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Liu M, Wang F, He B, Hu J, Dai Y, Chen W, Yi M, Zhang H, Ye Y, Cui Z, Zheng X, Wang P, Xing W, Zhang Z. Targeting Magnaporthe oryzae effector MoErs1 and host papain-like protease OsRD21 interaction to combat rice blast. NATURE PLANTS 2024; 10:618-632. [PMID: 38409290 DOI: 10.1038/s41477-024-01642-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
Effector proteins secreted by plant pathogenic fungi are important artilleries against host immunity, but there is no precedent of such effectors being explored as antifungal targets. Here we demonstrate that MoErs1, a species-specific effector protein secreted by the rice blast fungus Magnaporthe oryzae, inhibits the function of rice papain-like cysteine protease OsRD21 involved in rice immunity. Disrupting MoErs1-OsRD21 interaction effectively controls rice blast. In addition, we show that FY21001, a structure-function-based designer compound, specifically binds to and inhibits MoErs1 function. FY21001 significantly and effectively controls rice blast in field tests. Our study revealed a novel concept of targeting pathogen-specific effector proteins to prevent and manage crop diseases.
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Affiliation(s)
- Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Fangfang Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Bo He
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Jiexiong Hu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Ying Dai
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Weizhong Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Mingxi Yi
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Yonghao Ye
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Zhongli Cui
- College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Ping Wang
- Departments of Microbiology, Immunology and Parasitology, and Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Weiman Xing
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China.
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Chepsergon J, Moleleki LN. "Order from disordered": Potential role of intrinsically disordered regions in phytopathogenic oomycete intracellular effector proteins. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102402. [PMID: 37329857 DOI: 10.1016/j.pbi.2023.102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023]
Abstract
There is a continuous arms race between pathogens and their host plants. However, successful pathogens, such as phytopathogenic oomycetes, secrete effector proteins to manipulate host defense responses for disease development. Structural analyses of these effector proteins reveal the existence of regions that fail to fold into three-dimensional structures, intrinsically disordered regions (IDRs). Because of their flexibility, these regions are involved in important biological functions of effector proteins, such as effector-host protein interactions that perturb host immune responses. Despite their significance, the role of IDRs in phytopathogenic oomycete effector-host protein interactions is not clear. This review, therefore, searched the literature for functionally characterized oomycete intracellular effectors with known host interactors. We further classify regions that mediate effector-host protein interactions into globular or disordered binding sites in these proteins. To fully appreciate the potential role of IDRs, five effector proteins encoding potential disordered binding sites were used as case studies. We also propose a pipeline that can be used to identify, classify as well as characterize potential binding regions in effector proteins. Understanding the role of IDRs in these effector proteins can aid in the development of new disease-control strategies.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
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Nur M, Wood K, Michelmore R. EffectorO: Motif-Independent Prediction of Effectors in Oomycete Genomes Using Machine Learning and Lineage Specificity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:397-410. [PMID: 36853198 DOI: 10.1094/mpmi-11-22-0236-ta] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Oomycete plant pathogens cause a wide variety of diseases, including late blight of potato, sudden oak death, and downy mildews of plants. These pathogens are major contributors to loss in numerous food crops. Oomycetes secrete effector proteins to manipulate their hosts to the advantage of the pathogen. Plants have evolved to recognize effectors, resulting in an evolutionary cycle of defense and counter-defense in plant-microbe interactions. This selective pressure results in highly diverse effector sequences that can be difficult to computationally identify using only sequence similarity. We developed a novel effector prediction tool, EffectorO, that uses two complementary approaches to predict effectors in oomycete pathogen genomes: i) a machine learning-based pipeline that predicts effector probability based on the biochemical properties of the N-terminal amino-acid sequence of a protein and ii) a pipeline based on lineage specificity to find proteins that are unique to one species or genus, a sign of evolutionary divergence due to adaptation to the host. We tested EffectorO on Bremia lactucae, which causes lettuce downy mildew, and Phytophthora infestans, which causes late blight of potato and tomato, and predicted many novel effector candidates while recovering the majority of known effector candidates. EffectorO will be useful for discovering novel families of oomycete effectors without relying on sequence similarity to known effectors. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Munir Nur
- The Genome Center, University of California, Davis, CA, U.S.A
| | - Kelsey Wood
- The Genome Center, University of California, Davis, CA, U.S.A
- Integrative Genetics & Genomics Graduate Group, University of California, Davis, CA, U.S.A
| | - Richard Michelmore
- The Genome Center, University of California, Davis, CA, U.S.A
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA, U.S.A
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Rai P, Prasad L, Rai PK. Fungal effectors versus defense-related genes of B. juncea and the status of resistant transgenics against fungal pathogens. FRONTIERS IN PLANT SCIENCE 2023; 14:1139009. [PMID: 37360735 PMCID: PMC10285668 DOI: 10.3389/fpls.2023.1139009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023]
Abstract
Oilseed brassica has become instrumental in securing global food and nutritional security. B. juncea, colloquially known as Indian mustard, is cultivated across tropics and subtropics including Indian subcontinent. The production of Indian mustard is severely hampered by fungal pathogens which necessitates human interventions. Chemicals are often resorted to as they are quick and effective, but due to their economic and ecological unsustainability, there is a need to explore their alternatives. The B. juncea-fungal pathosystem is quite diverse as it covers broad-host range necrotrophs (Sclerotinia sclerotiorum), narrow-host range necrotrophs (Alternaria brassicae and A. brassicicola) and biotrophic oomycetes (Albugo candida and Hyaloperonospora brassica). Plants ward off fungal pathogens through two-step resistance mechanism; PTI which involves recognition of elicitors and ETI where the resistance gene (R gene) interacts with the fungal effectors. The hormonal signalling is also found to play a vital role in defense as the JA/ET pathway is initiated at the time of necrotroph infection and SA pathway is induced when the biotrophs attack plants. The review discuss the prevalence of fungal pathogens of Indian mustard and the studies conducted on effectoromics. It covers both pathogenicity conferring genes and host-specific toxins (HSTs) that can be used for a variety of purposes such as identifying cognate R genes, understanding pathogenicity and virulence mechanisms, and establishing the phylogeny of fungal pathogens. It further encompasses the studies on identifying resistant sources and characterisation of R genes/quantitative trait loci and defense-related genes identified in Brassicaceae and unrelated species which, upon introgression or overexpression, confer resistance. Finally, the studies conducted on developing resistant transgenics in Brassicaceae have been covered in which chitinase and glucanase genes are mostly used. The knowledge gained from this review can further be used for imparting resistance against major fungal pathogens.
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Affiliation(s)
- Prajjwal Rai
- Division of Plant Pathology, Indian Agriculture Research Institute, New Delhi, India
| | - Laxman Prasad
- Division of Plant Pathology, Indian Agriculture Research Institute, New Delhi, India
| | - Pramod Kumar Rai
- Division of Plant Pathology, Directorate of Rapeseed-Mustard Research, Bharatpur, India
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Hou X, He Z, Che Z, Li H, Tan X, Wang Q. Molecular mechanisms of Phytophthora sojae avirulence effectors escaping host recognition. Front Microbiol 2023; 13:1111774. [PMID: 36699593 PMCID: PMC9868715 DOI: 10.3389/fmicb.2022.1111774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
Phytophthora sojae is a well-known destructive oomycete pathogen, which causes soybean stem and root rot and poses a serious threat to global food security. Growing soybean cultivars with the appropriate resistance to P. sojae (Rps) genes are the primary management strategy to reduce losses. In most Phytophthora pathosystems, host resistance protein encoded by a specific R gene in the plant recognizes corresponding RxLR effector protein, encoded by an avirulence gene. This gene-for-gene relationship has been exploited to help breeders and agronomists deploy soybean cultivars. To date, 6 Rps genes have been incorporated into commercial soybean germplasm and trigger plant immunity in response to 8 P. sojae avirulence effectors. The incorporation of Rps genes in the soybean population creates selection pressure in favor of novel pathotypes of P. sojae. The 8 avirulence genes evolved to evade the host immune system, driven by genetic selection pressures. Understanding the evading strategies has important reference value for the prevention and control of Phytophthora stem and root rot. This investigation primarily highlights the research on the strategies of P. sojae avirulence effector evasion of host recognition, looking forward to creating durable resistance genes and thereby enabling successful disease management.
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Affiliation(s)
- Xiaoyuan Hou
- Shandong Province Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Zheng He
- Shandong Province Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Zhengzheng Che
- Shandong Province Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Hengjing Li
- Shandong Province Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Xinwei Tan
- Shandong Province Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Qunqing Wang
- Shandong Province Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China,*Correspondence: Qunqing Wang,
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Bai B, Zhang G, Li Y, Wang Y, Sujata S, Zhang X, Wang L, Zhao L, Wu Y. The 'Candidatus Phytoplasma tritici' effector SWP12 degrades the transcription factor TaWRKY74 to suppress wheat resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1473-1488. [PMID: 36380696 DOI: 10.1111/tpj.16029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
'Candidatus Phytoplasma tritici' ('Ca. P. tritici') is an insect-borne obligate pathogen that infects wheat (Triticum aestivum) causing wheat blue dwarf disease, and leads to yield losses. SWP12 is a potential effector secreted by 'Ca. P. tritici' that manipulates host processes to create an environment conducive to phytoplasma colonization, but the detailed mechanism of action remains to be investigated. In this study, the expression of SWP12 weakened the basal immunity of Nicotiana benthamiana and promoted leaf colonization by Phytophthora parasitica, Sclerotinia sclerotiorum, and tobacco mild green mosaic virus. Moreover, the expression of SWP12 in wheat plants promoted phytoplasma colonization. Triticum aestivum WRKY74 and N. benthamiana WRKY17 were identified as host targets of SWP12. The expression of TaWRKY74 triggered reactive oxygen species bursts, upregulated defense-related genes, and decreased TaCRR6 transcription, leading to reductions in NADH dehydrogenase complex (NDH) activity. Expression of TaWRKY74 in wheat increased plant resistance to 'Ca. P. tritici', and silencing of TaWRKY74 enhanced plant susceptibility, which indicates that TaWRKY74 is a positive regulator of wheat resistance to 'Ca. P. tritici'. We showed that SWP12 weakens plant resistance and promotes 'Ca. P. tritici' colonization by destabilizing TaWRKY74.
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Affiliation(s)
- Bixin Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Guoding Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yue Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanbin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shrestha Sujata
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xudong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Licheng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lei Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
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Qian Y, Zheng X, Wang X, Yang J, Zheng X, Zeng Q, Li J, Zhuge Q, Xiong Q. Systematic identification and functional characterization of the CFEM proteins in poplar fungus Marssonina brunnea. Front Cell Infect Microbiol 2022; 12:1045615. [PMID: 36439212 PMCID: PMC9684206 DOI: 10.3389/fcimb.2022.1045615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/21/2022] [Indexed: 01/10/2024] Open
Abstract
Proteins containing Common in Fungal Extracellular Membrane (CFEM) domains uniquely exist in fungi and play significant roles in their whole life history. In this study, a total of 11 MbCFEM proteins were identified from Marssonina brunnea f. sp. multigermtubi (MULT), a hemibiotrophic pathogenic fungus on poplars that causes severe leaf diseases. Phylogenic analysis showed that the 11 proteins (MbCFEM1-11) were divided into three clades based on the trans-membrane domain and the CFEM domain. Sequence alignment and WebLogo analysis of CFEM domains verified the amino acids conservatism therein. All of them possess eight cysteines except MbCFEM4 and MbCFEM11, which lack two cysteines each. Six MbCFEM proteins with a signal peptide and without trans-membrane domain were considered as candidate effectors for further functional analysis. Three-dimensional (3D) models of their CFEM domains presented a helical-basket structure homologous to the crucial virulence factor Csa2 of Candida albicans. Afterward, four (MbCFEM1, 6, 8, and 9) out of six candidate effectors were successfully cloned and a yeast signal sequence trap (YSST) assay confirmed their secretion activity. Pathogen challenge assays demonstrated that the transient expression of four candidate MbCFEM effectors in Nicotiana benthamiana promoted Fusarium proliferatum infection, respectively. In an N. benthamiana heterogeneous expression system, MbCFEM1, MbCFEM6, and MbCFEM9 appeared to suppress both BAX/INF1-triggered PCD, whereas MbCFEM8 could only defeat BAX-triggered PCD. Additionally, subcellular localization analysis indicated that the four candidate MbCFEM effectors accumulate in the cell membrane, nucleus, chloroplast, and cytosolic bodies. These results demonstrate that MbCFEM1, MbCFEM6, MbCFEM8, and MbCFEM9 are effectors of M. brunnea and provide valuable targets for further dissection of the molecular mechanisms underlying the poplar-M. brunnea interaction.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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Cox MP, Guo Y, Winter DJ, Sen D, Cauldron NC, Shiller J, Bradley EL, Ganley AR, Gerth ML, Lacey RF, McDougal RL, Panda P, Williams NM, Grunwald NJ, Mesarich CH, Bradshaw RE. Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families. Front Microbiol 2022; 13:1038444. [PMID: 36406440 PMCID: PMC9667082 DOI: 10.3389/fmicb.2022.1038444] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/11/2022] [Indexed: 01/25/2023] Open
Abstract
Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.
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Affiliation(s)
- Murray P. Cox
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yanan Guo
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - David J. Winter
- Institute of Environmental Science and Research (ESR), Porirua, New Zealand
| | | | - Nicholas C. Cauldron
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | | | - Ellie L. Bradley
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Austen R. Ganley
- School of Biological Sciences and Digital Life Institute, University of Auckland, Auckland, New Zealand
| | - Monica L. Gerth
- Bioprotection Aotearoa, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Randy F. Lacey
- Bioprotection Aotearoa, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | | | | | - Niklaus J. Grunwald
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, OR, United States
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Rosie E. Bradshaw
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand,*Correspondence: Rosie E. Bradshaw,
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Exploiting breakdown in nonhost effector-target interactions to boost host disease resistance. Proc Natl Acad Sci U S A 2022; 119:e2114064119. [PMID: 35994659 PMCID: PMC9436328 DOI: 10.1073/pnas.2114064119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Plant nonhost resistance (NHR) prevents infection by all members of most microbial species, but its molecular mechanisms are not well understood. We found that effector proteins from the potato blight pathogen Phytophthora infestans, which enhance infection in host plants, fail to enhance susceptibility in nonhost Arabidopsis. These P. infestans effectors often failed to interact with Arabidopsis orthologs of their potato target proteins, whereas many interactions were detected between these Arabidopsis orthologs and effectors from its adapted pathogen Hyaloperonospora arabidopsidis. Thus, breakdown in effector–target interactions in distantly related nonhost plants is likely a key component of NHR. Importantly, we demonstrate that exploiting this breakdown and expressing nonhost target orthologs in host plants provide a strategy to prevent crop disease. Plants are resistant to most microbial species due to nonhost resistance (NHR), providing broad-spectrum and durable immunity. However, the molecular components contributing to NHR are poorly characterised. We address the question of whether failure of pathogen effectors to manipulate nonhost plants plays a critical role in NHR. RxLR (Arg-any amino acid-Leu-Arg) effectors from two oomycete pathogens, Phytophthora infestans and Hyaloperonospora arabidopsidis, enhanced pathogen infection when expressed in host plants (Nicotiana benthamiana and Arabidopsis, respectively) but the same effectors performed poorly in distantly related nonhost pathosystems. Putative target proteins in the host plant potato were identified for 64 P. infestans RxLR effectors using yeast 2-hybrid (Y2H) screens. Candidate orthologues of these target proteins in the distantly related non-host plant Arabidopsis were identified and screened using matrix Y2H for interaction with RxLR effectors from both P. infestans and H. arabidopsidis. Few P. infestans effector-target protein interactions were conserved from potato to candidate Arabidopsis target orthologues (cAtOrths). However, there was an enrichment of H. arabidopsidis RxLR effectors interacting with cAtOrths. We expressed the cAtOrth AtPUB33, which unlike its potato orthologue did not interact with P. infestans effector PiSFI3, in potato and Nicotiana benthamiana. Expression of AtPUB33 significantly reduced P. infestans colonization in both host plants. Our results provide evidence that failure of pathogen effectors to interact with and/or correctly manipulate target proteins in distantly related non-host plants contributes to NHR. Moreover, exploiting this breakdown in effector-nonhost target interaction, transferring effector target orthologues from non-host to host plants is a strategy to reduce disease.
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Short Linear Motifs (SLiMs) in “Core” RxLR Effectors of
Phytophthora parasitica
var.
nicotianae
: a Case of PpRxLR1 Effector. Microbiol Spectr 2022; 10:e0177421. [PMID: 35404090 PMCID: PMC9045269 DOI: 10.1128/spectrum.01774-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Oomycetes of the genus Phytophthora encompass several of the most successful plant pathogens described to date. The success of infection by Phytophthora species is attributed to the pathogens’ ability to secrete effector proteins that alter the host’s physiological processes. Structural analyses of effector proteins mainly from bacterial and viral pathogens have revealed the presence of intrinsically disordered regions that host short linear motifs (SLiMs). These motifs play important biological roles by facilitating protein-protein interactions as well as protein translocation. Nonetheless, SLiMs in Phytophthora species RxLR effectors have not been investigated previously and their roles remain unknown. Using a bioinformatics pipeline, we identified 333 candidate RxLR effectors in the strain INRA 310 of Phytophthora parasitica. Of these, 71 (21%) were also found to be present in 10 other genomes of P. parasitica, and hence, these were designated core RxLR effectors (CREs). Within the CRE sequences, the N terminus exhibited enrichment in intrinsically disordered regions compared to the C terminus, suggesting a potential role of disorder in effector translocation. Although the disorder content was reduced in the C-terminal regions, it is important to mention that most SLiMs were in this terminus. PpRxLR1 is one of the 71 CREs identified in this study, and its genes encode a 6-amino acid (aa)-long SLiM at the C terminus. We showed that PpRxLR1 interacts with several host proteins that are implicated in defense. Structural analysis of this effector using homology modeling revealed the presence of potential ligand-binding sites. Among key residues that were predicted to be crucial for ligand binding, L102 and Y106 were of interest since they form part of the 6-aa-long PpRxLR1 SLiM. In silico substitution of these two residues to alanine was predicted to have a significant effect on both the function and the structure of PpRxLR1 effector. Molecular docking simulations revealed possible interactions between PpRxLR1 effector and ubiquitin-associated proteins. The ubiquitin-like SLiM carried in this effector was shown to be a potential mediator of these interactions. Further studies are required to validate and elucidate the underlying molecular mechanism of action. IMPORTANCE The continuous gain and loss of RxLR effectors makes the control of Phytophthora spp. difficult. Therefore, in this study, we endeavored to identify RxLR effectors that are highly conserved among species, also known as “core” RxLR effectors (CREs). We reason that these highly conserved effectors target conserved proteins or processes; thus, they can be harnessed in breeding for durable resistance in plants. To further understand the mechanisms of action of CREs, structural dissection of these proteins is crucial. Intrinsically disordered regions (IDRs) that do not adopt a fixed, three-dimensional fold carry short linear motifs (SLiMs) that mediate biological functions of proteins. The presence and potential role of these SLiMs in CREs of Phytophthora spp. have been overlooked. To our knowledge, we have effectively identified CREs as well as SLiMs with the potential of promoting effector virulence. Together, this work has advanced our comprehension of Phytophthora RxLR effector function and may facilitate the development of innovative and effective control strategies.
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Fabro G. Oomycete intracellular effectors: specialised weapons targeting strategic plant processes. THE NEW PHYTOLOGIST 2022; 233:1074-1082. [PMID: 34705271 DOI: 10.1111/nph.17828] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Oomycete phytopathogens have adapted to colonise plants using effectors as their molecular weapons. Intracellular effectors, mostly proteins but also small ribonucleic acids, are delivered by the pathogens into the host cell cytoplasm where they interfere with normal plant physiology. The diverse host processes emerging as 'victims' of these 'specialised bullets' include gene transcription and RNA-mediated silencing, cell death, protein stability, protein secretion and autophagy. Some effector targets are directly involved in defence execution, while others participate in fundamental metabolisms whose alteration collaterally affects defences. Other effector targets are susceptibility factors (SFs), that is host components that make plants vulnerable to pathogens. SFs are mostly negative regulators of immunity, but some seem necessary to sustain or promote pathogen colonisation.
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Affiliation(s)
- Georgina Fabro
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
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12
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Haq F, Xu X, Ma W, Shah SMA, Liu L, Zhu B, Zou L, Chen G. A Xanthomonas transcription activator-like effector is trapped in nonhost plants for immunity. PLANT COMMUNICATIONS 2022; 3:100249. [PMID: 35059629 PMCID: PMC8760140 DOI: 10.1016/j.xplc.2021.100249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/29/2021] [Accepted: 10/13/2021] [Indexed: 05/10/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight in rice, delivers transcription activator-like effector (TALE) proteins into host cells to activate susceptibility or resistance (R) genes that promote disease or immunity, respectively. Nonhost plants serve as potential reservoirs of R genes; consequently, nonhost R genes may trap TALEs to trigger an immune response. In this study, we screened 17 Xoo TALEs for their ability to induce a hypersensitive response (HR) in the nonhost plant Nicotiana benthamiana (Nb); only AvrXa10 elicited an HR when transiently expressed in Nb. The HR generated by AvrXa10 required both the central repeat region and the activation domain, suggesting a specific interaction between AvrXa10 and a potential R-like gene in nonhost plants. Evans blue staining and ion leakage measurements confirmed that the AvrXa10-triggered HR was a form of cell death, and the transient expression of AvrXa10 in Nb induced immune responses. Genes targeted by AvrXa10 in the Nb genome were identified by transcriptome profiling and prediction of effector binding sites. Using several approaches (in vivo reporter assays, electrophoretic mobility-shift assays, targeted designer TALEs, and on-spot gene silencing), we confirmed that AvrXa10 targets NbZnFP1, a C2H2-type zinc finger protein that resides in the nucleus. Functional analysis indicated that overexpression of NbZnFP1 and its rice orthologs triggered cell death in rice protoplasts. An NbZnFP1 ortholog was also identified in tomato and was specifically activated by AvrXa10. These results demonstrate that NbZnFP1 is a nonhost R gene that traps AvrXa10 to promote plant immunity in Nb.
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Affiliation(s)
- Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Wenxiu Ma
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Linlin Liu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Bo Zhu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Urban Agriculture of the Ministry of Agriculture, Shanghai, 200240, China
- Corresponding author
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13
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Chepsergon J, Motaung TE, Moleleki LN. "Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants? Virulence 2021; 12:1921-1935. [PMID: 34304703 PMCID: PMC8516161 DOI: 10.1080/21505594.2021.1948277] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Phytopathogenic oomycetes are known to successfully infect their hosts due to their ability to secrete effector proteins. Of interest to many researchers are effectors with the N-terminal RxLR motif (Arginine-any amino acid-Leucine-Arginine). Owing to advances in genome sequencing, we can now comprehend the high level of diversity among oomycete effectors, and similarly, their conservation within and among species referred to here as "core" RxLR effectors (CREs). Currently, there is a considerable number of CREs that have been identified in oomycetes. Functional characterization of these CREs propose their virulence role with the potential of targeting central cellular processes that are conserved across diverse plant species. We reason that effectors that are highly conserved and recognized by the host, could be harnessed in engineering plants for durable as well as broad-spectrum resistance.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Thabiso E. Motaung
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
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14
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Yuan X, Hulin MT, Sundin GW. Effectors, chaperones, and harpins of the Type III secretion system in the fire blight pathogen Erwinia amylovora: a review. JOURNAL OF PLANT PATHOLOGY 2021; 103:25-39. [PMID: 0 DOI: 10.1007/s42161-020-00623-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 05/20/2023]
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15
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Yang B, Yang S, Guo B, Wang Y, Zheng W, Tian M, Dai K, Liu Z, Wang H, Ma Z, Wang Y, Ye W, Dong S, Wang Y. The Phytophthora effector Avh241 interacts with host NDR1-like proteins to manipulate plant immunity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1382-1396. [PMID: 33586843 DOI: 10.1111/jipb.13082] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/12/2021] [Indexed: 05/27/2023]
Abstract
Plant pathogens rely on effector proteins to suppress host innate immune responses and facilitate colonization. Although the Phytophthora sojae RxLR effector Avh241 promotes Phytophthora infection, the molecular basis of Avh241 virulence remains poorly understood. Here we identified non-race specific disease resistance 1 (NDR1)-like proteins, the critical components in plant effector-triggered immunity (ETI) responses, as host targets of Avh241. Avh241 interacts with NDR1 in the plasma membrane and suppresses NDR1-participated ETI responses. Silencing of GmNDR1s increases the susceptibility of soybean to P. sojae infection, and overexpression of GmNDR1s reduces infection, which supports its positive role in plant immunity against P. sojae. Furthermore, we demonstrate that GmNDR1 interacts with itself, and Avh241 probably disrupts the self-association of GmNDR1. These data highlight an effective counter-defense mechanism by which a Phytophthora effector suppresses plant immune responses, likely by disturbing the function of NDR1 during infection.
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Affiliation(s)
- Bo Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sen Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baodian Guo
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuyin Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenyue Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengjun Tian
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaixin Dai
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zehan Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haonan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenchuan Ma
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
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16
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Chen S, Ma T, Song S, Li X, Fu P, Wu W, Liu J, Gao Y, Ye W, Dry IB, Lu J. Arabidopsis downy mildew effector HaRxLL470 suppresses plant immunity by attenuating the DNA-binding activity of bZIP transcription factor HY5. THE NEW PHYTOLOGIST 2021; 230:1562-1577. [PMID: 33586184 DOI: 10.1111/nph.17280] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 05/27/2023]
Abstract
The oomycete pathogen Hyaloperonospora arabidopsidis delivers diverse effector proteins into host plant cells to suppress the plant's innate immunity. In this study, we investigate the mechanism of action of a conserved RxLR effector, HaRxLL470, in suppressing plant immunity. Genomic, molecular and biochemical analyses were performed to investigate the function of HaRxLL470 and the mechanism of the interaction between HaRxLL470 and the target host protein during H. arabidopsidis infection. We report that HaRxLL470 enhances plant susceptibility to H. arabidopsidis isolate Noco2 by interacting with the host photomorphogenesis regulator protein HY5. Our results demonstrate that HY5 is not only an important component in the regulation of light signalling, but also positively regulates host plant immunity against H. arabidopsidis by transcriptional activation of defense-related genes. We show that the interaction between HaRxLL470 and HY5 compromises the function of HY5 as a transcription factor by attenuating its DNA-binding activity. The present study demonstrates that HY5 positively regulates host plant defense against H. arabidopsidis whereas HaRxLL470, a conserved RxLR effector across oomycete pathogens, enhances pathogenicity by interacting with HY5 and suppressing transcriptional activation of defense-related genes.
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Affiliation(s)
- Shuyun Chen
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Ma
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiren Song
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinlong Li
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peining Fu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiaqi Liu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu Gao
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenxiu Ye
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ian B Dry
- CSIRO Agriculture & Food, Urrbrae, SA, 5064, Australia
| | - Jiang Lu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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17
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Ghareeb H, El-Sayed M, Pound M, Tetyuk O, Hanika K, Herrfurth C, Feussner I, Lipka V. Quantitative Hormone Signaling Output Analyses of Arabidopsis thaliana Interactions With Virulent and Avirulent Hyaloperonospora arabidopsidis Isolates at Single-Cell Resolution. FRONTIERS IN PLANT SCIENCE 2020; 11:603693. [PMID: 33240308 PMCID: PMC7677359 DOI: 10.3389/fpls.2020.603693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
The phytohormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) are central regulators of biotic and abiotic stress responses in Arabidopsis thaliana. Here, we generated modular fluorescent protein-based reporter lines termed COLORFUL-PR1pro, -VSP2pro, and -PDF1.2apro. These feature hormone-controlled nucleus-targeted transcriptional output sensors and the simultaneous constitutive expression of spectrally separated nuclear reference and plasma membrane-localized reporters. This set-up allowed the study of cell-type specific hormone activities, cellular viability and microbial invasion. Moreover, we developed a software-supported high-throughput confocal microscopy imaging protocol for output quantification to resolve the spatio-temporal dynamics of respective hormonal signaling activities at single-cell resolution. Proof-of-principle analyses in A. thaliana leaves revealed distinguished hormone sensitivities in mesophyll, epidermal pavement and stomatal guard cells, suggesting cell type-specific regulatory protein activities. In plant-microbe interaction studies, we found that virulent and avirulent Hyaloperonospora arabidopsidis (Hpa) isolates exhibit different invasion dynamics and induce spatio-temporally distinct hormonal activity signatures. On the cellular level, these hormone-controlled reporter signatures demarcate the nascent sites of Hpa entry and progression, and highlight initiation, transduction and local containment of immune signals.
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Affiliation(s)
- Hassan Ghareeb
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
- Department of Plant Biotechnology, National Research Centre, Cairo, Egypt
| | - Mohamed El-Sayed
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
- Department of Plant Biotechnology, National Research Centre, Cairo, Egypt
| | - Michael Pound
- School of Computer Science, University of Nottingham, Nottingham, United Kingdom
| | - Olena Tetyuk
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Katharina Hanika
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Volker Lipka
- Department of Plant Cell Biology, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
- Central Microscopy Facility of the Faculty of Biology and Psychology, University of Göttingen, Göttingen, Germany
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18
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Guo Y, Dupont P, Mesarich CH, Yang B, McDougal RL, Panda P, Dijkwel P, Studholme DJ, Sambles C, Win J, Wang Y, Williams NM, Bradshaw RE. Functional analysis of RXLR effectors from the New Zealand kauri dieback pathogen Phytophthora agathidicida. MOLECULAR PLANT PATHOLOGY 2020; 21:1131-1148. [PMID: 32638523 PMCID: PMC7411639 DOI: 10.1111/mpp.12967] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 05/08/2023]
Abstract
New Zealand kauri is an ancient, iconic, gymnosperm tree species that is under threat from a lethal dieback disease caused by the oomycete Phytophthora agathidicida. To gain insight into this pathogen, we determined whether proteinaceous effectors of P. agathidicida interact with the immune system of a model angiosperm, Nicotiana, as previously shown for Phytophthora pathogens of angiosperms. From the P. agathidicida genome, we defined and analysed a set of RXLR effectors, a class of proteins that typically have important roles in suppressing or activating the plant immune system. RXLRs were screened for their ability to activate or suppress the Nicotiana plant immune system using Agrobacterium tumefaciens transient transformation assays. Nine P. agathidicida RXLRs triggered cell death or suppressed plant immunity in Nicotiana, of which three were expressed in kauri. For the most highly expressed, P. agathidicida (Pa) RXLR24, candidate cognate immune receptors associated with cell death were identified in Nicotiana benthamiana using RNA silencing-based approaches. Our results show that RXLRs of a pathogen of gymnosperms can interact with the immune system of an angiosperm species. This study provides an important foundation for studying the molecular basis of plant-pathogen interactions in gymnosperm forest trees, including kauri.
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Affiliation(s)
- Yanan Guo
- Bio‐Protection Research CentreSchool of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | | | - Carl H. Mesarich
- Bio‐Protection Research CentreSchool of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | - Bo Yang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | | | - Preeti Panda
- Scion (New Zealand Forest Research Institute Ltd.)RotoruaNew Zealand
- The New Zealand Institute for Plant and Food ResearchAucklandNew Zealand
| | - Paul Dijkwel
- Bio‐Protection Research CentreSchool of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | | | | | - Joe Win
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Yuanchao Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Nari M. Williams
- Scion (New Zealand Forest Research Institute Ltd.)RotoruaNew Zealand
- The New Zealand Institute for Plant and Food ResearchAucklandNew Zealand
| | - Rosie E. Bradshaw
- Bio‐Protection Research CentreSchool of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
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Ai G, Yang K, Ye W, Tian Y, Du Y, Zhu H, Li T, Xia Q, Shen D, Peng H, Jing M, Xia A, Dou D. Prediction and Characterization of RXLR Effectors in Pythium Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1046-1058. [PMID: 32330072 DOI: 10.1094/mpmi-01-20-0010-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
RXLR effectors, a class of secreted proteins that are transferred into host cells to manipulate host immunity, have been reported to widely exist in oomycetes, including those from genera Phytophthora, Hyaloperonospora, Albugo, and Saprolegnia. However, in Pythium species, no RXLR effector has yet been characterized, and the origin and evolution of such virulent effectors are still unknown. Here, we developed a modified regular expression method for de novo identification of RXLRs and characterized 359 putative RXLR effectors in nine Pythium species. Phylogenetic analysis revealed that all oomycetous RXLRs formed a single superfamily, suggesting that they might have a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures, and genome locations. In particular, there were significantly more RXLR proteins in the mosquito biological control agent P. guiyangense than in the other eight Pythium species, and P. guiyangense RXLRs might be the result of gene duplication and genome rearrangement events, as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts of the majority of the predicted RXLR genes, with some RXLR effectors induced in infection stages and one RXLR showing necrosis-inducing activity. Furthermore, all predicted RXLR genes were cloned from two biocontrol agents, P. oligandrum and P. periplocum, and three of the RXLR genes were found to induce a defense response in Nicotiana benthamiana. Taken together, our findings represent the first evidence of RXLR effectors in Pythium species, providing valuable information on their evolutionary patterns and the mechanisms of their interactions with diverse hosts.
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Affiliation(s)
- Gan Ai
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwu Ye
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuee Tian
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Protection, Henan University of Science and Technology, Luoyang 471000, China
| | - Yaxin Du
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai Zhu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingyue Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, U.S.A
| | - Maofeng Jing
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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Klein J, Neilen M, van Verk M, Dutilh BE, Van den Ackerveken G. Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering. PLoS One 2020; 15:e0225808. [PMID: 32396560 PMCID: PMC7217449 DOI: 10.1371/journal.pone.0225808] [Citation(s) in RCA: 10] [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: 11/12/2019] [Accepted: 04/24/2020] [Indexed: 01/27/2023] Open
Abstract
Peronospora effusa (previously known as P. farinosa f. sp. spinaciae, and here referred to as Pfs) is an obligate biotrophic oomycete that causes downy mildew on spinach (Spinacia oleracea). To combat this destructive many disease resistant cultivars have been bred and used. However, new Pfs races rapidly break the employed resistance genes. To get insight into the gene repertoire of Pfs and identify infection-related genes, the genome of the first reference race, Pfs1, was sequenced, assembled, and annotated. Due to the obligate biotrophic nature of this pathogen, material for DNA isolation can only be collected from infected spinach leaves that, however, also contain many other microorganisms. The obtained sequences can, therefore, be considered a metagenome. To filter and obtain Pfs sequences we utilized the CAT tool to taxonomically annotate ORFs residing on long sequences of a genome pre-assembly. This study is the first to show that CAT filtering performs well on eukaryotic contigs. Based on the taxonomy, determined on multiple ORFs, contaminating long sequences and corresponding reads were removed from the metagenome. Filtered reads were re-assembled to provide a clean and improved Pfs genome sequence of 32.4 Mbp consisting of 8,635 scaffolds. Transcript sequencing of a range of infection time points aided the prediction of a total of 13,277 gene models, including 99 RxLR(-like) effector, and 14 putative Crinkler genes. Comparative analysis identified common features in the predicted secretomes of different obligate biotrophic oomycetes, regardless of their phylogenetic distance. Their secretomes are generally smaller, compared to hemi-biotrophic and necrotrophic oomycete species. We observe a reduction in proteins involved in cell wall degradation, in Nep1-like proteins (NLPs), proteins with PAN/apple domains, and host translocated effectors. The genome of Pfs1 will be instrumental in studying downy mildew virulence and for understanding the molecular adaptations by which new isolates break spinach resistance.
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Affiliation(s)
- Joël Klein
- Department of Biology, Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
| | - Manon Neilen
- Department of Biology, Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
| | - Marcel van Verk
- Department of Biology, Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
- Crop Data Science, KeyGene, Wageningen, The Netherlands
| | - Bas E. Dutilh
- Department of Biology, Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Guido Van den Ackerveken
- Department of Biology, Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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21
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Situ J, Jiang L, Fan X, Yang W, Li W, Xi P, Deng Y, Kong G, Jiang Z. An RXLR effector PlAvh142 from Peronophythora litchii triggers plant cell death and contributes to virulence. MOLECULAR PLANT PATHOLOGY 2020; 21:415-428. [PMID: 31912634 PMCID: PMC7036370 DOI: 10.1111/mpp.12905] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 05/09/2023]
Abstract
Litchi downy blight, caused by the phytopathogenic oomycete Peronophythora litchii, results in tremendous economic loss in litchi production every year. To successfully colonize the host cell, Phytophthora species secret hundreds of RXLR effectors that interfere with plant immunity and facilitate the infection process. Previous work has already predicted 245 candidate RXLR effector-encoding genes in P. litchii, 212 of which have been cloned and tested for plant cell death-inducing activity in this study. We found three such RXLR effectors could trigger plant cell death through transient expression in Nicotiana benthamiana. Further experiments demonstrated that PlAvh142 could induce cell death and immune responses in several plants. We also found that PlAvh142 localized in both the cytoplasm and nucleus of plant cells. The cytoplasmic localization was critical for its cell death-inducing activity. Moreover, deletion either of the two internal repeats in PlAvh142 abolished the cell death-inducing activity. Virus-induced gene silencing assays showed that cell death triggered by PlAvh142 was dependent on the plant transduction components RAR1 (require for Mla12 resistance), SGT1 (suppressor of the G2 allele of skp1) and HSP90 (heat shock protein 90). Finally, knockout of PlAvh142 resulted in significantly attenuated P. litchii virulence on litchi plants, whereas the PlAvh142-overexpressed mutants were more aggressive. These data indicated that PlAvh142 could be recognized in plant cytoplasm and is an important virulence RXLR effector of P. litchii.
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Affiliation(s)
- Junjian Situ
- Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
| | - Liqun Jiang
- Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
- Guangdong Province Key Laboratory of New Technology in Rice Breeding/Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Xiaoning Fan
- Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
| | - Wensheng Yang
- Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
| | - Wen Li
- Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
| | - Pinggen Xi
- Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
| | - Yizhen Deng
- Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
| | - Guanghui Kong
- Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
| | - Zide Jiang
- Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhouChina
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22
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Lu S, Yu J, Ma L, Dou D. Two phosphatidylinositol 3-kinase components are involved in interactions between Nicotiana benthamiana and Phytophthora by regulating pathogen effectors and host cell death. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:293-302. [PMID: 32054565 DOI: 10.1071/fp19155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Phosphatidylinositol 3-phosphate (PtdIns(3)P) has been reported to regulate different physiological processes in plants. PtdIns(3)P is synthesised by the phosphatidylinositol 3-kinase (PI3K) complex which includes common subunits of vacuolar protein sorting (VPS)15, VPS30 and VPS34. Here, we characterised the roles of the important genes NbVPS15, -30 and -34 encoding PI3K components during interactions between Nicotiana benthamiana and Phytophthora pathogens. NbVPS15 and NbVPS34 were upregulated during infection, and plants deficient in these two genes displayed higher resistance to two different Phytophthora pathogens. Silencing NbVPS15 and NbVPS34 decreased the content of PtdIns(3)P in plant cells and the stability of three RxLR (containing the characteristic amino-terminal motif of arginine-X-leucine-arginine, X is any amino acid) effectors. Furthermore, NbVPS15, -30 and -34 were essential for autolysosome formation during Phytophthora capsici infection and limiting programmed cell death (PCD) induced by effectors and elicitors. Taken together, these findings suggest that NbVPS15 and NbVPS34 play a critical role in the resistance of N. benthamiana to Phytophthora pathogens by regulating PtdIns(3)P contents and host PCD.
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Affiliation(s)
- Shan Lu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; and Corresponding author.
| | - Jia Yu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Lina Ma
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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23
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Zhang X, Liu B, Zou F, Shen D, Yin Z, Wang R, He F, Wang Y, Tyler BM, Fan W, Qian W, Dou D. Whole Genome Re-sequencing Reveals Natural Variation and Adaptive Evolution of Phytophthora sojae. Front Microbiol 2019; 10:2792. [PMID: 31849921 PMCID: PMC6895562 DOI: 10.3389/fmicb.2019.02792] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022] Open
Abstract
Due to the monocultural basis of agricultural crops, mutated plant microbes with increased pathogenicity can easily spread in the field and lead to serious yield losses. As a major threat to a wide range of crop plants, oomycete pathogens continuously undergo adaptive evolution to overcome plant defense barriers. However, the genetic basis of their evolution at the molecular level remains largely unknown. Here, we investigated the nature variation and the population genomics of the soybean pathogen Phytophthora sojae by high-throughput genome re-sequencing. Genomic variation analysis revealed uneven “two-speed” evolutionary pattern with genes in gene-sparse regions (GSRs) showing higher rates of structural polymorphisms and positive selection. GSRs are enriched in effector genes and transposase-related genes. Our results also suggested that the NADH oxidase and MIP transporter gene families undergo rapid and diversifying selection. Furthermore, we demonstrated that P. sojae isolates possess varying numbers of RxLR effectors with diverse sequences, totaling 471 members. Among them, 42 core RxLR effectors are assumed to be important for infection. Finally, we observed that Avr genes exhibit abundant sequence variation in P. sojae isolates. Several novel variants lead to the evading of host resistance, including a complete deletion in Avr3c and amino acid mutations in Avr1a. Taken together, our results provide an adaptive landscape of P. sojae at single-nucleotide resolution, as well as resources for further resistance breeding and disease prevention against this important plant pathogen.
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Affiliation(s)
- Xiong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Bo Liu
- Agricultural Genomic Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fen Zou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyuan Yin
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Rongbo Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Feng He
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Wei Fan
- Agricultural Genomic Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wanqiang Qian
- Agricultural Genomic Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Department of Plant Pathology, China Agricultural University, Beijing, China
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24
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Biotechnological potential of engineering pathogen effector proteins for use in plant disease management. Biotechnol Adv 2019; 37:107387. [DOI: 10.1016/j.biotechadv.2019.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 11/19/2022]
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25
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Li T, Wang Q, Feng R, Li L, Ding L, Fan G, Li W, Du Y, Zhang M, Huang G, Schäfer P, Meng Y, Tyler BM, Shan W. Negative regulators of plant immunity derived from cinnamyl alcohol dehydrogenases are targeted by multiple Phytophthora Avr3a-like effectors. THE NEW PHYTOLOGIST 2019. [PMID: 31436314 DOI: 10.1111/nph.16139] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/15/2019] [Indexed: 05/21/2023]
Abstract
Oomycete pathogens secrete numerous effectors to manipulate host immunity. While some effectors share a conserved structural fold, it remains unclear if any have conserved host targets. Avr3a-like family effectors, which are related to Phytophthora infestans effector PiAvr3a and are widely distributed across diverse clades of Phytophthora species, were used to study this question. By using yeast-two-hybrid, bimolecular fluorescence complementation and co-immunoprecipitation assays, we identified members of the plant cinnamyl alcohol dehydrogenase 7 (CAD7) subfamily as targets of multiple Avr3a-like effectors from Phytophthora pathogens. The CAD7 subfamily has expanded in plant genomes but lost the lignin biosynthetic activity of canonical CAD subfamilies. In turn, we identified CAD7s as negative regulators of plant immunity that are induced by Phytophthora infection. Moreover, AtCAD7 was stabilized by Avr3a-like effectors and involved in suppression of pathogen-associated molecular pattern-triggered immunity, including callose deposition, reactive oxygen species burst and WRKY33 expression. Our results reveal CAD7 subfamily proteins as negative regulators of plant immunity that are exploited by multiple Avr3a-like effectors to promote infection in different host plants.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ruirui Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Licai Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Liwen Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guangjin Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weiwei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yu Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Meixiang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guiyan Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, UK
| | - Yuling Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
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26
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Zhang P, Jia Y, Shi J, Chen C, Ye W, Wang Y, Ma W, Qiao Y. The WY domain in the Phytophthora effector PSR1 is required for infection and RNA silencing suppression activity. THE NEW PHYTOLOGIST 2019; 223:839-852. [PMID: 30963588 DOI: 10.1111/nph.15836] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/29/2019] [Indexed: 05/27/2023]
Abstract
Phytophthora pathogens manipulate host innate immunity by secreting numerous RxLR effectors, thereby facilitating pathogen colonization. Predicted single and tandem repeats of WY domains are the most prominent C-terminal motifs conserved across the Phytophthora RxLR superfamily. However, the functions of individual WY domains in effectors remain poorly understood. The Phytophthora sojae effector PSR1 promotes infection by suppressing small RNA biogenesis in plant hosts. We identified one single WY domain following the RxLR motif in PSR1. This domain was required for RNA silencing suppression activity and infection in Nicotiana benthamiana, Arabidopsis and soybean. Mutations of the conserved residues in the WY domain did not affect the subcellular localization of PSR1 but abolished its effect on plant development and resistance to viral and Phytophthora pathogens. This is at least in part due to decreased protein stability of the PSR1 mutants in planta. The identification of the WY domain in PSR1 allows predicts that a family of PSR1-like effectors also possess RNA silencing suppression activity. Mutation of the conserved residues in two members of this family, PpPSR1L from P. parasitica and PcPSR1L from P. capsici, perturbed their biological functions, indicating that the WY domain is critical in Phytophthora PSR1 and PSR1-like effectors.
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Affiliation(s)
- Peng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Yijuan Jia
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jinxia Shi
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chen Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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27
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Lan X, Liu Y, Song S, Yin L, Xiang J, Qu J, Lu J. Plasmopara viticola effector PvRXLR131 suppresses plant immunity by targeting plant receptor-like kinase inhibitor BKI1. MOLECULAR PLANT PATHOLOGY 2019; 20:765-783. [PMID: 30945786 PMCID: PMC6637860 DOI: 10.1111/mpp.12790] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The grapevine downy mildew pathogen Plasmopara viticola secretes a set of RXLR effectors (PvRXLRs) to overcome host immunity and facilitate infection, but how these effectors function is unclear. Here, the biological function of PvRXLR131 was investigated via heterologous expression. Constitutive expression of PvRXLR131 in Colletotrichum gloeosporioides significantly enhanced its pathogenicity on grapevine leaves. Constitutive expression of PvRXLR131 in Arabidopsis promoted Pseudomonas syringae DC3000 and P. syringae DC3000 (hrcC- ) growth as well as suppressed defence-related callose deposition. Transient expression of PvRXLR131 in Nicotiana benthamiana leaves could also suppress different elicitor-triggered cell death and inhibit plant resistance to Phytophthora capsici. Further analysis revealed that PvRXLR131 interacted with host Vitis vinifera BRI1 kinase inhibitor 1 (VvBKI1), and its homologues in N. benthamiana (NbBKI1) and Arabidopsis (AtBKI1). Moreover, bimolecular fluorescence complementation analysis revealed that PvRXLR131 interacted with VvBKI1 in the plasma membrane. Deletion assays showed that the C-terminus of PvRXLR131 was responsible for the interaction and mutation assays showed that phosphorylation of a conserved tyrosine residue in BKI1s disrupted the interaction. BKI1 was a receptor inhibitor of growth- and defence-related brassinosteroid (BR) and ERECTA (ER) signalling. When silencing of NbBKI1 in N. benthamiana, the virulence function of PvRXLR131 was eliminated, demonstrating that the effector activity is mediated by BKI1. Moreover, PvRXLR131-transgenic plants displayed BKI1-overexpression dwarf phenotypes and suppressed BR and ER signalling. These physiological and genetic data clearly demonstrate that BKI1 is a virulence target of PvRXLR131. We propose that P. viticola secretes PvRXLR131 to target BKI1 as a strategy for promoting infection.
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Affiliation(s)
- Xia Lan
- College of Food Science and Nutritional EngineeringChina Agricultural UniversityBeijingChina
- Center for Viticulture and Enology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yunxiao Liu
- College of Food Science and Nutritional EngineeringChina Agricultural UniversityBeijingChina
- Center for Viticulture and Enology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Shiren Song
- Center for Viticulture and Enology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ling Yin
- Guangxi Crop Genetic Improvement and Biotechnology LaboratoryGuangxi Academy of Agricultural SciencesNanningChina
| | - Jiang Xiang
- Center for Viticulture and Enology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology LaboratoryGuangxi Academy of Agricultural SciencesNanningChina
| | - Jiang Lu
- Center for Viticulture and Enology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
- Guangxi Crop Genetic Improvement and Biotechnology LaboratoryGuangxi Academy of Agricultural SciencesNanningChina
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28
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Mohd-Assaad N, McDonald BA, Croll D. The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses. Environ Microbiol 2019; 21:2677-2695. [PMID: 30838748 DOI: 10.1111/1462-2920.14583] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 01/28/2023]
Abstract
Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species-specific and the evolutionary trajectories are poorly understood. Here, we investigate the necrosis-inducing protein 1 (NIP1) effector in the multihost pathogen genus Rhynchosporium. We retraced the evolutionary history of the NIP1 locus using whole-genome assemblies of 146 strains covering four closely related species. NIP1 orthologues were present in all species but the locus consistently segregated presence-absence polymorphisms suggesting long-term balancing selection. We also identified previously unknown paralogues of NIP1 that were shared among multiple species and showed substantial copy-number variation within R. commune. The NIP1A paralogue was under significant positive selection suggesting that NIP1A is the dominant effector variant coevolving with host immune receptors. Consistent with this prediction, we found that copy number variation at NIP1A had a stronger effect on virulence than NIP1B. Our analyses unravelled the origins and diversification mechanisms of a pathogen effector family shedding light on how pathogens gain adaptive genetic variation.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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29
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Liu L, Xu L, Jia Q, Pan R, Oelmüller R, Zhang W, Wu C. Arms race: diverse effector proteins with conserved motifs. PLANT SIGNALING & BEHAVIOR 2019; 14:1557008. [PMID: 30621489 PMCID: PMC6351098 DOI: 10.1080/15592324.2018.1557008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Effector proteins play important roles in the infection by pathogenic oomycetes and fungi or the colonization by endophytic and mycorrhizal fungi. They are either translocated into the host plant cells via specific translocation mechanisms and function in the host's cytoplasm or nucleus, or they reside in the apoplast of the plant cells and act at the extracellular host-microbe interface. Many effector proteins possess conserved motifs (such as the RXLR, CRN, LysM, RGD, DELD, EAR, RYWT, Y/F/WXC or CFEM motifs) localized in their N- or C-terminal regions. Analysis of the functions of effector proteins, especially so-called "core effectors", is crucial for the understanding of pathogenicity/symbiosis mechanisms and plant defense strategies, and helps to develop breeding strategies for pathogen-resistant cultivars, and to increase crop yield and quality as well as abiotic stress resistance. This review summarizes current knowledge about these effector proteins with the conversed motifs and their involvement in pathogenic or mutualistic plant/fungal interactions.
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Affiliation(s)
- Liping Liu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Le Xu
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Qie Jia
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Ralf Oelmüller
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
- CONTACT Wenying Zhang Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou 434025, China; Chu Wu College of Horticulture & Gardening, Yangtze University, Jingzhou 434025, China
| | - Chu Wu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
- Institute of Plant Ecology and Environmental Restoration, Yangtze University, Jingzhou, China
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30
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Deb D, Mackey D, Opiyo SO, McDowell JM. Application of alignment-free bioinformatics methods to identify an oomycete protein with structural and functional similarity to the bacterial AvrE effector protein. PLoS One 2018; 13:e0195559. [PMID: 29641586 PMCID: PMC5895030 DOI: 10.1371/journal.pone.0195559] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/23/2018] [Indexed: 11/23/2022] Open
Abstract
Diverse plant pathogens export effector proteins to reprogram host cells. One of the most challenging goals in the molecular plant-microbe field is to functionally characterize the complex repertoires of effectors secreted by these pathogens. For bacterial pathogens, the predominant class of effectors is delivered to host cells by Type III secretion. For oomycetes, the predominant class of effectors is defined by a signal peptide that mediates secretion from the oomycete and a conserved RxLR motif. Downy mildew pathogens and Phytophthora species maintain hundreds of candidate RxLR effector genes in their genomes. Although no primary sequence similarity is evident between bacterial Type III effectors (T3Es) and oomycete RXLR effectors, some bacterial and oomycete effectors have convergently evolved to target the same host proteins. Such effectors might have evolved domains that are functionally similar but sequence-unrelated. We reasoned that alignment-free bioinformatics approaches could be useful to identify structural similarities between bacterial and oomycete effectors. To test this approach, we used partial least squares regression, alignment-free bioinformatics methods to identify effector proteins from the genome of the oomycete Hyaloperonospora arabidopsidis that are similar to the well-studied AvrE1 effector from Pseudomonas syringae. This approach identified five RxLR proteins with putative structural similarity to AvrE1. We focused on one, HaRxL23, because it is an experimentally validated effector and it is conserved between distantly related oomycetes. Several experiments indicate that HaRxL23 is functionally similar to AvrE1, including the ability to partially rescue an AvrE1 loss-of-function mutant. This study provides an example of how an alignment-free bioinformatics approach can identify functionally similar effector proteins in the absence of primary sequence similarity. This approach could be useful to identify effectors that have convergently evolved regardless of whether the shared host target is known.
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Affiliation(s)
- Devdutta Deb
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - David Mackey
- Departments of Horticulture and Crop Science and Molecular Genetics, Ohio State University, Columbus, Ohio, United States of America
| | - Stephen O. Opiyo
- Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center, Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (SOO); (JMM)
| | - John M. McDowell
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail: (SOO); (JMM)
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