattern Recognition Receptors for Broad-Spectrum Disease Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:257-286. [PMID: 28617654 DOI: 10.1146/annurev-phyto-080614-120106] [Citation(s) in RCA: 393] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants are constantly exposed to would-be pathogens and pests, and thus have a sophisticated immune system to ward off these threats, which otherwise can have devastating ecological and economic consequences on ecosystems and agriculture. Plants employ receptor kinases (RKs) and receptor-like proteins (RLPs) as pattern recognition receptors (PRRs) to monitor their apoplastic environment and detect non-self and damaged-self patterns as signs of potential danger. Plant PRRs contribute to both basal and non-host resistances, and treatment with pathogen-/microbe-associated molecular patterns (PAMPs/MAMPs) or damage-associated molecular patterns (DAMPs) recognized by plant PRRs induces both local and systemic immunity. Here, we comprehensively review known PAMPs/DAMPs recognized by plants as well as the plant PRRs described to date. In particular, we describe the different methods that can be used to identify PAMPs/DAMPs and PRRs. Finally, we emphasize the emerging biotechnological potential use of PRRs to improve broad-spectrum, and potentially durable, disease resistance in crops.
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Affiliation(s)
- Freddy Boutrot
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
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188
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Thynne E, Saur IML, Simbaqueba J, Ogilvie HA, Gonzalez‐Cendales Y, Mead O, Taranto A, Catanzariti A, McDonald MC, Schwessinger B, Jones DA, Rathjen JP, Solomon PS. Fungal phytopathogens encode functional homologues of plant rapid alkalinization factor (RALF) peptides. MOLECULAR PLANT PATHOLOGY 2017; 18:811-824. [PMID: 27291634 PMCID: PMC6638259 DOI: 10.1111/mpp.12444] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 05/19/2023]
Abstract
In this article, we describe the presence of genes encoding close homologues of an endogenous plant peptide, rapid alkalinization factor (RALF), within the genomes of 26 species of phytopathogenic fungi. Members of the RALF family are key growth factors in plants, and the sequence of the RALF active region is well conserved between plant and fungal proteins. RALF1-like sequences were observed in most cases; however, RALF27-like sequences were present in the Sphaerulina musiva and Septoria populicola genomes. These two species are pathogens of poplar and, interestingly, the closest relative to their respective RALF genes is a poplar RALF27-like sequence. RALF peptides control cellular expansion during plant development, but were originally defined on the basis of their ability to induce rapid alkalinization in tobacco cell cultures. To test whether the fungal RALF peptides were biologically active in plants, we synthesized RALF peptides corresponding to those encoded by two sequenced genomes of the tomato pathogen Fusarium oxysporum f. sp. lycopersici. One of these peptides inhibited the growth of tomato seedlings and elicited responses in tomato and Nicotiana benthamiana typical of endogenous plant RALF peptides (reactive oxygen species burst, induced alkalinization and mitogen-activated protein kinase activation). Gene expression analysis confirmed that a RALF-encoding gene in F. oxysporum f. sp. lycopersici was expressed during infection on tomato. However, a subsequent reverse genetics approach revealed that the RALF peptide was not required by F. oxysporum f. sp. lycopersici for infection on tomato roots. This study has demonstrated the presence of functionally active RALF peptides encoded within phytopathogens that harbour an as yet undetermined role in plant-pathogen interactions.
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Affiliation(s)
- Elisha Thynne
- Plant Sciences DivisionThe Australian National UniversityCanberra2601Australia
| | - Isabel M. L. Saur
- Plant Sciences DivisionThe Australian National UniversityCanberra2601Australia
| | - Jaime Simbaqueba
- Plant Sciences DivisionThe Australian National UniversityCanberra2601Australia
| | - Huw A. Ogilvie
- Evolution, Ecology and Genetics Division, Research School of BiologyThe Australian National UniversityCanberra2601Australia
- Computational Evolution Group, The University of AucklandAuckland1142New Zealand
| | | | - Oliver Mead
- Plant Sciences DivisionThe Australian National UniversityCanberra2601Australia
| | - Adam Taranto
- Plant Sciences DivisionThe Australian National UniversityCanberra2601Australia
| | | | - Megan C. McDonald
- Plant Sciences DivisionThe Australian National UniversityCanberra2601Australia
| | | | - David A. Jones
- Plant Sciences DivisionThe Australian National UniversityCanberra2601Australia
| | - John P. Rathjen
- Plant Sciences DivisionThe Australian National UniversityCanberra2601Australia
| | - Peter S. Solomon
- Plant Sciences DivisionThe Australian National UniversityCanberra2601Australia
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189
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Abstract
The interactions between fungi and plants encompass a spectrum of ecologies ranging from saprotrophy (growth on dead plant material) through pathogenesis (growth of the fungus accompanied by disease on the plant) to symbiosis (growth of the fungus with growth enhancement of the plant). We consider pathogenesis in this article and the key roles played by a range of pathogen-encoded molecules that have collectively become known as effectors.
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190
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Zhang L, Ni H, Du X, Wang S, Ma XW, Nürnberger T, Guo HS, Hua C. The Verticillium-specific protein VdSCP7 localizes to the plant nucleus and modulates immunity to fungal infections. THE NEW PHYTOLOGIST 2017; 215:368-381. [PMID: 28407259 DOI: 10.1111/nph.14537] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/21/2017] [Indexed: 05/05/2023]
Abstract
Fungal pathogens secrete effector proteins to suppress plant basal defense for successful colonization. Resistant plants, however, can recognize effectors by cognate R proteins to induce effector-triggered immunity (ETI). By analyzing secretomes of the vascular fungal pathogen Verticillium dahliae, we identified a novel secreted protein VdSCP7 that targets the plant nucleus. The green fluorescent protein (GFP)-tagged VdSCP7 gene with either a mutated nuclear localization signal motif or with additional nuclear export signal was transiently expressed in Nicotiana benthamiana, and investigated for induction of plant immunity. The role of VdSCP7 in V. dahliae pathogenicity was characterized by gene knockout and complementation, and GFP labeling. Expression of the VdSCP7 gene in N. benthamiana activated both salicylic acid and jasmonate signaling, and altered the plant's susceptibility to the pathogens Botrytis cinerea and Phytophthora capsici. The immune response activated by VdSCP7 was highly dependent on its initial extracellular secretion and subsequent nuclear localization in plants. Knockout of the VdSCP7 gene significantly enhanced V. dahliae aggressiveness on cotton. GFP-labeled VdSCP7 is secreted by V. dahliae and accumulates in the plant nucleus. We conclude that VdSCP7 is a novel effector protein that targets the host nucleus to modulate plant immunity, and suggest that plants can recognize VdSCP7 to activate ETI during fungal infection.
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Affiliation(s)
- Lisha Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, D-72076, Germany
| | - Hao Ni
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Du
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Wei Ma
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, D-72076, Germany
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenlei Hua
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, D-72076, Germany
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191
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Depotter JRL, Seidl MF, van den Berg GCM, Thomma BPHJ, Wood TA. A distinct and genetically diverse lineage of the hybrid fungal pathogen Verticillium longisporum population causes stem striping in British oilseed rape. Environ Microbiol 2017; 19:3997-4009. [PMID: 28523726 DOI: 10.1111/1462-2920.13801] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/11/2017] [Accepted: 05/13/2017] [Indexed: 11/30/2022]
Abstract
Population genetic structures illustrate evolutionary trajectories of organisms adapting to differential environmental conditions. Verticillium stem striping disease on oilseed rape was mainly observed in continental Europe, but has recently emerged in the United Kingdom. The disease is caused by the hybrid fungal species Verticillium longisporum that originates from at least three separate hybridization events, yet hybrids between Verticillium progenitor species A1 and D1 are mainly responsible for Verticillium stem striping. We reveal a hitherto un-described dichotomy within V. longisporum lineage A1/D1 that correlates with the geographic distribution of the isolates with an 'A1/D1 West' and an 'A1/D1 East' cluster. Genome comparison between representatives of the A1/D1 West and East clusters excluded population distinctiveness through separate hybridization events. Remarkably, the A1/D1 West population that is genetically more diverse than the entire A1/D1 East cluster caused the sudden emergence of Verticillium stem striping in the UK, whereas in continental Europe Verticillium stem striping is predominantly caused by the more genetically uniform A1/D1 East population. The observed genetic diversity of the A1/D1 West population argues against a recent introduction of the pathogen into the UK, but rather suggests that the pathogen previously established in the UK and remained latent or unnoticed as oilseed rape pathogen until recently.
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Affiliation(s)
- Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.,Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Thomas A Wood
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
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192
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Zhou R, Zhu T, Han L, Liu M, Xu M, Liu Y, Han D, Qiu D, Gong Q, Liu X. The asparagine-rich protein NRP interacts with the Verticillium effector PevD1 and regulates the subcellular localization of cryptochrome 2. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3427-3440. [PMID: 28633330 DOI: 10.1093/jxb/erx192] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/16/2017] [Indexed: 05/20/2023]
Abstract
The soil-borne fungal pathogen Verticillium dahliae infects a wide range of dicotyledonous plants including cotton, tobacco, and Arabidopsis. Among the effector proteins secreted by V. dahliae, the 16 kDa PevD1 induces a hypersensitive response in tobacco. Here we report the high-resolution structure of PevD1 with folds resembling a C2 domain-like structure with a calcium ion bound to the C-terminal acidic pocket. A yeast two-hybrid screen, designed to probe for molecular functions of PevD1, identified Arabidopsis asparagine-rich protein (NRP) as the interacting partner of PevD1. Extending the pathway of V. dahliae effects, which include induction of early flowering in cotton and Arabidopsis, NRP was found to interact with cryptochrome 2 (CRY2), leading to increased cytoplasmic accumulation of CRY2 in a blue light-independent manner. Further physiological and genetic evidence suggests that PevD1 indirectly activates CRY2 by antagonizing NRP functions. The promotion of CRY2-mediated flowering by a fungal effector outlines a novel pathway by which an external stimulus is recognized and transferred in changing a developmental program.
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Affiliation(s)
- Ruimin Zhou
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tong Zhu
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lei Han
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Institute of Plant Protection, Beijing 100081, China
| | - Mengjie Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Institute of Plant Protection, Beijing 100081, China
| | - Mengyuan Xu
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yanli Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Dandan Han
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Dewen Qiu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Institute of Plant Protection, Beijing 100081, China
| | - Qingqiu Gong
- Tianjin Key Laboratory of Protein Science, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xinqi Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
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193
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Xie C, Li Q, Yang X. Characterization of VdASP F2 Secretory Factor from Verticillium dahliae by a Fast and Easy Gene Knockout System. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:444-454. [PMID: 28291379 DOI: 10.1094/mpmi-01-17-0007-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The vascular wilt fungus Verticillium dahliae produces persistent resting structures known as microsclerotia, which enable long-term survival of this plant pathogen in soil. The completed genome sequence of V. dahliae has facilitated large-scale investigations of individual gene functions using gene-disruption strategies based on Agrobacterium tumefaciens-mediated transformation. However, the construction of gene-deletion vectors and screening of deletion mutants have remained challenging in V. dahliae. In this study, we developed a fast and easy gene knockout system for V. dahliae using ligation-independent cloning and fluorescent screening. We identified secretory factor VdASP F2 in a T-DNA insertion library of V. dahliae and deleted the VdASP F2 gene using the developed knockout system. Phenotypic analysis suggests that VdASP F2 is not necessary for V. dahliae growth on potato dextrose agar under various stress conditions. However, on semisynthetic medium or under limited nutrient conditions at lower temperatures, the VdASP F2 deletion mutant exhibited vigorous mycelium growth, less branching, and a significant delay in melanized microsclerotial formation. Further assessment revealed that VdASP F2 was required for the expression of VDH1 and VMK1, two genes involved in microsclerotial formation. Cotton inoculated with the VdASP F2 deletion mutant wilted, demonstrating that VdASP F2 is not associated with pathogenicity under normal conditions. However, after inducing microsclerotial formation and incubation at low temperatures, cotton infected with the VdASP F2 deletion mutant did not exhibit wilt symptoms. In conclusion, our results show that VdASP F2 plays an important role in the response of V. dahliae to adverse environmental conditions and is involved in a transition to a dormant form for prolonged survival.
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Affiliation(s)
- Chengjian Xie
- 1 School of Life Sciences and
- 2 The Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China; and
| | - Qiaoling Li
- 3 Chongqing Institute of Medicinal Plant Cultivation, Chongqing 408435, China
| | - Xingyong Yang
- 1 School of Life Sciences and
- 2 The Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China; and
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194
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Franco-Orozco B, Berepiki A, Ruiz O, Gamble L, Griffe LL, Wang S, Birch PRJ, Kanyuka K, Avrova A. A new proteinaceous pathogen-associated molecular pattern (PAMP) identified in Ascomycete fungi induces cell death in Solanaceae. THE NEW PHYTOLOGIST 2017; 214:1657-1672. [PMID: 28386988 DOI: 10.1111/nph.14542] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 02/15/2017] [Indexed: 05/09/2023]
Abstract
Pathogen-associated molecular patterns (PAMPs) are detected by plant pattern recognition receptors (PRRs), which gives rise to PAMP-triggered immunity (PTI). We characterized a novel fungal PAMP, Cell Death Inducing 1 (RcCDI1), identified in the Rhynchosporium commune transcriptome sampled at an early stage of barley (Hordeum vulgare) infection. The ability of RcCDI1 and its homologues from different fungal species to induce cell death in Nicotiana benthamiana was tested following agroinfiltration or infiltration of recombinant proteins produced by Pichia pastoris. Virus-induced gene silencing (VIGS) and transient expression of Phytophthora infestans effectors PiAVR3a and PexRD2 were used to assess the involvement of known components of PTI in N. benthamiana responses to RcCDI1. RcCDI1 was highly upregulated early during barley colonization with R. commune. RcCDI1 and its homologues from different fungal species, including Zymoseptoria tritici, Magnaporthe oryzae and Neurospora crassa, exhibited PAMP activity, inducing cell death in Solanaceae but not in other families of dicots or monocots. RcCDI1-triggered cell death was shown to require N. benthamiana Brassinosteroid insensitive 1-Associated Kinase 1 (NbBAK1), N. benthamiana suppressor of BIR1-1 (NbSOBIR1) and N. benthamiana SGT1 (NbSGT1), but was not suppressed by PiAVR3a or PexRD2. We report the identification of a novel Ascomycete PAMP, RcCDI1, recognized by Solanaceae but not by monocots, which activates cell death through a pathway that is distinct from that triggered by the oomycete PAMP INF1.
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Affiliation(s)
- Barbara Franco-Orozco
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Adokiye Berepiki
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Olaya Ruiz
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Louise Gamble
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Lucie L Griffe
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Shumei Wang
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Paul R J Birch
- Division of Plant Sciences, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Kostya Kanyuka
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Anna Avrova
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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195
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Mustafa R, Hamza M, Kamal H, Mansoor S, Scheffler J, Amin I. Tobacco Rattle Virus-Based Silencing of Enoyl-CoA Reductase Gene and Its Role in Resistance Against Cotton Wilt Disease. Mol Biotechnol 2017; 59:241-250. [DOI: 10.1007/s12033-017-0014-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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196
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Deng CH, Plummer KM, Jones DAB, Mesarich CH, Shiller J, Taranto AP, Robinson AJ, Kastner P, Hall NE, Templeton MD, Bowen JK. Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range. BMC Genomics 2017; 18:339. [PMID: 28464870 PMCID: PMC5412055 DOI: 10.1186/s12864-017-3699-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/11/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuticular space without penetrating plant cells, it is assumed that effectors that contribute to virulence and determination of host range will be secreted into this plant-pathogen interface. Thus the predicted secretomes of a range of isolates of Venturia with distinct host-ranges were interrogated to reveal putative proteins involved in virulence and pathogenicity. RESULTS Genomes of Venturia pirina (one European pear scab isolate) and Venturia inaequalis (three apple scab, and one loquat scab, isolates) were sequenced and the predicted secretomes of each isolate identified. RNA-Seq was conducted on the apple-specific V. inaequalis isolate Vi1 (in vitro and infected apple leaves) to highlight virulence and pathogenicity components of the secretome. Genes encoding over 600 small secreted proteins (candidate effectors) were identified, most of which are novel to Venturia, with expansion of putative effector families a feature of the genus. Numerous genes with similarity to Leptosphaeria maculans AvrLm6 and the Verticillium spp. Ave1 were identified. Candidates for avirulence effectors with cognate resistance genes involved in race-cultivar specificity were identified, as were putative proteins involved in host-species determination. Candidate effectors were found, on average, to be in regions of relatively low gene-density and in closer proximity to repeats (e.g. transposable elements), compared with core eukaryotic genes. CONCLUSIONS Comparative secretomics has revealed candidate effectors from Venturia fungal plant pathogens that attack pome fruit. Effectors that are putative determinants of host range were identified; both those that may be involved in race-cultivar and host-species specificity. Since many of the effector candidates are in close proximity to repetitive sequences this may point to a possible mechanism for the effector gene family expansion observed and a route to diversification via transposition and repeat-induced point mutation.
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Affiliation(s)
- Cecilia H. Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Kim M. Plummer
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Plant Biosecurity Cooperative Research Centre, Bruce, ACT Australia
| | - Darcy A. B. Jones
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Present Address: The Centre for Crop and Disease Management, Curtin University, Bentley, Australia
| | - Carl H. Mesarich
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Present Address: Institute of Agriculture & Environment, Massey University, Palmerston North, New Zealand
| | - Jason Shiller
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Present Address: INRA-Angers, Beaucouzé, Cedex, France
| | - Adam P. Taranto
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, Australia
| | - Andrew J. Robinson
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative (VLSCI), Victoria, Australia
| | - Patrick Kastner
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
| | - Nathan E. Hall
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative (VLSCI), Victoria, Australia
| | - Matthew D. Templeton
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanna K. Bowen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
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197
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Hartmann FE, Sánchez-Vallet A, McDonald BA, Croll D. A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements. THE ISME JOURNAL 2017; 11:1189-1204. [PMID: 28117833 PMCID: PMC5437930 DOI: 10.1038/ismej.2016.196] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/10/2016] [Accepted: 11/25/2016] [Indexed: 11/09/2022]
Abstract
Fungal pathogens can rapidly evolve virulence towards resistant crops in agricultural ecosystems. Gains in virulence are often mediated by the mutation or deletion of a gene encoding a protein recognized by the plant immune system. However, the loci and the mechanisms of genome evolution enabling rapid virulence evolution are poorly understood. We performed genome-wide association mapping on a global collection of 106 strains of Zymoseptoria tritici, the most damaging pathogen of wheat in Europe, to identify polymorphisms linked to virulence on two wheat varieties. We found 25 distinct genomic loci associated with reproductive success of the pathogen. However, no locus was shared between the host genotypes, suggesting host specialization. The main locus associated with virulence encoded a highly expressed, small secreted protein. Population genomic analyses showed that the gain in virulence was explained by a segregating gene deletion polymorphism. The deletion was likely adaptive by preventing detection of the encoded protein. Comparative genomics of closely related species showed that the locus emerged de novo since speciation. A large cluster of transposable elements in direct proximity to the locus generated extensive rearrangements leading to multiple independent gene losses. Our study demonstrates that rapid turnover in the chromosomal structure of a pathogen can drive host specialization.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, Zurich, Switzerland
| | | | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, Zurich, Switzerland
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, Zurich, Switzerland
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198
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Gui YJ, Chen JY, Zhang DD, Li NY, Li TG, Zhang WQ, Wang XY, Short DPG, Li L, Guo W, Kong ZQ, Bao YM, Subbarao KV, Dai XF. Verticillium dahliae manipulates plant immunity by glycoside hydrolase 12 proteins in conjunction with carbohydrate-binding module 1. Environ Microbiol 2017; 19:1914-1932. [PMID: 28205292 DOI: 10.1111/1462-2920.13695] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 01/06/2023]
Abstract
Glycoside hydrolase 12 (GH12) proteins act as virulence factors and pathogen-associated molecular patterns (PAMPs) in oomycetes. However, the pathogenic mechanisms of fungal GH12 proteins have not been characterized. In this study, we demonstrated that two of the six GH12 proteins produced by the fungus Verticillium dahliae Vd991, VdEG1 and VdEG3 acted as PAMPs to trigger cell death and PAMP-triggered immunity (PTI) independent of their enzymatic activity in Nicotiana benthamiana. A 63-amino-acid peptide of VdEG3 was sufficient for cell death-inducing activity, but this was not the case for the corresponding peptide of VdEG1. Further study indicated that VdEG1 and VdEG3 trigger PTI in different ways: BAK1 is required for VdEG1- and VdEG3-triggered immunity, while SOBIR1 is specifically required for VdEG1-triggered immunity in N. benthamiana. Unlike oomycetes, which employ RXLR effectors to suppress host immunity, a carbohydrate-binding module family 1 (CBM1) protein domain suppressed GH12 protein-induced cell death. Furthermore, during infection of N. benthamiana and cotton, VdEG1 and VdEG3 acted as PAMPs and virulence factors, respectively indicative of host-dependent molecular functions. These results suggest that VdEG1 and VdEG3 associate differently with BAK1 and SOBIR1 receptor-like kinases to trigger immunity in N. benthamiana, and together with CBM1-containing proteins manipulate plant immunity.
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Affiliation(s)
- Yue-Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Nan-Yang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ting-Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wen-Qi Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xin-Yan Wang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dylan P G Short
- Department of Plant Pathology, University of California, Davis, United States of America
| | - Lei Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei Guo
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhi-Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yu-Ming Bao
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, United States of America
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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199
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Kombrink A, Rovenich H, Shi‐Kunne X, Rojas‐Padilla E, van den Berg GCM, Domazakis E, de Jonge R, Valkenburg D, Sánchez‐Vallet A, Seidl MF, Thomma BPHJ. Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts. MOLECULAR PLANT PATHOLOGY 2017; 18:596-608. [PMID: 27911046 PMCID: PMC6638240 DOI: 10.1111/mpp.12520] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Chitin-binding lysin motif (LysM) effectors contribute to the virulence of various plant-pathogenic fungi that are causal agents of foliar diseases. Here, we report the LysM effectors of the soil-borne fungal vascular wilt pathogen Verticillium dahliae. Comparative genomics revealed three core LysM effectors that are conserved in a collection of V. dahliae strains. Remarkably, and in contrast with the previously studied LysM effectors of other plant pathogens, no expression of core LysM effectors was monitored in planta in a taxonomically diverse panel of host plants. Moreover, targeted deletion of the individual LysM effector genes in V. dahliae strain JR2 did not compromise virulence in infections on Arabidopsis, tomato or Nicotiana benthamiana. Interestingly, an additional lineage-specific LysM effector is encoded in the genome of V. dahliae strain VdLs17, but not in any other V. dahliae strain sequenced to date. Remarkably, this lineage-specific effector is expressed in planta and contributes to the virulence of V. dahliae strain VdLs17 on tomato, but not on Arabidopsis or N. benthamiana. Functional analysis revealed that this LysM effector binds chitin, is able to suppress chitin-induced immune responses and protects fungal hyphae against hydrolysis by plant hydrolytic enzymes. Thus, in contrast with the core LysM effectors of V. dahliae, this lineage-specific LysM effector of strain VdLs17 contributes to virulence in planta.
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Affiliation(s)
- Anja Kombrink
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Hanna Rovenich
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Xiaoqian Shi‐Kunne
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Eduardo Rojas‐Padilla
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Grardy C. M. van den Berg
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Emmanouil Domazakis
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Ronnie de Jonge
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Dirk‐Jan Valkenburg
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Andrea Sánchez‐Vallet
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Michael F. Seidl
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
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200
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Santhanam P, Boshoven JC, Salas O, Bowler K, Islam MT, Saber MK, van den Berg GCM, Bar‐Peled M, Thomma BPHJ. Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae. MOLECULAR PLANT PATHOLOGY 2017; 18:347-362. [PMID: 26996832 PMCID: PMC6638212 DOI: 10.1111/mpp.12401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/17/2016] [Accepted: 03/17/2016] [Indexed: 05/05/2023]
Abstract
The initial interaction of a pathogenic fungus with its host is complex and involves numerous metabolic pathways and regulatory proteins. Considerable attention has been devoted to proteins that play a crucial role in these interactions, with an emphasis on so-called effector molecules that are secreted by the invading microbe to establish the symbiosis. However, the contribution of other types of molecules, such as glycans, is less well appreciated. Here, we present a random genetic screen that enabled us to identify 58 novel candidate genes that are involved in the pathogenic potential of the fungal pathogen Verticillium dahliae, which causes vascular wilt diseases in over 200 dicotyledonous plant species, including economically important crops. One of the candidate genes that was identified concerns a putative biosynthetic gene involved in nucleotide sugar precursor formation, as it encodes a putative nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER). This enzyme has homology to bacterial enzymes involved in the biosynthesis of the nucleotide sugar deoxy-thymidine diphosphate (dTDP)-rhamnose, a precursor of L-rhamnose, which has been shown to be required for virulence in several human pathogenic bacteria. Rhamnose is known to be a minor cell wall glycan in fungi and has therefore not been suspected as a crucial molecule in fungal-host interactions. Nevertheless, our study shows that deletion of the VdNRS/ER gene from the V. dahliae genome results in complete loss of pathogenicity on tomato and Nicotiana benthamiana plants, whereas vegetative growth and sporulation are not affected. We demonstrate that VdNRS/ER is a functional enzyme in the biosynthesis of uridine diphosphate (UDP)-rhamnose, and further analysis has revealed that VdNRS/ER deletion strains are impaired in the colonization of tomato roots. Collectively, our results demonstrate that rhamnose, although only a minor cell wall component, is essential for the pathogenicity of V. dahliae.
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Affiliation(s)
- Parthasarathy Santhanam
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Jordi C. Boshoven
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Omar Salas
- Complex Carbohydrate Research Center, University of GeorgiaAthensGA30602USA
| | - Kyle Bowler
- Complex Carbohydrate Research Center, University of GeorgiaAthensGA30602USA
| | - Md Tohidul Islam
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Mojtaba Keykha Saber
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Grardy C. M. van den Berg
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Maor Bar‐Peled
- Complex Carbohydrate Research Center, University of GeorgiaAthensGA30602USA
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
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