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Dodds PN, Chen J, Outram MA. Pathogen perception and signaling in plant immunity. THE PLANT CELL 2024; 36:1465-1481. [PMID: 38262477 PMCID: PMC11062475 DOI: 10.1093/plcell/koae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/19/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Plant diseases are a constant and serious threat to agriculture and ecological biodiversity. Plants possess a sophisticated innate immunity system capable of detecting and responding to pathogen infection to prevent disease. Our understanding of this system has grown enormously over the past century. Early genetic descriptions of plant disease resistance and pathogen virulence were embodied in the gene-for-gene hypothesis, while physiological studies identified pathogen-derived elicitors that could trigger defense responses in plant cells and tissues. Molecular studies of these phenomena have now coalesced into an integrated model of plant immunity involving cell surface and intracellular detection of specific pathogen-derived molecules and proteins culminating in the induction of various cellular responses. Extracellular and intracellular receptors engage distinct signaling processes but converge on many similar outputs with substantial evidence now for integration of these pathways into interdependent networks controlling disease outcomes. Many of the molecular details of pathogen recognition and signaling processes are now known, providing opportunities for bioengineering to enhance plant protection from disease. Here we provide an overview of the current understanding of the main principles of plant immunity, with an emphasis on the key scientific milestones leading to these insights.
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Affiliation(s)
- Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Megan A Outram
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
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2
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Jones JDG, Staskawicz BJ, Dangl JL. The plant immune system: From discovery to deployment. Cell 2024; 187:2095-2116. [PMID: 38670067 DOI: 10.1016/j.cell.2024.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/08/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
Plant diseases cause famines, drive human migration, and present challenges to agricultural sustainability as pathogen ranges shift under climate change. Plant breeders discovered Mendelian genetic loci conferring disease resistance to specific pathogen isolates over 100 years ago. Subsequent breeding for disease resistance underpins modern agriculture and, along with the emergence and focus on model plants for genetics and genomics research, has provided rich resources for molecular biological exploration over the last 50 years. These studies led to the identification of extracellular and intracellular receptors that convert recognition of extracellular microbe-encoded molecular patterns or intracellular pathogen-delivered virulence effectors into defense activation. These receptor systems, and downstream responses, define plant immune systems that have evolved since the migration of plants to land ∼500 million years ago. Our current understanding of plant immune systems provides the platform for development of rational resistance enhancement to control the many diseases that continue to plague crop production.
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Affiliation(s)
- Jonathan D G Jones
- Sainsbury Lab, University of East Anglia, Colney Lane, Norwich NR4 7UH, UK.
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology and Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill and Howard Hughes Medical Institute, Chapel Hill, NC 27599, USA
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3
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Jost M, Outram MA, Dibley K, Zhang J, Luo M, Ayliffe M. Plant and pathogen genomics: essential approaches for stem rust resistance gene stacks in wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1223504. [PMID: 37727853 PMCID: PMC10505659 DOI: 10.3389/fpls.2023.1223504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/27/2023] [Indexed: 09/21/2023]
Abstract
The deployment of disease resistance genes is currently the most economical and environmentally sustainable method of crop protection. However, disease resistance genes can rapidly break down because of constant pathogen evolution, particularly when they are deployed singularly. Polygenic resistance is, therefore, considered the most durable, but combining and maintaining these genes by breeding is a laborious process as effective genes are usually unlinked. The deployment of polygenic resistance with single-locus inheritance is a promising innovation that overcomes these difficulties while enhancing resistance durability. Because of major advances in genomic technologies, increasing numbers of plant resistance genes have been cloned, enabling the development of resistance transgene stacks (RTGSs) that encode multiple genes all located at a single genetic locus. Gene stacks encoding five stem rust resistance genes have now been developed in transgenic wheat and offer both breeding simplicity and potential resistance durability. The development of similar genomic resources in phytopathogens has advanced effector gene isolation and, in some instances, enabled functional validation of individual resistance genes in RTGS. Here, the wheat stem rust pathosystem is used as an illustrative example of how host and pathogen genomic advances have been instrumental in the development of RTGS, which is a strategy applicable to many other agricultural crop species.
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Affiliation(s)
| | | | | | | | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
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McCombe CL, Catanzariti AM, Greenwood JR, Desai AM, Outram MA, Yu DS, Ericsson DJ, Brenner SE, Dodds PN, Kobe B, Jones DA, Williams SJ. A rust-fungus Nudix hydrolase effector decaps mRNA in vitro and interferes with plant immune pathways. THE NEW PHYTOLOGIST 2023; 239:222-239. [PMID: 36631975 DOI: 10.1111/nph.18727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/02/2023] [Indexed: 06/02/2023]
Abstract
To infect plants, pathogenic fungi secrete small proteins called effectors. Here, we describe the catalytic activity and potential virulence function of the Nudix hydrolase effector AvrM14 from the flax rust fungus (Melampsora lini). We completed extensive in vitro assays to characterise the enzymatic activity of the AvrM14 effector. Additionally, we used in planta transient expression of wild-type and catalytically dead AvrM14 versions followed by biochemical assays, phenotypic analysis and RNA sequencing to unravel how the catalytic activity of AvrM14 impacts plant immunity. AvrM14 is an extremely selective enzyme capable of removing the protective 5' cap from mRNA transcripts in vitro. Homodimerisation of AvrM14 promoted biologically relevant mRNA cap cleavage in vitro and this activity was conserved in related effectors from other Melampsora spp. In planta expression of wild-type AvrM14, but not the catalytically dead version, suppressed immune-related reactive oxygen species production, altered the abundance of some circadian-rhythm-associated mRNA transcripts and reduced the hypersensitive cell-death response triggered by the flax disease resistance protein M1. To date, the decapping of host mRNA as a virulence strategy has not been described beyond viruses. Our results indicate that some fungal pathogens produce Nudix hydrolase effectors with in vitro mRNA-decapping activity capable of interfering with plant immunity.
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Affiliation(s)
- Carl L McCombe
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ann-Maree Catanzariti
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Julian R Greenwood
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Anna M Desai
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Megan A Outram
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel S Yu
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Australian Synchrotron, Macromolecular Crystallography, Clayton, Vic., 3168, Australia
| | - Steven E Brenner
- Plant and Microbial Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld, 4072, Australia
| | - David A Jones
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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5
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Zhang Y, Zhang Y, Ge X, Yuan Y, Jin Y, Wang Y, Zhao L, Han X, Hu W, Yang L, Gao C, Wei X, Li F, Yang Z. Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton. Genome Biol 2023; 24:111. [PMID: 37165460 PMCID: PMC10170703 DOI: 10.1186/s13059-023-02950-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Verticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen, Verticillium dahliae, yet the related genetic mechanism remains unknown. RESULTS By genome-wide association studies of 419 accessions of the upland cotton, Gossypium hirsutum, we identify ten loci that are associated with resistance against Verticillium wilt. Among these loci, SHZDI1/SHZDP2/AYDP1 from chromosome A10 is located on a fragment introgressed from Gossypium arboreum. We characterize a large cluster of Toll/interleukin 1 (TIR) nucleotide-binding leucine-rich repeat receptors in this fragment. We then identify a dual-TIR domain gene from this cluster, GhRVD1, which triggers an effector-independent cell death and is induced by Verticillium dahliae. We confirm that GhRVD1 is one of the causal gene for SHZDI1. Allelic variation in the TIR domain attenuates GhRVD1-mediated resistance against Verticillium dahliae. Homodimerization between TIR1-TIR2 mediates rapid immune response, while disruption of its αD- and αE-helices interface eliminates the autoactivity and self-association of TIR1-TIR2. We further demonstrate that GhTIRP1 inhibits the autoactivity and self-association of TIR1-TIR2 by competing for binding to them, thereby preventing the resistance to Verticillium dahliae. CONCLUSIONS We propose the first working model for TIRP1 involved self-association and autoactivity of dual-TIR domain proteins that confer compromised pathogen resistance of dual-TIR domain proteins in plants. The findings reveal a novel mechanism on Verticillium dahliae resistance and provide genetic basis for breeding in future.
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Affiliation(s)
- Yihao Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yaning Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Xiaoyang Ge
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuan Yuan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuying Jin
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ye Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lihong Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiao Han
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chenxu Gao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Xi Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Umer MJ, Zheng J, Yang M, Batool R, Abro AA, Hou Y, Xu Y, Gebremeskel H, Wang Y, Zhou Z, Cai X, Liu F, Zhang B. Insights to Gossypium defense response against Verticillium dahliae: the Cotton Cancer. Funct Integr Genomics 2023; 23:142. [PMID: 37121989 DOI: 10.1007/s10142-023-01065-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
The soil-borne pathogen Verticillium dahliae, also referred as "The Cotton Cancer," is responsible for causing Verticillium wilt in cotton crops, a destructive disease with a global impact. To infect cotton plants, the pathogen employs multiple virulence mechanisms such as releasing enzymes that degrade cell walls, activating genes that contribute to virulence, and using protein effectors. Conversely, cotton plants have developed numerous defense mechanisms to combat the impact of V. dahliae. These include strengthening the cell wall by producing lignin and depositing callose, discharging reactive oxygen species, and amassing hormones related to defense. Despite the efforts to develop resistant cultivars, there is still no permanent solution to Verticillium wilt due to a limited understanding of the underlying molecular mechanisms that drive both resistance and pathogenesis is currently prevalent. To address this challenge, cutting-edge technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), host-induced gene silencing (HIGS), and gene delivery via nano-carriers could be employed as effective alternatives to control the disease. This article intends to present an overview of V. dahliae virulence mechanisms and discuss the different cotton defense mechanisms against Verticillium wilt, including morphophysiological and biochemical responses and signaling pathways including jasmonic acid (JA), salicylic acid (SA), ethylene (ET), and strigolactones (SLs). Additionally, the article highlights the significance of microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs) in gene expression regulation, as well as the different methods employed to identify and functionally validate genes to achieve resistance against this disease. Gaining a more profound understanding of these mechanisms could potentially result in the creation of more efficient strategies for combating Verticillium wilt in cotton crops.
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Affiliation(s)
- Muhammad Jawad Umer
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jie Zheng
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory, China/National Nanfan, Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572025, China
| | - Mengying Yang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Raufa Batool
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aamir Ali Abro
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Haileslassie Gebremeskel
- Mehoni Agricultural Research Center, Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Yuhong Wang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - ZhongLi Zhou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory, China/National Nanfan, Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572025, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Hainan Yazhou Bay Seed Laboratory, China/National Nanfan, Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572025, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.
| | - Baohong Zhang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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Xiao G, Wang W, Liu M, Li Y, Liu J, Franceschetti M, Yi Z, Zhu X, Zhang Z, Lu G, Banfield MJ, Wu J, Zhou B. The Piks allele of the NLR immune receptor Pik breaks the recognition of AvrPik effectors of rice blast fungus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:810-824. [PMID: 36178632 DOI: 10.1111/jipb.13375] [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] [Received: 07/20/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Arms race co-evolution of plant-pathogen interactions evolved sophisticated recognition mechanisms between host immune receptors and pathogen effectors. Different allelic haplotypes of an immune receptor in the host mount distinct recognition against sequence or non-sequence related effectors in pathogens. We report the molecular characterization of the Piks allele of the rice immune receptor Pik against rice blast pathogen, which requires two head-to-head arrayed nucleotide-binding sites and leucine-rich repeat proteins. Like other Pik alleles, both Piks-1 and Piks-2 are necessary and sufficient for mediating resistance. However, unlike other Pik alleles, Piks does not recognize any known AvrPik variants of Magnaporthe oryzae. Sequence analysis of the genome of an avirulent isolate V86010 further revealed that its cognate avirulence (Avr) gene most likely has no significant sequence similarity to known AvrPik variants. Piks-1 and Pikm-1 have only two amino acid differences within the integrated heavy metal-associated (HMA) domain. Pikm-HMA interacts with AvrPik-A, -D, and -E in vitro and in vivo, whereas Piks-HMA does not bind any AvrPik variants. Characterization of two amino acid residues differing Piks-1 from Pikm-1 reveal that Piks-E229Q derived from the exchange of Glu229 to Gln229 in Piks-1 gains recognition specificity against AvrPik-D but not AvrPik-A or -E, indicating that Piks-E229Q partially restores the Pikm spectrum. By contrast, Piks-A261V derived from the exchange of Ala261 to Val261 in Piks-1 retains Piks recognition specificity. We conclude that Glu229 in Piks-1 is critical for Piks breaking the canonical Pik/AvrPik recognition pattern. Intriguingly, binding activity and ectopic cell death induction is maintained between Piks-A261V and AvrPik-D, implying that positive outcomes from ectopic assays might be insufficient to deduce its immune activity against the relevant effectors in rice and rice blast interaction.
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Affiliation(s)
- Gui Xiao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410128, China
- International Rice Research Institute, Metro Manila, 1301, Philippines
| | - Wenjuan Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Ya Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianbin Liu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410128, China
| | - Marina Franceschetti
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Zhaofeng Yi
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410128, China
| | - Xiaoyuan Zhu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, 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, Ministry of Education, Nanjing, 210095, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mark J Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jun Wu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410128, China
| | - Bo Zhou
- International Rice Research Institute, Metro Manila, 1301, Philippines
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8
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Wen TY, Wu XQ, Ye JR, Qiu YJ, Rui L, Zhang Y. Two Novel Bursaphelenchus xylophilus Kunitz Effector Proteins Using Different Infection and Survival Strategies to Suppress Immunity in Pine. PHYTOPATHOLOGY 2023; 113:539-548. [PMID: 36976314 DOI: 10.1094/phyto-04-22-0127-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Pine wilt disease, caused by Bursaphelenchus xylophilus, results in tremendous economic loss in conifer production every year. To disturb the host immune responses, plant pathogens secrete a mass of effector proteins that facilitate the infection process. Although several effectors of B. xylophilus have been identified, detailed mechanisms of their functions remain largely unexplored. Here, we reveal two novel B. xylophilus Kunitz effectors, named BxKU1 and BxKU2, using different infection strategies to suppress immunity in Pinus thunbergii. We found that both BxKU1 and BxKU2 could suppress PsXEG1-triggered cell death and were present in the nucleus and cytoplasm in Nicotiana benthamiana. However, they had different three-dimensional structures and various expression patterns in B. xylophilus infection. In situ hybridization experiments showed that BxKU2 was expressed in the esophageal glands and ovaries, whereas BxKU1 was only expressed in the esophageal glands of females. We further confirmed that the morbidity was significantly decreased in P. thunbergii infected with B. xylophilus when BxKU1 and BxKU2 were silenced. The silenced BxKU2I, but not BxKU1, affected the reproduction and feeding rate of B. xylophilus. Moreover, BxKU1 and BxKU2 targeted to different proteins in P. thunbergii, but they all interacted with thaumatin-like protein 4 (TLP4) according to yeast two-hybrid screening. Collectively, our study showed that B. xylophilus could incorporate two Kunitz effectors in a multilayer strategy to counter immune response in P. thunbergii, which could help us better understand the interaction between plant and B. xylophilus.
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Affiliation(s)
- Tong-Yue Wen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, 210037, China
| | - Jian-Ren Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, 210037, China
| | - Yi-Jun Qiu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, 210037, China
| | - Lin Rui
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, 210037, China
| | - Yan Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, 210037, China
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9
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Zeng Y, Song H, Xia L, Yang L, Zhang S. The responses of poplars to fungal pathogens: A review of the defensive pathway. FRONTIERS IN PLANT SCIENCE 2023; 14:1107583. [PMID: 36875570 PMCID: PMC9978395 DOI: 10.3389/fpls.2023.1107583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Long-lived tree species need to cope with changing environments and pathogens during their lifetime. Fungal diseases cause damage to trees growth and forest nurseries. As model system for woody plants, poplars are also hosts of a large variety of fungus. The defense strategies to fungus are generally associated with the type of fungus, therefore, the defense strategies of poplar against necrotrophic and biotrophic fungus are different. Poplars initiate constitutive defenses and induced defenses based on recognition of the fungus, hormone signaling network cascades, activation of defense-related genes and transcription factors and production of phytochemicals. The means of sensing fungus invasion in poplars are similar with herbs, both of which are mediated by receptor proteins and resistance (R) proteins, leading to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), but poplars have evolved some unique defense mechanisms compared with Arabidopsis due to their longevity. In this paper, current researches on poplar defensive responses to necrotrophic and biotrophic fungus, which mainly include the physiological and genetic aspects, and the role of noncoding RNA (ncRNA) in fungal resistance are reviewed. This review also provides strategies to enhance poplar disease resistance and some new insights into future research directions.
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Affiliation(s)
- Yi Zeng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Haifeng Song
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Linchao Xia
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Le Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Sheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Advances in Fungal Elicitor-Triggered Plant Immunity. Int J Mol Sci 2022; 23:ijms231912003. [PMID: 36233304 PMCID: PMC9569958 DOI: 10.3390/ijms231912003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 11/17/2022] Open
Abstract
There is an array of pathogenic fungi in the natural environment of plants, which produce some molecules including pathogen-associated molecular patterns (PAMPs) and effectors during infection. These molecules, which can be recognized by plant specific receptors to activate plant immunity, including PTI (PAMP-triggered immunity) and ETI (effector-triggered immunity), are called elicitors. Undoubtedly, identification of novel fungal elicitors and their plant receptors and comprehensive understanding about fungal elicitor-triggered plant immunity will be of great significance to effectively control plant diseases. Great progress has occurred in fungal elicitor-triggered plant immunity, especially in the signaling pathways of PTI and ETI, in recent years. Here, recent advances in fungal elicitor-triggered plant immunity are summarized and their important contribution to the enlightenment of plant disease control is also discussed.
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Zhan Z, Liu H, Yang Y, Liu S, Li X, Piao Z. Identification and characterization of putative effectors from Plasmodiophora brassicae that suppress or induce cell death in Nicotiana benthamiana. FRONTIERS IN PLANT SCIENCE 2022; 13:881992. [PMID: 36204052 PMCID: PMC9530463 DOI: 10.3389/fpls.2022.881992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Clubroot, caused by Plasmodiophora brassicae, is a major disease of crucifers. Effector proteins are important virulence factors in host recognition of pathogens and the interactions between pathogens and hosts. Secretory proteins, as effector candidates, have been studied in the interaction between Plasmodiophora brassicae and its hosts. In this study, 518 secretary proteins were screened from the Plasmodiophora brassicae genome. A total of 63 candidate effectors that induce or suppress cell death were identified using agroinfiltration-mediated transient expression in Nicothiana benthamiana. The candidate effectors, Pb4_102097 and Pb4_108104 showed high expressing level in the stage of rest spore maturity, could induce cell death and were associated with H2O2 accumulation in N. benthamiana leaves. In addition, 55 candidate effectors that could suppress BAX (Bcl-2-associated X protein) induced cell death, and 21 out of which could suppress the immunity caused by bacterial pathogen Pseudomonas syringae pv. tomato strain DC3000 expressing avrRps4 in Arabidopsis. Based on the expression pattern in different stages, 28 candidate effectors showed high expression levels during the primary and secondary infection stage. Five candidate effectors containing the RXLR motif functioned in the cytoplasm and cell membrane.
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Zhang D, Wang Z, Yamamoto N, Wang M, Yi X, Li P, Lin R, Nasimi Z, Okada K, Mochida K, Noutoshi Y, Zheng A. Secreted Glycosyltransferase RsIA_GT of Rhizoctonia solani AG-1 IA Inhibits Defense Responses in Nicotiana benthamiana. Pathogens 2022; 11:pathogens11091026. [PMID: 36145458 PMCID: PMC9501517 DOI: 10.3390/pathogens11091026] [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] [Received: 08/07/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Anastomosis group AG-1 IA of Rhizoctonia solani Khün has a wide host range and threatens crop production. Various glycosyltransferases secreted by phytopathogenic fungi play an essential role in pathogenicity. Previously, we identified a glycosyltransferase RsIA_GT (AG11A_09161) as a secreted protein-encoding gene of R. solani AG-1 IA, whose expression levels increased during infection in rice. In this study, we further characterized the virulence function of RsIA_GT. It is conserved not only in Basidiomycota, including multiple anastomosis groups of R. solani, but also in other primary fungal taxonomic categories. RsIA_GT possesses a signal peptide (SP) for protein secretion, and its functionality was proven using yeast and Nicotiana benthamiana. The SP-truncated form of RsIA_GT (RsIA_GT(ΔS)) expressed in Escherichia coli-induced lesion-like phenotype in rice leaves when applied to punched leaves. However, Agrobacterium-mediated transient expressions of both the full-length RsIA_GT and RsIA_GT(ΔS) did not induce cell death in N. benthamiana leaves. Instead, only RsIA_GT(ΔS) suppressed the cell death induced by two reference cell death factors BAX and INF1 in N.benthamiana. RsIA_GT(ΔS)R154A D168A D170A, a mutant RsIA_GT(ΔS) for the glycosyltransferase catalytic domain, still suppressed the BAX- or INF1-induced cell death, suggesting that the cell death suppression activity of RsIA_GT(ΔS) would be independent from its enzymatic activity. RsIA_GT(ΔS) also suppressed the H2O2 production and callose deposition and showed an effect on the induction of defense genes associated with the expression of BAX and INF1. The transient expression of RsIA_GT(ΔS) in N. benthamiana enhanced the lesion area caused by R. solani AG-1 IA. The secreted glycosyltransferase, RsIA_GT, of R. solani AG-1 IA is likely to have a dual role in virulence inside and outside of host cells.
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Affiliation(s)
- Danhua Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhaoyilin Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Naoki Yamamoto
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingyue Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoqun Yi
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Ping Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zohreh Nasimi
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Kazunori Okada
- Agro-Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama 2300045, Japan
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama 2300045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 2440813, Japan
- School of Information and Data Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Aiping Zheng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Correspondence:
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13
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Tarallo M, McDougal RL, Chen Z, Wang Y, Bradshaw RE, Mesarich CH. Characterization of two conserved cell death elicitor families from the Dothideomycete fungal pathogens Dothistroma septosporum and Fulvia fulva (syn. Cladosporium fulvum). Front Microbiol 2022; 13:964851. [PMID: 36160260 PMCID: PMC9493481 DOI: 10.3389/fmicb.2022.964851] [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] [Received: 06/09/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Dothistroma septosporum (Ds) and Fulvia fulva (Ff; previously called Cladosporium fulvum) are two closely related Dothideomycete fungal species that cause Dothistroma needle blight in pine and leaf mold in tomato, respectively. During host colonization, these pathogens secrete virulence factors termed effectors to promote infection. In the presence of corresponding host immune receptors, however, these effectors activate plant defenses, including a localized cell death response that halts pathogen growth. We identified two apoplastic effector protein families, Ecp20 and Ecp32, which are conserved between the two pathogens. The Ecp20 family has four paralogues in both species, while the Ecp32 family has four paralogues in D. septosporum and five in F. fulva. Both families have members that are highly expressed during host infection. Members of the Ecp20 family have predicted structural similarity to proteins with a β-barrel fold, including the Alt a 1 allergen from Alternaria alternata, while members of the Ecp32 family have predicted structural similarity to proteins with a β-trefoil fold, such as trypsin inhibitors and lectins. Using Agrobacterium tumefaciens-mediated transient transformation assays, each family member was assessed for its ability to trigger cell death in leaves of the non-host species Nicotiana benthamiana and N. tabacum. Using this approach, FfEcp20-2, DsEcp20-3, and FfEcp20-3 from the Ecp20 family, and all members from the Ecp32 family, except for the Ds/FfEcp32-4 pair, triggered cell death in both species. This cell death was dependent on secretion of the effectors to the apoplast. In line with recognition by an extracellular immune receptor, cell death triggered by Ds/FfEcp20-3 and FfEcp32-3 was compromised in N. benthamiana silenced for BAK1 or SOBIR1, which encode extracellular co-receptors involved in transducing defense response signals following apoplastic effector recognition. We then investigated whether DsEcp20-3 and DsEcp20-4 triggered cell death in the host species Pinus radiata by directly infiltrating purified protein into pine needles. Strikingly, as in the non-host species, DsEcp20-3 triggered cell death, while DsEcp20-4 did not. Collectively, our study describes two new candidate effector families with cell death-eliciting activity from D. septosporum and F. fulva and provides evidence that members of these families are recognized by plant immune receptors.
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Affiliation(s)
- Mariana Tarallo
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
- *Correspondence: Mariana Tarallo,
| | | | - Zhiyuan Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Rosie E. Bradshaw
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Rosie E. Bradshaw,
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Carl H. Mesarich,
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Xia C, Qiu A, Wang M, Liu T, Chen W, Chen X. Current Status and Future Perspectives of Genomics Research in the Rust Fungi. Int J Mol Sci 2022; 23:ijms23179629. [PMID: 36077025 PMCID: PMC9456177 DOI: 10.3390/ijms23179629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management.
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Affiliation(s)
- Chongjing Xia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
| | - Age Qiu
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430, USA
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
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Direct recognition of pathogen effectors by plant NLR immune receptors and downstream signalling. Essays Biochem 2022; 66:471-483. [PMID: 35731245 PMCID: PMC9528080 DOI: 10.1042/ebc20210072] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Plants deploy extracellular and intracellular immune receptors to sense and restrict pathogen attacks. Rapidly evolving pathogen effectors play crucial roles in suppressing plant immunity but are also monitored by intracellular nucleotide-binding, leucine-rich repeat immune receptors (NLRs), leading to effector-triggered immunity (ETI). Here, we review how NLRs recognize effectors with a focus on direct interactions and summarize recent research findings on the signalling functions of NLRs. Coiled-coil (CC)-type NLR proteins execute immune responses by oligomerizing to form membrane-penetrating ion channels after effector recognition. Some CC-NLRs function in sensor-helper networks with the sensor NLR triggering oligomerization of the helper NLR. Toll/interleukin-1 receptor (TIR)-type NLR proteins possess catalytic activities that are activated upon effector recognition-induced oligomerization. Small molecules produced by TIR activity are detected by additional signalling partners of the EDS1 lipase-like family (enhanced disease susceptibility 1), leading to activation of helper NLRs that trigger the defense response.
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Ngou BPM, Ding P, Jones JDG. Thirty years of resistance: Zig-zag through the plant immune system. THE PLANT CELL 2022; 34:1447-1478. [PMID: 35167697 PMCID: PMC9048904 DOI: 10.1093/plcell/koac041] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/02/2022] [Indexed: 05/05/2023]
Abstract
Understanding the plant immune system is crucial for using genetics to protect crops from diseases. Plants resist pathogens via a two-tiered innate immune detection-and-response system. The first plant Resistance (R) gene was cloned in 1992 . Since then, many cell-surface pattern recognition receptors (PRRs) have been identified, and R genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) have been cloned. Here, we provide a list of characterized PRRs and NLRs. In addition to immune receptors, many components of immune signaling networks were discovered over the last 30 years. We review the signaling pathways, physiological responses, and molecular regulation of both PRR- and NLR-mediated immunity. Recent studies have reinforced the importance of interactions between the two immune systems. We provide an overview of interactions between PRR- and NLR-mediated immunity, highlighting challenges and perspectives for future research.
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Affiliation(s)
| | - Pingtao Ding
- Author for correspondence: (B.P.M.N.); (P.D.); (J.J.)
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17
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Bai Q, Wang M, Xia C, See DR, Chen X. Identification of Secreted Protein Gene-Based SNP Markers Associated with Virulence Phenotypes of Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen. Int J Mol Sci 2022; 23:ijms23084114. [PMID: 35456934 PMCID: PMC9033109 DOI: 10.3390/ijms23084114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 01/14/2023] Open
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a destructive disease that occurs throughout the major wheat-growing regions of the world. This pathogen is highly variable due to the capacity of virulent races to undergo rapid changes in order to circumvent resistance in wheat cultivars and genotypes and to adapt to different environments. Intensive efforts have been made to study the genetics of wheat resistance to this disease; however, no known avirulence genes have been molecularly identified in Pst so far. To identify molecular markers for avirulence genes, a Pst panel of 157 selected isolates representing 126 races with diverse virulence spectra was genotyped using 209 secreted protein gene-based single nucleotide polymorphism (SP-SNP) markers via association analysis. Nineteen SP-SNP markers were identified for significant associations with 12 avirulence genes: AvYr1, AvYr6, AvYr7, AvYr9, AvYr10, AvYr24, AvYr27, AvYr32, AvYr43, AvYr44, AvYrSP, and AvYr76. Some SP-SNPs were associated with two or more avirulence genes. These results further confirmed that association analysis in combination with SP-SNP markers is a powerful tool for identifying markers for avirulence genes. This study provides genomic resources for further studies on the cloning of avirulence genes, understanding the mechanisms of host–pathogen interactions, and developing functional markers for tagging specific virulence genes and race groups.
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Affiliation(s)
- Qing Bai
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
| | - Chongjing Xia
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Deven R. See
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, USA
- Correspondence: ; Tel.: +1-509-335-8086
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Wilkerson DG, Crowell CR, Carlson CH, McMullen PW, Smart CD, Smart LB. Comparative transcriptomics and eQTL mapping of response to Melampsora americana in selected Salix purpurea F2 progeny. BMC Genomics 2022; 23:71. [PMID: 35065596 PMCID: PMC8783449 DOI: 10.1186/s12864-021-08254-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
Background Melampsora spp. rusts are the greatest pathogen threat to shrub willow (Salix spp.) bioenergy crops. Genetic resistance is key to limit the effects of these foliar diseases on host response and biomass yield, however, the genetic basis of host resistance has not been characterized. The addition of new genomic resources for Salix provides greater power to investigate the interaction between S. purpurea and M. americana, species commonly found in the Northeast US. Here, we utilize 3′ RNA-seq to investigate host-pathogen interactions following controlled inoculations of M. americana on resistant and susceptible F2S. purpurea genotypes identified in a recent QTL mapping study. Differential gene expression, network analysis, and eQTL mapping were used to contrast the response to inoculation and to identify associated candidate genes. Results Controlled inoculation in a replicated greenhouse study identified 19 and 105 differentially expressed genes between resistant and susceptible genotypes at 42 and 66 HPI, respectively. Defense response gene networks were activated in both resistant and susceptible genotypes and enriched for many of the same defense response genes, yet the hub genes of these common response modules showed greater mean expression among the resistant plants. Further, eight and six eQTL hotspots were identified at 42 and 66 HPI, respectively. The combined results of three analyses highlight 124 candidate genes in the host for further analysis while analysis of pathogen RNA showed differential expression of 22 genes, two of which are candidate pathogen effectors. Conclusions We identified two differentially expressed M. americana transcripts and 124 S. purpurea genes that are good candidates for future studies to confirm their role in conferring resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08254-1.
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Ma A, Zhang D, Wang G, Wang K, Li Z, Gao Y, Li H, Bian C, Cheng J, Han Y, Yang S, Gong Z, Qi J. Verticillium dahliae effector VDAL protects MYB6 from degradation by interacting with PUB25 and PUB26 E3 ligases to enhance Verticillium wilt resistance. THE PLANT CELL 2021; 33:3675-3699. [PMID: 34469582 PMCID: PMC8643689 DOI: 10.1093/plcell/koab221] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/26/2021] [Indexed: 05/30/2023]
Abstract
Verticillium wilt is a severe plant disease that causes massive losses in multiple crops. Increasing the plant resistance to Verticillium wilt is a critical challenge worldwide. Here, we report that the hemibiotrophic Verticillium dahliae-secreted Asp f2-like protein VDAL causes leaf wilting when applied to cotton leaves in vitro but enhances the resistance to V. dahliae when overexpressed in Arabidopsis or cotton without affecting the plant growth and development. VDAL protein interacts with Arabidopsis E3 ligases plant U-box 25 (PUB25) and PUB26 and is ubiquitinated by PUBs in vitro. However, VDAL is not degraded by PUB25 or PUB26 in planta. Besides, the pub25 pub26 double mutant shows higher resistance to V. dahliae than the wild-type. PUBs interact with the transcription factor MYB6 in a yeast two-hybrid screen. MYB6 promotes plant resistance to Verticillium wilt while PUBs ubiquitinate MYB6 and mediate its degradation. VDAL competes with MYB6 for binding to PUBs, and the role of VDAL in increasing Verticillium wilt resistance depends on MYB6. Taken together, these results suggest that plants evolute a strategy to utilize the invaded effector protein VDAL to resist the V. dahliae infection without causing a hypersensitive response (HR); alternatively, hemibiotrophic pathogens may use some effectors to keep plant cells alive during its infection in order to take nutrients from host cells. This study provides the molecular mechanism for plants increasing disease resistance when overexpressing some effector proteins without inducing HR, and may promote searching for more genes from pathogenic fungi or bacteria to engineer plant disease resistance.
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Affiliation(s)
- Aifang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Dingpeng Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Neurosurgery, University of Florida, Gainesville, Florida 32608, USA
| | - Guangxing Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Kai Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuanhui Gao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hengchang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chao Bian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yinan Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- College of Life Science, Hebei University, Baoding 071002, China
| | - Junsheng Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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20
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Louet C, Saubin M, Andrieux A, Persoons A, Gorse M, Pétrowski J, Fabre B, De Mita S, Duplessis S, Frey P, Halkett F. A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown. Mol Ecol 2021; 32:2472-2483. [PMID: 34843142 DOI: 10.1111/mec.16294] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 01/29/2023]
Abstract
The deployment of plant varieties carrying resistance genes (R) exerts strong selection pressure on pathogen populations. Rapidly evolving avirulence genes (Avr) allow pathogens to escape R-mediated plant immunity through a variety of mechanisms, leading to virulence. The poplar rust fungus Melampsora larici-populina is a damaging pathogen of poplars in Europe. It underwent a major adaptive event in 1994, with the breakdown of the poplar RMlp7 resistance gene. Population genomics studies identified a locus in the genome of M. larici-populina that probably corresponds to the candidate avirulence gene AvrMlp7. Here, to further characterize this effector, we used a population genetics approach on a comprehensive set of 281 individuals recovered throughout a 28-year period encompassing the resistance breakdown event. Using two dedicated molecular tools, genotyping at the candidate locus highlighted two different alterations of a predominant allele found mainly before the resistance breakdown: a nonsynonymous mutation and a complete deletion of this locus. This results in six diploid genotypes: three genotypes related to the avirulent phenotype and three related to the virulent phenotype. The temporal survey of the candidate locus revealed that both alterations were found in association during the resistance breakdown event. They pre-existed before the breakdown in a heterozygous state with the predominant allele cited above. Altogether, these results suggest that the association of both alterations at the candidate locus AvrMlp7 drove the poplar rust adaptation to RMlp7-mediated immunity. This study demonstrates for the first time a case of adaptation from standing genetic variation in rust fungi during a qualitative resistance breakdown.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, Nancy, France
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21
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Jones DAB, Moolhuijzen PM, Hane JK. Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi. Microb Genom 2021; 7. [PMID: 34468307 PMCID: PMC8715435 DOI: 10.1099/mgen.0.000637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plant diseases caused by fungal pathogens are typically initiated by molecular interactions between 'effector' molecules released by a pathogen and receptor molecules on or within the plant host cell. In many cases these effector-receptor interactions directly determine host resistance or susceptibility. The search for fungal effector proteins is a developing area in fungal-plant pathology, with more than 165 distinct confirmed fungal effector proteins in the public domain. For a small number of these, novel effectors can be rapidly discovered across multiple fungal species through the identification of known effector homologues. However, many have no detectable homology by standard sequence-based search methods. This study employs a novel comparison method (RemEff) that is capable of identifying protein families with greater sensitivity than traditional homology-inference methods, leveraging a growing pool of confirmed fungal effector data to enable the prediction of novel fungal effector candidates by protein family association. Resources relating to the RemEff method and data used in this study are available from https://figshare.com/projects/Effector_protein_remote_homology/87965.
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Affiliation(s)
- Darcy A B Jones
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia
| | - Paula M Moolhuijzen
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia
| | - James K Hane
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia.,Curtin Institute for Computation, Curtin University, Perth, Australia
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Duplessis S, Lorrain C, Petre B, Figueroa M, Dodds PN, Aime MC. Host Adaptation and Virulence in Heteroecious Rust Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:403-422. [PMID: 34077239 DOI: 10.1146/annurev-phyto-020620-121149] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rust fungi (Pucciniales, Basidiomycota) are obligate biotrophic pathogens that cause rust diseases in plants, inflicting severe damage to agricultural crops. Pucciniales possess the most complex life cycles known in fungi. These include an alternation of generations, the development of up to five different sporulating stages, and, for many species, the requirement of infecting two unrelated host plants during different parts of their life cycle, termed heteroecism. These fungi have been extensively studied in the past century through microscopy and inoculation studies, providing precise descriptions of their infection processes, although the molecular mechanisms underlying their unique biology are poorly understood. In this review, we cover recent genomic and life cycle transcriptomic studies in several heteroecious rust species, which provide insights into the genetic tool kits associated with host adaptation and virulence, opening new avenues for unraveling their unique evolution.
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Affiliation(s)
- Sebastien Duplessis
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Cecile Lorrain
- Plant Pathology Group, ETH Zurich, 8092 Zurich, Switzerland;
| | - Benjamin Petre
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Melania Figueroa
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA;
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Kumar J, Ramlal A, Kumar K, Rani A, Mishra V. Signaling Pathways and Downstream Effectors of Host Innate Immunity in Plants. Int J Mol Sci 2021; 22:ijms22169022. [PMID: 34445728 PMCID: PMC8396522 DOI: 10.3390/ijms22169022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Phytopathogens, such as biotrophs, hemibiotrophs and necrotrophs, pose serious stress on the development of their host plants, compromising their yields. Plants are in constant interaction with such phytopathogens and hence are vulnerable to their attack. In order to counter these attacks, plants need to develop immunity against them. Consequently, plants have developed strategies of recognizing and countering pathogenesis through pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Pathogen perception and surveillance is mediated through receptor proteins that trigger signal transduction, initiated in the cytoplasm or at the plasma membrane (PM) surfaces. Plant hosts possess microbe-associated molecular patterns (P/MAMPs), which trigger a complex set of mechanisms through the pattern recognition receptors (PRRs) and resistance (R) genes. These interactions lead to the stimulation of cytoplasmic kinases by many phosphorylating proteins that may also be transcription factors. Furthermore, phytohormones, such as salicylic acid, jasmonic acid and ethylene, are also effective in triggering defense responses. Closure of stomata, limiting the transfer of nutrients through apoplast and symplastic movements, production of antimicrobial compounds, programmed cell death (PCD) are some of the primary defense-related mechanisms. The current article highlights the molecular processes involved in plant innate immunity (PII) and discusses the most recent and plausible scientific interventions that could be useful in augmenting PII.
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Affiliation(s)
- Jitendra Kumar
- Bangalore Bioinnovation Centre, Life Sciences Park, Electronics City Phase 1, Bengaluru 560100, India;
| | - Ayyagari Ramlal
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi 110012, India;
| | - Kamal Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110066, India;
| | - Anita Rani
- Department of Botany, Dyal Singh College, University of Delhi, Delhi 110003, India;
| | - Vachaspati Mishra
- Department of Botany, Dyal Singh College, University of Delhi, Delhi 110003, India;
- Correspondence:
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24
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Zheng W, Peng Z, Peng S, Yu Z, Cao Z. Multinuclei Occurred Under Cryopreservation and Enhanced the Pathogenicity of Melampsora larici-populina. Front Microbiol 2021; 12:650902. [PMID: 34248868 PMCID: PMC8270653 DOI: 10.3389/fmicb.2021.650902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
Melampsora larici-populina is a macrocyclic rust, and the haploid stage with two nuclei and the diploid of mononuclear sequentially occur annually. During the preservation of dry urediniospores at −80°C, we found that one isolate, ΔTs06, was different from the usual wild-type isolate Ts06 at −20°C because it has mixed polykaryotic urediniospores. However, the other spores, including the 0, I, III, and IV stages of a life cycle, were the same as Ts06. After five generations of successive inoculation and harvest of urediniospores from the compatible host Populus purdomii, the isolate ΔTs06 steadily maintained more than 20% multiple nucleus spores. To test the pathogenesis variation of ΔTs06, an assay of host poplars was applied to evaluate the differences between ΔTs06 and Ts06. After ΔTs06 and Ts06 inoculation, leaves of P. purdomii were used to detect the expression of small secreted proteins (SSPs) and fungal biomasses using quantitative real-time PCR (qRT-PCR) and trypan blue staining. ΔTs06 displayed stronger expression of five SSPs and had a shorter latent period, a higher density of uredinia, and higher DNA mass. A transcriptomic comparison between ΔTs06 and Ts06 revealed that 3,224 were differentially expressed genes (DEGs), 55 of which were related to reactive oxygen species metabolism, the Mitogen-activated protein kinase (MAPK) signaling pathway, and the meiosis pathway. Ten genes in the mitotic and meiotic pathways and another two genes associated with the “response to DNA damage stimulus” all had an upward expression, which were detected by qRT-PCR in ΔTs06 during cryopreservation. Gas chromatography–mass spectrometry (GC-MS) confirmed that the amounts of hexadecanoic acid and octadecadienoic acid were much more in ΔTs06 than in Ts06. In addition, using spectrophotometry, hydrogen peroxide (H2O2) was also present in greater quantities in ΔTs06 compared with those found in Ts06. Increased fatty acids metabolism could prevent damage to urediniospores in super-low temperatures, but oxidant species that involved H2O2 may destroy tube proteins of mitosis and meiosis, which could cause abnormal nuclear division and lead to multinucleation, which has a different genotype. Therefore, the multinuclear isolate is different from the wild-type isolate in terms of phenotype and genotype; this multinucleation phenomenon in urediniospores improves the pathogenesis and environmental fitness of M. larici-populina.
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Affiliation(s)
- Wei Zheng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zijia Peng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Shaobing Peng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zhongdong Yu
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zhimin Cao
- College of Forestry, Northwest A&F University, Yangling, China
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dos Santos KCG, Pelletier G, Séguin A, Guillemette F, Hawkes J, Desgagné-Penix I, Germain H. Unrelated Fungal Rust Candidate Effectors Act on Overlapping Plant Functions. Microorganisms 2021; 9:microorganisms9050996. [PMID: 34063040 PMCID: PMC8148019 DOI: 10.3390/microorganisms9050996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/30/2021] [Indexed: 11/21/2022] Open
Abstract
Rust fungi cause epidemics that threaten the production of important plant species, such as wheat and soy. Melampsora larici-populina (Mlp) causes the poplar rust and encodes at least 1184 candidate effectors (CEs) whose functions are poorly known. In this study, we sequenced the transcriptome and used mass spectrometry to analyze the metabolome of Arabidopsis plants constitutively expressing 14 Mlp CEs and of a control line to discover alterations leading to plant susceptibility. We found 2299 deregulated genes across the experiment. Genes involved in pattern-triggered immunity, such as FRK1, PR1, RBOHD, and WRKY33, as well as AUX/IAA genes were down-regulated. We further observed that 680 metabolites were deregulated in at least one CE-expressing transgenic line, with “highly unsaturated and phenolic compounds” and “peptides” enriched among down- and up-regulated metabolites. Interestingly, transgenic lines expressing unrelated CEs had correlated patterns of gene and metabolite deregulation, while expression of CEs belonging to the same family deregulated different genes and metabolites. Thus, our results uncouple effector sequence similarity and function. This supports that effector functional investigation in the context of their virulence activity and effect on plant susceptibility requires the investigation of the individual effector and precludes generalization based on sequence similarity.
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Affiliation(s)
- Karen Cristine Goncalves dos Santos
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada; (K.C.G.d.S.); (I.D.-P.)
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada
| | - Gervais Pelletier
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC G1V 4C7, Canada; (G.P.); (A.S.)
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC G1V 4C7, Canada; (G.P.); (A.S.)
| | - François Guillemette
- Centre for Research on Aquatic Ecosystem Interactions (RIVE), Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada;
| | - Jeffrey Hawkes
- Department of Chemistry—BMC, Analytical Chemistry, Uppsala University, VJ2J+92 Uppsala, Sweden;
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada; (K.C.G.d.S.); (I.D.-P.)
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada; (K.C.G.d.S.); (I.D.-P.)
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada
- Correspondence:
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Hatta MAM, Arora S, Ghosh S, Matny O, Smedley MA, Yu G, Chakraborty S, Bhatt D, Xia X, Steuernagel B, Richardson T, Mago R, Lagudah ES, Patron NJ, Ayliffe M, Rouse MN, Harwood WA, Periyannan S, Steffenson BJ, Wulff BB. The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:273-284. [PMID: 32744350 PMCID: PMC7868974 DOI: 10.1111/pbi.13460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 06/17/2020] [Indexed: 05/16/2023]
Abstract
In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley's genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley.
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Affiliation(s)
- M. Asyraf Md Hatta
- John Innes CentreNorwich Research ParkNorwichUK
- Department of Agriculture TechnologyFaculty of AgricultureUniversiti Putra MalaysiaSerdangMalaysia
| | - Sanu Arora
- John Innes CentreNorwich Research ParkNorwichUK
| | - Sreya Ghosh
- John Innes CentreNorwich Research ParkNorwichUK
| | - Oadi Matny
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
| | | | - Guotai Yu
- John Innes CentreNorwich Research ParkNorwichUK
| | - Soma Chakraborty
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Dhara Bhatt
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Xiaodi Xia
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Terese Richardson
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Evans S. Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Matthew N. Rouse
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
- USDA‐ARS Cereal Disease LaboratorySt. PaulMNUSA
| | | | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Brian J. Steffenson
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
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27
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In-depth secretome analysis of Puccinia striiformis f. sp. tritici in infected wheat uncovers effector functions. Biosci Rep 2020; 40:226968. [PMID: 33275764 PMCID: PMC7724613 DOI: 10.1042/bsr20201188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 11/17/2022] Open
Abstract
The importance of wheat yellow rust disease, caused by Puccinia striiformis f. sp. tritici (Pst), has increased substantially due to the emergence of aggressive new Pst races in the last couple of decades. In an era of escalating human populations and climate change, it is vital to understand the infection mechanism of Pst in order to develop better strategies to combat wheat yellow disease. The present study focuses on the identification of small secreted proteins (SSPs) and candidate-secreted effector proteins (CSEPs) that are used by the pathogen to support infection and control disease development. We generated de novo assembled transcriptomes of Pst collected from wheat fields in central Anatolia. We inoculated both susceptible and resistant seedlings with Pst and analyzed haustoria formation. At 10 days post-inoculation (dpi), we analyzed the transcriptomes and identified 10550 Differentially Expressed Unigenes (DEGs), of which 6072 were Pst-mapped. Among those Pst-related genes, 227 were predicted as PstSSPs. In silico characterization was performed using an approach combining the transcriptomic data and data mining results to provide a reliable list to narrow down the ever-expanding repertoire of predicted effectorome. The comprehensive analysis detected 14 Differentially Expressed Small-Secreted Proteins (DESSPs) that overlapped with the genes in available literature data to serve as the best CSEPs for experimental validation. One of the CSEPs was cloned and studied to test the reliability of the presented data. Biological assays show that the randomly selected CSEP, Unigene17495 (PSTG_10917), localizes in the chloroplast and is able to suppress cell death induced by INF1 in a Nicotiana benthamiana heterologous expression system.
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NOD-like receptor-mediated plant immunity: from structure to cell death. Nat Rev Immunol 2020; 21:305-318. [PMID: 33293618 DOI: 10.1038/s41577-020-00473-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2020] [Indexed: 12/25/2022]
Abstract
Animal and plant immune systems use intracellular nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) to detect pathogens, resulting in the activation of immune responses that are often associated with localized host cell death. Whereas vertebrate NLRs detect evolutionarily conserved molecular patterns and have undergone comparatively little copy number expansion, plant NLRs detect virulence factors that have often diversified in plant pathogen populations, and thus plant NLRs have been subject to parallel diversification. Plant NLRs sense the presence of virulence factors with enzymatic virulence activity often indirectly through their modification of host target proteins. By contrast, phytopathogenic virulence factors without enzymatic activity are usually recognized by NLRs directly by their structure. Structural and biochemical analyses have shown that both indirect and direct recognition of plant pathogens trigger the oligomerization of plant NLRs into active complexes. Assembly into three-layered ring-like structures has emerged as a common principle of NLR activation in plants and animals, but with distinct amino-terminal domains initiating different signalling pathways. Collectively, these analyses point to host cell membranes as a convergence point for activated plant NLRs and the disruption of cellular ion homeostasis as a possible major factor in NLR-triggered cell death signalling.
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29
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Leaping into the Unknown World of Sporisorium scitamineum Candidate Effectors. J Fungi (Basel) 2020; 6:jof6040339. [PMID: 33291820 PMCID: PMC7762069 DOI: 10.3390/jof6040339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Sporisorium scitamineum is a biotrophic fungus causing sugarcane smut disease. In this study, we set up a pipeline and used genomic and dual transcriptomic data previously obtained by our group to identify candidate effectors of S. scitamineum and their expression profiles in infected smut-resistant and susceptible sugarcane plants. The expression profile of different genes after infection in contrasting sugarcane genotypes assessed by RT-qPCR depended on the plant genotypes and disease progression. Three candidate effector genes expressed earlier only in resistant plants, four expressed in both genotypes, and three later in susceptible plants. Ten genes were cloned and transiently expressed in N. benthamiana leaves to determine their subcellular location, while four localized in more than one compartment. Two candidates, g3890 having a nucleoplasmic and mitochondrial location and g5159 targeting the plant cell wall, were selected to obtain their possible corresponding host targets using co-immunoprecipitation (CoIP) experiments and mass spectrometry. Various potential interactors were identified, including subunits of the protein phosphatase 2A and an endochitinase. We investigated the presence of orthologs in sugarcane and using transcriptome data present their expression profiles. Orthologs of sugarcane shared around 70% similarity. Identifying a set of putative fungal effectors and their plant targets provides a valuable resource for functional characterization of the molecular events leading to smut resistance in sugarcane plants and uncovers further opportunities for investigation.
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30
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Wang X, Zhang H, Nyamesorto B, Luo Y, Mu X, Wang F, Kang Z, Lagudah E, Huang L. A new mode of NPR1 action via an NB-ARC-NPR1 fusion protein negatively regulates the defence response in wheat to stem rust pathogen. THE NEW PHYTOLOGIST 2020; 228:959-972. [PMID: 32544264 PMCID: PMC7589253 DOI: 10.1111/nph.16748] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/01/2020] [Indexed: 05/20/2023]
Abstract
NPR1 has been found to be a key transcriptional regulator in some plant defence responses. There are nine NPR1 homologues (TaNPR1) in wheat, but little research has been done to understand the function of those NPR1-like genes in the wheat defence response against stem rust (Puccinia graminis f. sp. tritici) pathogens. We used bioinformatics and reverse genetics approaches to study the expression and function of each TaNPR1. We found six members of TaNPR1 located on homoeologous group 3 chromosomes (designated as TaG3NPR1) and three on homoeologous group 7 chromosomes (designated as TaG7NPR1). The group 3 NPR1 proteins regulate transcription of SA-responsive PR genes. Downregulation of all the TaNPR1 homologues via virus-induced gene co-silencing resulted in enhanced resistance to stem rust. More specifically downregulating TaG7NPR1 homeologues or Ta7ANPR1 expression resulted in stem rust resistance phenotype. By contrast, knocking down TaG3NPR1 alone did not show visible phenotypic changes in response to the rust pathogen. Knocking out Ta7ANPR1 enhanced resistance to stem rust. The Ta7ANPR1 locus is alternatively spliced under pathogen inoculated conditions. We discovered a new mode of NPR1 action in wheat at the Ta7ANPR1 locus through an NB-ARC-NPR1 fusion protein negatively regulating the defence to stem rust infection.
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Affiliation(s)
- Xiaojing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life SciencesNorthwest A&F UniversityYanglingShaanxi712100China
- Department of Plant Sciences and Plant PathologyMontana State UniversityBozemanMT59717‐3150USA
| | - Hongtao Zhang
- Department of Plant Sciences and Plant PathologyMontana State UniversityBozemanMT59717‐3150USA
| | - Bernard Nyamesorto
- Department of Plant Sciences and Plant PathologyMontana State UniversityBozemanMT59717‐3150USA
| | - Yi Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life SciencesNorthwest A&F UniversityYanglingShaanxi712100China
| | - Xiaoqian Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life SciencesNorthwest A&F UniversityYanglingShaanxi712100China
| | - Fangyan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life SciencesNorthwest A&F UniversityYanglingShaanxi712100China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxi712100China
| | - Evans Lagudah
- CSIRO Agriculture & FoodGPO Box 1700CanberraACT2601Australia
| | - Li Huang
- Department of Plant Sciences and Plant PathologyMontana State UniversityBozemanMT59717‐3150USA
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31
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Bentham AR, De la Concepcion JC, Mukhi N, Zdrzałek R, Draeger M, Gorenkin D, Hughes RK, Banfield MJ. A molecular roadmap to the plant immune system. J Biol Chem 2020; 295:14916-14935. [PMID: 32816993 PMCID: PMC7606695 DOI: 10.1074/jbc.rev120.010852] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/17/2020] [Indexed: 12/15/2022] Open
Abstract
Plant diseases caused by pathogens and pests are a constant threat to global food security. Direct crop losses and the measures used to control disease (e.g. application of pesticides) have significant agricultural, economic, and societal impacts. Therefore, it is essential that we understand the molecular mechanisms of the plant immune system, a system that allows plants to resist attack from a wide variety of organisms ranging from viruses to insects. Here, we provide a roadmap to plant immunity, with a focus on cell-surface and intracellular immune receptors. We describe how these receptors perceive signatures of pathogens and pests and initiate immune pathways. We merge existing concepts with new insights gained from recent breakthroughs on the structure and function of plant immune receptors, which have generated a shift in our understanding of cell-surface and intracellular immunity and the interplay between the two. Finally, we use our current understanding of plant immunity as context to discuss the potential of engineering the plant immune system with the aim of bolstering plant defenses against disease.
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Affiliation(s)
- Adam R Bentham
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | | | - Nitika Mukhi
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Rafał Zdrzałek
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Markus Draeger
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Danylo Gorenkin
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Richard K Hughes
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom.
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32
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He Q, Liu Y, Liang P, Liao X, Li X, Li X, Shi D, Liu W, Lin C, Zheng F, Miao W. A novel chorismate mutase from Erysiphe quercicola performs dual functions of synthesizing amino acids and inhibiting plant salicylic acid synthesis. Microbiol Res 2020; 242:126599. [PMID: 33010586 DOI: 10.1016/j.micres.2020.126599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 07/17/2020] [Accepted: 09/15/2020] [Indexed: 11/28/2022]
Abstract
Pathogens secrete effectors to establish a successful interaction with their host. It is well understood that plant pathogens recruit classically secreted chorismate mutase (Cmu) as an effector to disrupt plant salicylic acid (SA) synthesis. However, the identity and function of the Cmu effector from powdery mildew fungi remain unknown. Here, we identified a novel secreted Cmu effector, EqCmu, from rubber (Hevea brasiliensis Muell) powdery mildew fungus (Erysiphe quercicola). Unlike the classically secreted Cmu, EqCmu lack signal peptide, and exhibited characteristics of non-classically secreted proteins. EqCmu could fully complement a Saccharomyces cerevisiae ScAro7 mutant that was deficient in the synthesis of phenylalanine and tyrosine. In addition, transient expression of EqCmu could promote infection by Phytophthora capsici and reduce the levels of SA and the mRNA of PR1 gene in Nicotiana benthamiana in response to P. capsici infection, while confocal observations showed that EqCmu was localized within the cytoplasm and nucleus of transfected N. benthamiana leaf cells. These non-homologous systems assays provide evidences that EqCmu may serve as a "moonlighting" protein, which is not only a key enzyme in the synthesis of phenylalanine and tyrosine within fungal cells, but also has the function of regulating plant SA synthesis within plant cells. This is the first study to identify and functionally validate a candidate effector from E. quercicola. Overall, the non-classical secretion pathway is a novel mechanism for powdery mildew fungal effectors secretion and might play an important role in host-pathogen interactions.
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Affiliation(s)
- Qiguang He
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Yao Liu
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Peng Liang
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Xiaomiao Liao
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Xiang Li
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Xiao Li
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Dou Shi
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Wenbo Liu
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Chunhua Lin
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Fucong Zheng
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China
| | - Weiguo Miao
- College of Plant Protection, Hainan University, Haikou 570228, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou 570228, China.
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Zhang Y, Wei J, Qi Y, Li J, Amin R, Yang W, Liu D. Predicating the Effector Proteins Secreted by Puccinia triticina Through Transcriptomic Analysis and Multiple Prediction Approaches. Front Microbiol 2020; 11:538032. [PMID: 33072007 PMCID: PMC7536266 DOI: 10.3389/fmicb.2020.538032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/26/2020] [Indexed: 11/17/2022] Open
Abstract
Wheat leaf rust caused by Puccinia triticina is one of the most common and serious diseases in wheat production. The constantly changing pathogens overcome the plant resistance to P. triticina. Plant pathogens secrete effector proteins that alter the structure of the host cell, interfere plant defenses, or modify the physiology of plant cells. Therefore, the identification of effector proteins is critical to reveal the pathogenic mechanism. We used SignalP v4.1, TargetP v1.1, TMHMM v2.0, and EffectorP v2.0 to screen the candidate effector proteins in P. triticina isolates – KHTT, JHKT, and THSN. As a result, a total of 635 candidate effector proteins were obtained. Structural analysis showed that effector proteins were small in size (50AA to 422AA) and of diverse sequences, and the conserved sequential elements or clear common elements were not involved, regardless of their secretion from the pathogen to the host. There were 427 candidate effector proteins that contain more than or equal to 4 cysteine residues, and 339 candidate effector proteins contained the known motifs. Sixteen families, 9 domains, and 53 other known functional types were found in 186 candidate effector proteins using the Pfam search. Three novel motifs were found by MEME. Heterogeneous expression system was performed to verify the functions of 30 candidate effectors by inhibiting the programmed cell death (PCD) induced by BAX (the mouse-apoptotic gene elicitor) on Nicotiana benthamiana. Hypersensitive response (HR) can be induced by the six effectors in the wheat leaf rust resistance near isogenic lines, and this would be shown by the method of transient expression through Agrobacterium tumefaciens infiltration. The quantitative reverse transcription PCR (qRT-PCR) analysis of 14 candidate effector proteins secreted after P. triticina inoculation showed that the tested effectors displayed different expression patterns in different stages, suggesting that they may be involved in the wheat–P. triticina interaction. The results showed that the prediction of P. triticina effector proteins based on transcriptomic analysis and multiple bioinformatics software is effective and more accurate, laying the foundation of revealing the pathogenic mechanism of Pt and controlling disease.
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Affiliation(s)
- Yue Zhang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Jie Wei
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Yue Qi
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Jianyuan Li
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China.,College of Biological Sciences and Engineering, Hebei Xingtai College, Xingtai, China
| | - Raheela Amin
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Wenxiang Yang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Daqun Liu
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
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Li J, Cornelissen B, Rep M. Host-specificity factors in plant pathogenic fungi. Fungal Genet Biol 2020; 144:103447. [PMID: 32827756 DOI: 10.1016/j.fgb.2020.103447] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 01/18/2023]
Abstract
Fortunately, no fungus can cause disease on all plant species, and although some plant-pathogenic fungi have quite a broad host range, most are highly limited in the range of plant species or even cultivars that they cause disease in. The mechanisms of host specificity have been extensively studied in many plant-pathogenic fungi, especially in fungal pathogens causing disease on economically important crops. Specifically, genes involved in host specificity have been identified during the last few decades. In this overview, we describe and discuss these host-specificity genes. These genes encode avirulence (Avr) proteins, proteinaceous host-specific toxins or secondary metabolites. We discuss the genomic context of these genes, their expression, polymorphism, horizontal transfer and involvement in pathogenesis.
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Affiliation(s)
- Jiming Li
- Molecular Plant Pathology, University of Amsterdam, Amsterdam 1098 XH, the Netherlands
| | - Ben Cornelissen
- Molecular Plant Pathology, University of Amsterdam, Amsterdam 1098 XH, the Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, University of Amsterdam, Amsterdam 1098 XH, the Netherlands.
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An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population. mSphere 2020; 5:5/3/e00128-20. [PMID: 32554716 PMCID: PMC7300351 DOI: 10.1128/msphere.00128-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe (yellow) rust, is an obligate, biotrophic fungus. It was difficult to study the genetics of the pathogen due to the lack of sexual reproduction. The recent discovery of alternate hosts for P. striiformis f. sp. tritici makes it possible to study inheritance and map genes involved in its interaction with plant hosts. To identify avirulence (Avr) genes in P. striiformis f. sp. tritici, we developed a segregating population by selfing isolate 12-368 on barberry (Berberis vulgaris) plants under controlled conditions. The dikaryotic sexual population segregated for avirulent/virulent phenotypes on nine Yr single-gene lines. The parental and progeny isolates were whole-genome sequenced at >30× coverage using Illumina HiSeq PE150 technology. A total of 2,637 high-quality markers were discovered by mapping the whole-genome sequencing (WGS) reads to the reference genome of strain 93-210 and used to construct a genetic map, consisting of 41 linkage groups, spanning 7,715.0 centimorgans (cM) and covering 68 Mb of the reference genome. The recombination rate was estimated to be 1.81 ± 2.32 cM/10 kb. Quantitative trait locus analysis mapped six Avr gene loci to the genetic map, including an Avr cluster harboring four Avr genes, AvYr7, AvYr43, AvYr44, and AvYrExp2 Aligning the genetic map to the reference genome identified Avr candidates and narrowed them to a small genomic region (<200 kb). The discovery of the Avr gene cluster is useful for understanding pathogen evolution, and the identification of candidate genes is an important step toward cloning Avr genes for studying molecular mechanisms of pathogen-host interactions.IMPORTANCE Stripe rust is a destructive disease of wheat worldwide. Growing resistant cultivars is the most effective, easy-to-use, economical, and environmentally friendly strategy for the control of the disease. However, P. striiformis f. sp. tritici can produce new virulent races that may circumvent race-specific resistance. Therefore, understanding the genetic basis of the interactions between wheat genes for resistance and P. striiformis f. sp. tritici genes for avirulence is useful for improving cultivar resistance for more effective control of the disease. This study developed a high-quality map that facilitates genomic and genetic studies of important traits related to pathogen pathogenicity and adaptation to different environments and crop cultivars carrying different resistance genes. The information on avirulence/virulence genes identified in this study can be used for guiding breeding programs to select combinations of genes for developing new cultivars with effective resistance to mitigate this devastating disease.
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Li Y, Xia C, Wang M, Yin C, Chen X. Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates. BMC Genomics 2020; 21:247. [PMID: 32197579 PMCID: PMC7085141 DOI: 10.1186/s12864-020-6677-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/13/2020] [Indexed: 12/30/2022] Open
Abstract
Background The stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), threats world wheat production. Resistance to Pst is often overcome by pathogen virulence changes, but the mechanisms of variation are not clearly understood. To determine the role of mutation in Pst virulence changes, in previous studies 30 mutant isolates were developed from a least virulent isolate using ethyl methanesulfonate (EMS) mutagenesis and phenotyped for virulence changes. The progenitor isolate was sequenced, assembled and annotated for establishing a high-quality reference genome. In the present study, the 30 mutant isolates were sequenced and compared to the wide-type isolate to determine the genomic variation and identify candidates for avirulence (Avr) genes. Results The sequence reads of the 30 mutant isolates were mapped to the wild-type reference genome to identify genomic changes. After selecting EMS preferred mutations, 264,630 and 118,913 single nucleotide polymorphism (SNP) sites and 89,078 and 72,513 Indels (Insertion/deletion) were detected among the 30 mutant isolates compared to the primary scaffolds and haplotigs of the wild-type isolate, respectively. Deleterious variants including SNPs and Indels occurred in 1866 genes. Genome wide association analysis identified 754 genes associated with avirulence phenotypes. A total of 62 genes were found significantly associated to 16 avirulence genes after selection through six criteria for putative effectors and degree of association, including 48 genes encoding secreted proteins (SPs) and 14 non-SP genes but with high levels of association (P ≤ 0.001) to avirulence phenotypes. Eight of the SP genes were identified as avirulence-associated effectors with high-confidence as they met five or six criteria used to determine effectors. Conclusions Genome sequence comparison of the mutant isolates with the progenitor isolate unraveled a large number of mutation sites along the genome and identified high-confidence effector genes as candidates for avirulence genes in Pst. Since the avirulence gene candidates were identified from associated SNPs and Indels caused by artificial mutagenesis, these avirulence gene candidates are valuable resources for elucidating the mechanisms of the pathogen pathogenicity, and will be studied to determine their functions in the interactions between the wheat host and the Pst pathogen.
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Affiliation(s)
- Yuxiang Li
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Chongjing Xia
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA. .,USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA, 99164-6430, USA.
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Abstract
Among the thousands of rust species described, many are known for their devastating effects on their hosts, which include major agriculture crops and trees. Hence, for over a century, these basidiomycete pathogenic fungi have been researched and experimented with. However, due to their biotrophic nature, they are challenging organisms to work with and, needing their hosts for propagation, represent pathosystems that are not easily experimentally accessible. Indeed, efforts to perform genetics have been few and far apart for the rust fungi, though one study performed in the 1940s was famously instrumental in formulating the gene-for-gene hypothesis describing pathogen-host interactions. By taking full advantage of the molecular genetic tools developed in the 1980s, research on many plant pathogenic microbes thrived, yet similar work on the rusts remained very challenging though not without some successes. However, the genomics era brought real breakthrough research for the biotrophic fungi and with innovative experimentation and the use of heterologous systems, molecular genetic analyses over the last 2 decades have significantly advanced our insight into the function of many rust fungus genes and their role in the interaction with their hosts. This has allowed optimizing efforts for resistance breeding and the design and testing of various novel strategies to reduce the devastating diseases they cause.
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Affiliation(s)
- Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research & Development Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0
| | - Les J Szabo
- U.S. Department of Agriculture-Agriculture Research Service, Cereal Disease Laboratory and University of Minnesota, 1551 Lindig Street, St. Paul, MN 55108, U.S.A
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Sharma Poudel R, Richards J, Shrestha S, Solanki S, Brueggeman R. Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance. BMC Genomics 2019; 20:985. [PMID: 31842749 PMCID: PMC6915985 DOI: 10.1186/s12864-019-6369-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 12/04/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its importance in human sustenance. This is the first extensive study utilizing a transcriptome-wide association mapping approach to identify candidate Puccinia graminis f. sp. tritici (Pgt) effectors/suppressors that elicit or suppress barley stem rust resistance genes. Here we focus on identifying Pgt elicitors that interact with the rpg4-mediated resistance locus (RMRL), the only effective source of Pgt race TTKSK resistance in barley. RESULTS Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses. CONCLUSIONS This transcriptomic study provided novel findings that help fill knowledge gaps in the understanding of stem rust virulence/avirulence and host resistance in barley. The pathogen transcriptome analysis suggested RMRL virulence might depend on the lack of avirulence genes, but evidence from pathogen association mapping analysis and host transcriptional analysis also suggested the alternate hypothesis that RMRL virulence may be due to the presence of suppressors of defense responses.
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Affiliation(s)
| | - Jonathan Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University, Baton Rouge, LA, USA
| | - Subidhya Shrestha
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
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Wu W, Nemri A, Blackman LM, Catanzariti AM, Sperschneider J, Lawrence GJ, Dodds PN, Jones DA, Hardham AR. Flax rust infection transcriptomics reveals a transcriptional profile that may be indicative for rust Avr genes. PLoS One 2019; 14:e0226106. [PMID: 31830116 PMCID: PMC6907798 DOI: 10.1371/journal.pone.0226106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/19/2019] [Indexed: 01/04/2023] Open
Abstract
Secreted effectors of fungal pathogens are essential elements for disease development. However, lack of sequence conservation among identified effectors has long been a problem for predicting effector complements in fungi. Here we have explored the expression characteristics of avirulence (Avr) genes and candidate effectors of the flax rust fungus, Melampsora lini. We performed transcriptome sequencing and real-time quantitative PCR (qPCR) on RNA extracted from ungerminated spores, germinated spores, isolated haustoria and flax seedlings inoculated with M. lini isolate CH5 during plant infection. Genes encoding two categories of M. lini proteins, namely Avr proteins and plant cell wall degrading enzymes (CWDEs), were investigated in detail. Analysis of the expression profiles of 623 genes encoding predicted secreted proteins in the M. lini transcriptome shows that the six known Avr genes (i.e. AvrM (avrM), AvrM14, AvrL2, AvrL567, AvrP123 (AvrP) and AvrP4) fall within a group of 64 similarly expressed genes that are induced in planta and show a peak of expression early in infection with a subsequent decline towards sporulation. Other genes within this group include two paralogues of AvrL2, an AvrL567 virulence allele, and a number of genes encoding putative effector proteins. By contrast, M. lini genes encoding CWDEs fall into different expression clusters with their distribution often unrelated to their catalytic activity or substrate targets. These results suggest that synthesis of M. lini Avr proteins may be regulated in a coordinated fashion and that the expression profiling-based analysis has significant predictive power for the identification of candidate Avr genes.
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Affiliation(s)
- Wenjie Wu
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
- * E-mail:
| | | | - Leila M. Blackman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Ann-Maree Catanzariti
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, the Australian National University, Canberra, Australia
| | | | | | - David A. Jones
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Adrienne R. Hardham
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
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van de Vossenberg BTLH, Prodhomme C, van Arkel G, van Gent-Pelzer MPE, Bergervoet M, Brankovics B, Przetakiewicz J, Visser RGF, van der Lee TAJ, Vossen JH. The Synchytrium endobioticum AvrSen1 Triggers a Hypersensitive Response in Sen1 Potatoes While Natural Variants Evade Detection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1536-1546. [PMID: 31246152 DOI: 10.1094/mpmi-05-19-0138-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synchytrium endobioticum is an obligate biotrophic fungus of division Chytridiomycota. It causes potato wart disease, has a worldwide quarantine status and is included on the Health and Human Services and United States Department of Agriculture Select Agent list. S. endobioticum isolates are grouped in pathotypes based on their ability to evade host resistance in a set of differential potato varieties. Thus far, 39 pathotypes are reported. A single dominant gene (Sen1) governs pathotype 1 (D1) resistance and we anticipated that the underlying molecular model would involve a pathogen effector (AvrSen1) that is recognized by the host. The S. endobioticum-specific secretome of 14 isolates representing six different pathotypes was screened for effectors specifically present in pathotype 1 (D1) isolates but absent in others. We identified a single AvrSen1 candidate. Expression of this candidate in potato Sen1 plants showed a specific hypersensitive response (HR), which cosegregated with the Sen1 resistance in potato populations. No HR was obtained with truncated genes found in pathotypes that evaded recognition by Sen1. These findings established that our candidate gene was indeed Avrsen1. The S. endobioticum AvrSen1 is a single-copy gene and encodes a 376-amino-acid protein without predicted function or functional domains, and is the first effector gene identified in Chytridiomycota, an extremely diverse yet underrepresented basal lineage of fungi.
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Affiliation(s)
- Bart T L H van de Vossenberg
- Wageningen University and Research, Biointeractions and Plant Health, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands
| | | | | | - Marga P E van Gent-Pelzer
- Wageningen University and Research, Biointeractions and Plant Health, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | | | - Balázs Brankovics
- Wageningen University and Research, Biointeractions and Plant Health, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jarosław Przetakiewicz
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, 05-870 Błonie, Warsaw, Poland
| | | | - Theo A J van der Lee
- Wageningen University and Research, Biointeractions and Plant Health, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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De Novo Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen Puccinia hordei Identifies Candidates for Three Avirulence Genes. G3-GENES GENOMES GENETICS 2019; 9:3263-3271. [PMID: 31444296 PMCID: PMC6778787 DOI: 10.1534/g3.119.400450] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Puccinia hordei (Ph) is a damaging pathogen of barley throughout the world. Despite its importance, almost nothing is known about the genomics of this pathogen, and a reference genome is lacking. In this study, the first reference genome was assembled for an Australian isolate of Ph ("Ph560") using long-read SMRT sequencing. A total of 838 contigs were assembled, with a total size of 207 Mbp. This included both haplotype collapsed and separated regions, consistent with an estimated haploid genome size of about 150Mbp. An annotation pipeline that combined RNA-Seq of Ph-infected host tissues and homology to proteins from four other Puccinia species predicted 25,543 gene models of which 1,450 genes were classified as encoding secreted proteins based on the prediction of a signal peptide and no transmembrane domain. Genome resequencing using short-read technology was conducted for four additional Australian strains, Ph612, Ph626, Ph608 and Ph584, which are considered to be simple mutational derivatives of Ph560 with added virulence to one or two of three barley leaf rust resistance genes (viz. Rph3, Rph13 and Rph19). To identify candidate genes for the corresponding avirulence genes AvrRph3, AvrRph13 and AvrRph19, genetic variation in predicted secreted protein genes between the strains was correlated to the virulence profiles of each, identifying 35, 29 and 46 candidates for AvrRph13, AvrRph3 and AvrRph19, respectively. The identification of these candidate genes provides a strong foundation for future efforts to isolate these three avirulence genes, investigate their biological properties, and develop new diagnostic tests for monitoring pathogen virulence.
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Horsefield S, Burdett H, Zhang X, Manik MK, Shi Y, Chen J, Qi T, Gilley J, Lai JS, Rank MX, Casey LW, Gu W, Ericsson DJ, Foley G, Hughes RO, Bosanac T, von Itzstein M, Rathjen JP, Nanson JD, Boden M, Dry IB, Williams SJ, Staskawicz BJ, Coleman MP, Ve T, Dodds PN, Kobe B. NAD + cleavage activity by animal and plant TIR domains in cell death pathways. Science 2019; 365:793-799. [PMID: 31439792 DOI: 10.1126/science.aax1911] [Citation(s) in RCA: 287] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/23/2019] [Indexed: 02/02/2023]
Abstract
SARM1 (sterile alpha and TIR motif containing 1) is responsible for depletion of nicotinamide adenine dinucleotide in its oxidized form (NAD+) during Wallerian degeneration associated with neuropathies. Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors recognize pathogen effector proteins and trigger localized cell death to restrict pathogen infection. Both processes depend on closely related Toll/interleukin-1 receptor (TIR) domains in these proteins, which, as we show, feature self-association-dependent NAD+ cleavage activity associated with cell death signaling. We further show that SARM1 SAM (sterile alpha motif) domains form an octamer essential for axon degeneration that contributes to TIR domain enzymatic activity. The crystal structures of ribose and NADP+ (the oxidized form of nicotinamide adenine dinucleotide phosphate) complexes of SARM1 and plant NLR RUN1 TIR domains, respectively, reveal a conserved substrate binding site. NAD+ cleavage by TIR domains is therefore a conserved feature of animal and plant cell death signaling pathways.
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Affiliation(s)
- Shane Horsefield
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Hayden Burdett
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiaoxiao Zhang
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia.,Plant Sciences Division, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Mohammad K Manik
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Jian Chen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia.,Plant Sciences Division, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Tiancong Qi
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathan Gilley
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, ED Adrian Building, Forvie Site, Robinson Way, Cambridge CB2 0PY, UK.,Babraham Institute, Babraham, Cambridge CB22 3AT, UK
| | - Jhih-Siang Lai
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Maxwell X Rank
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Lachlan W Casey
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.,Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD 4072, Australia
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel J Ericsson
- Macromolecular Crystallography (MX) Beamlines, Australian Synchrotron, Melbourne, VIC 3168, Australia
| | - Gabriel Foley
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert O Hughes
- Disarm Therapeutics, 400 Technology Square, Cambridge, MA 02139, USA
| | - Todd Bosanac
- Disarm Therapeutics, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - John P Rathjen
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Mikael Boden
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Ian B Dry
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Urrbrae, SA 5064, Australia
| | - Simon J Williams
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Michael P Coleman
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, ED Adrian Building, Forvie Site, Robinson Way, Cambridge CB2 0PY, UK.,Babraham Institute, Babraham, Cambridge CB22 3AT, UK
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia. .,Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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44
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Jones JDG. Flor-iculture: Ellis and Dodds' Illumination of Gene-for-Gene Biology. THE PLANT CELL 2019; 31:1204-1205. [PMID: 31036596 PMCID: PMC6588296 DOI: 10.1105/tpc.19.00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Jonathan D G Jones
- The Sainsbury Laboratory University of East AngliaNorwich, United Kingdom
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45
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Ma Z, Liu JJ, Zamany A. Identification and Functional Characterization of an Effector Secreted by Cronartium ribicola. PHYTOPATHOLOGY 2019; 109:942-951. [PMID: 31066346 DOI: 10.1094/phyto-11-18-0427-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cri-9402 was identified as a protein effector from Cronartium ribicola, based on the effect of its expression on growth of Pseudomonas syringae Psm ES4326 introduced into transiently transformed tobacco leaves and stably transformed Arabidopsis seedlings. In tobacco leaves transiently expressing its coding sequence, growth of P. syringae Psm ES4326 was inhibited. Expression of pathogenesis-related (PR) protein 2 (PR2), PR4a, endochitinase B, hypersensitive-related 201 (HSR201), HSR203J, and proteinase inhibitor 1 was upregulated but expression of PR1, coronatine insensitive 1, and abscisic acid 1 was significantly suppressed. In transformed Arabidopsis seedlings, the effector stimulated growth of P. syringae Psm ES4326; significantly suppressed expression of PR1, PR2, nonexpresser of pathogenesis-related genes 1 (NPR1), NPR3, NPR4, phytoalexin deficient 4, and salicylic acid induction deficient 2; and enhanced expression of plant defensin 1.2 (PDF1.2). The above results showed that the majority of responses to this effector in tobacco leaves were converse to those in transformed Arabidopsis. We could conclude that Cri-9402 promoted disease resistance in tobacco leaves and disease susceptibility in Arabidopsis seedlings. Its transcript was mainly expressed in aeciospores of C. ribicola and was probably involved in production or germination of aeciospores, and it was an effector potentially functioning in white pine-blister rust interactions.
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Affiliation(s)
- Zhenguo Ma
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Jun-Jun Liu
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Arezoo Zamany
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
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46
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Bourras S, Kunz L, Xue M, Praz CR, Müller MC, Kälin C, Schläfli M, Ackermann P, Flückiger S, Parlange F, Menardo F, Schaefer LK, Ben-David R, Roffler S, Oberhaensli S, Widrig V, Lindner S, Isaksson J, Wicker T, Yu D, Keller B. The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nat Commun 2019; 10:2292. [PMID: 31123263 PMCID: PMC6533294 DOI: 10.1038/s41467-019-10274-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/03/2019] [Indexed: 12/25/2022] Open
Abstract
The wheat Pm3 resistance gene against the powdery mildew pathogen occurs as an allelic series encoding functionally different immune receptors which induce resistance upon recognition of isolate-specific avirulence (AVR) effectors from the pathogen. Here, we describe the identification of five effector proteins from the mildew pathogens of wheat, rye, and the wild grass Dactylis glomerata, specifically recognized by the PM3B, PM3C and PM3D receptors. Together with the earlier identified AVRPM3A2/F2, the recognized AVRs of PM3B/C, (AVRPM3B2/C2), and PM3D (AVRPM3D3) belong to a large group of proteins with low sequence homology but predicted structural similarities. AvrPm3b2/c2 and AvrPm3d3 are conserved in all tested isolates of wheat and rye mildew, and non-host infection assays demonstrate that Pm3b, Pm3c, and Pm3d are also restricting the growth of rye mildew on wheat. Furthermore, divergent AVR homologues from non-adapted rye and Dactylis mildews are recognized by PM3B, PM3C, or PM3D, demonstrating their involvement in host specificity.
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Affiliation(s)
- Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
- Department of Forest Mycology and Plant Pathology, Division of Plant Pathology, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden.
| | - Lukas Kunz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Minfeng Xue
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China
- College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Coraline Rosalie Praz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Carol Kälin
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Michael Schläfli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Patrick Ackermann
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simon Flückiger
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | | | - Roi Ben-David
- Institute of Plant Science, ARO-Volcani Center, 50250, Bet Dagan, Israel
| | - Stefan Roffler
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simone Oberhaensli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Victoria Widrig
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Stefan Lindner
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Jonatan Isaksson
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Dazhao Yu
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China.
- College of Life Science, Wuhan University, Wuhan, 430072, China.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
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47
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Lorrain C, Gonçalves Dos Santos KC, Germain H, Hecker A, Duplessis S. Advances in understanding obligate biotrophy in rust fungi. THE NEW PHYTOLOGIST 2019; 222:1190-1206. [PMID: 30554421 DOI: 10.1111/nph.15641] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/13/2018] [Indexed: 05/18/2023]
Abstract
Contents Summary 1190 I. Introduction 1190 II. Rust fungi: a diverse and serious threat to agriculture 1191 III. The different facets of rust life cycles and unresolved questions about their evolution 1191 IV. The biology of rust infection 1192 V. Rusts in the genomics era: the ever-expanding list of candidate effector genes 1195 VI. Functional characterization of rust effectors 1197 VII. Putting rusts to sleep: Pucciniales research outlooks 1201 Acknowledgements 1202 References 1202 SUMMARY: Rust fungi (Pucciniales) are the largest group of plant pathogens and represent one of the most devastating threats to agricultural crops worldwide. Despite the economic importance of these highly specialized pathogens, many aspects of their biology remain obscure, largely because rust fungi are obligate biotrophs. The rise of genomics and advances in high-throughput sequencing technology have presented new options for identifying candidate effector genes involved in pathogenicity mechanisms of rust fungi. Transcriptome analysis and integrated bioinformatics tools have led to the identification of key genetic determinants of host susceptibility to infection by rusts. Thousands of genes encoding secreted proteins highly expressed during host infection have been reported for different rust species, which represents significant potential towards understanding rust effector function. Recent high-throughput in planta expression screen approaches (effectoromics) have pushed the field ahead even further towards predicting high-priority effectors and identifying avirulence genes. These new insights into rust effector biology promise to inform future research and spur the development of effective and sustainable strategies for managing rust diseases.
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Affiliation(s)
- Cécile Lorrain
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | | | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Quebec à Trois-Rivières, Trois-Rivières, QC, G9A 5H7, Canada
| | - Arnaud Hecker
- Université de Lorraine, UMR 1136 Université de Lorraine/INRA Interactions Arbres/Microorganismes, Vandoeuvre-lès-Nancy, France
| | - Sébastien Duplessis
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
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48
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Wan L, Koeck M, Williams SJ, Ashton AR, Lawrence GJ, Sakakibara H, Kojima M, Böttcher C, Ericsson DJ, Hardham AR, Jones DA, Ellis JG, Kobe B, Dodds PN. Structural and functional insights into the modulation of the activity of a flax cytokinin oxidase by flax rust effector AvrL567-A. MOLECULAR PLANT PATHOLOGY 2019; 20:211-222. [PMID: 30242946 PMCID: PMC6637871 DOI: 10.1111/mpp.12749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
During infection, plant pathogens secrete effector proteins to facilitate colonization. In comparison with our knowledge of bacterial effectors, the current understanding of how fungal effectors function is limited. In this study, we show that the effector AvrL567-A from the flax rust fungus Melampsora lini interacts with a flax cytosolic cytokinin oxidase, LuCKX1.1, using both yeast two-hybrid and in planta bimolecular fluorescence assays. Purified LuCKX1.1 protein shows catalytic activity against both N6-(Δ2-isopentenyl)-adenine (2iP) and trans-zeatin (tZ) substrates. Incubation of LuCKX1.1 with AvrL567-A results in increased catalytic activity against both substrates. The crystal structure of LuCKX1.1 and docking studies with AvrL567-A indicate that the AvrL567 binding site involves a flexible surface-exposed region that surrounds the cytokinin substrate access site, which may explain its effect in modulating LuCKX1.1 activity. Expression of AvrL567-A in transgenic flax plants gave rise to an epinastic leaf phenotype consistent with hormonal effects, although no difference in overall cytokinin levels was observed. We propose that, during infection, plant pathogens may differentially modify the levels of extracellular and intracellular cytokinins.
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Affiliation(s)
- Li Wan
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular BioscienceUniversity of QueenslandBrisbaneQLD4072Australia
- Department of BiologyUniversity of North CarolinaChapel HillNorth Carolina27599‐3280USA
| | - Markus Koeck
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraACT2601Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular BioscienceUniversity of QueenslandBrisbaneQLD4072Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Anthony R. Ashton
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraACT2601Australia
| | - Gregory J. Lawrence
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraACT2601Australia
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource ScienceYokohamaKanagawa230‐0045Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource ScienceYokohamaKanagawa230‐0045Japan
| | - Christine Böttcher
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodAdelaideSA5064Australia
| | - Daniel J. Ericsson
- Australian SynchrotronMacromolecular CrystallographyClaytonVictoria3168Australia
| | - Adrienne R. Hardham
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - David A. Jones
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Jeffrey G. Ellis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraACT2601Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular BioscienceUniversity of QueenslandBrisbaneQLD4072Australia
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraACT2601Australia
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49
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Kapos P, Devendrakumar KT, Li X. Plant NLRs: From discovery to application. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 279:3-18. [PMID: 30709490 DOI: 10.1016/j.plantsci.2018.03.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 05/09/2023]
Abstract
Plants require a complex immune system to defend themselves against a wide range of pathogens which threaten their growth and development. The nucleotide-binding leucine-rich repeat proteins (NLRs) are immune sensors that recognize effectors delivered by pathogens. The first NLR was cloned more than twenty years ago. Since this initial discovery, NLRs have been described as key components of plant immunity responsible for pathogen recognition and triggering defense responses. They have now been described in most of the well-studied mulitcellular plant species, with most having large NLR repertoires. As research has progressed so has the understanding of how NLRs interact with their recognition substrates and how they in turn activate downstream signalling. It has also become apparent that NLR regulation occurs at the transcriptional, post-transcriptional, translational, and post-translational levels. Even before the first NLR was cloned, breeders were utilising such genes to increase crop performance. Increased understanding of the mechanistic details of the plant immune system enable the generation of plants resistant against devastating pathogens. This review aims to give an updated summary of the NLR field.
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Affiliation(s)
- Paul Kapos
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Karen Thulasi Devendrakumar
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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50
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Saur IML, Bauer S, Lu X, Schulze-Lefert P. A cell death assay in barley and wheat protoplasts for identification and validation of matching pathogen AVR effector and plant NLR immune receptors. PLANT METHODS 2019; 15:118. [PMID: 31666804 PMCID: PMC6813131 DOI: 10.1186/s13007-019-0502-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/14/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant disease resistance to host-adapted pathogens is often mediated by host nucleotide-binding and leucine-rich repeat (NLR) receptors that detect matching pathogen avirulence effectors (AVR) inside plant cells. AVR-triggered NLR activation is typically associated with a rapid host cell death at sites of attempted infection and this response constitutes a widely used surrogate for NLR activation. However, it is challenging to assess this cell death in cereal hosts. RESULTS Here we quantify cell death upon NLR-mediated recognition of fungal pathogen AVRs in mesophyll leaf protoplasts of barley and wheat. We provide measurements for the recognition of the fungal AVRs AvrSr50 and AVR a1 by their respective cereal NLRs Sr50 and Mla1 upon overexpression of the AVR and NLR pairs in mesophyll protoplast of both, wheat and barley. CONCLUSIONS Our data demonstrate that the here described approach can be effectively used to detect and quantify death of wheat and barley cells induced by overexpression of NLR and AVR effectors or AVR effector candidate genes from diverse fungal pathogens within 24 h.
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Affiliation(s)
- Isabel M. L. Saur
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Saskia Bauer
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Xunli Lu
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Present Address: Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193 China
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
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