1
|
Henningsen EC, Lewis D, Nguyen DT, Sperschneider J, Kianian SF, Stone E, Dodds PN, Figueroa M. Virulence Patterns of Oat Crown Rust in Australia - Season 2022. PLANT DISEASE 2024; 108:1959-1963. [PMID: 38277650 DOI: 10.1094/pdis-09-23-1973-sc] [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: 01/28/2024]
Abstract
Puccinia coronata f. sp. avenae (Pca) is an important foliar pathogen of oat which causes crown rust disease. The virulence profile of 48 Pca isolates derived from different locations in Australia was characterized using a collection of oat lines often utilized in rust surveys in the United States and Australia. This analysis indicates that Pca populations in Eastern Australia are broadly virulent, which contrasts with the population in Western Australia (WA). Several oat lines/Pc genes are effective against all rust samples collected from WA, suggesting they may provide useful resistance in this region if deployed in combination. We identified 19 lines from the United States oat differential set that display disease resistance to Pca in WA, with some in agreement with previous rust survey reports. We adopted the 10-letter nomenclature system to define oat crown rust races in Australia and compare the frequency of those virulence traits to published data from the United States. Based on this nomenclature, 42 unique races were detected among the 48 isolates, reflecting the high diversity of virulence phenotypes for Pca in Australia. Nevertheless, the Pca population in the United States is substantially more broadly virulent than that of Australia. Close examination of resistance profiles for the oat differential set lines after infection with Pca supports hypotheses of allelism or redundancy among Pc genes or the presence of several resistance genes in some oat differential lines. These findings illustrate the need to deconvolute the oat differential set using molecular tools.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Eva C Henningsen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - David Lewis
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Duong T Nguyen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Adelaide, SA 5064, Australia
| | - Jana Sperschneider
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Shahryar F Kianian
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service, St. Paul, MN, U.S.A
| | - Eric Stone
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- Biological Data Science Institute, The Australian National University, Canberra, ACT 2601, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Melania Figueroa
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| |
Collapse
|
2
|
Nazarov T, Liu Y, Chen X, See DR. Molecular Mechanisms of the Stripe Rust Interaction with Resistant and Susceptible Wheat Genotypes. Int J Mol Sci 2024; 25:2930. [PMID: 38474176 DOI: 10.3390/ijms25052930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Rust fungi cause significant damage to wheat production worldwide. In order to mitigate disease impact and improve food security via durable resistance, it is important to understand the molecular basis of host-pathogen interactions. Despite a long history of research and high agricultural importance, still little is known about the interactions between the stripe rust fungus and wheat host on the gene expression level. Here, we present analysis of the molecular interactions between a major wheat pathogen-Puccinia striiformis f. sp. tritici (Pst)-in resistant and susceptible host backgrounds. Using plants with durable nonrace-specific resistance along with fully susceptible ones allowed us to show how gene expression patterns shift in compatible versus incompatible interactions. The pathogen showed significantly greater number and fold changes of overexpressed genes on the resistant host than the susceptible host. Stress-related pathways including MAPK, oxidation-reduction, osmotic stress, and stress granule formation were, almost exclusively, upregulated in the resistant host background, suggesting the requirement of the resistance-countermeasure mechanism facilitated by Pst. In contrast, the susceptible host background allowed for broad overrepresentation of the nutrient uptake pathways. This is the first study focused on the stripe rust pathogen-wheat interactions, on the whole transcriptome level, from the pathogen side. It lays a foundation for the better understanding of the resistant/susceptible hosts versus pathogenic fungus interaction in a broader sense.
Collapse
Affiliation(s)
- Taras Nazarov
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Yan Liu
- 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
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, USA
| | - Deven R See
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, USA
| |
Collapse
|
3
|
Qi M, Yu H, Bredow M, Chicowski AS, Fields LD, Whitham SA. Insights into Phakopsora pachyrhizi Effector-Effector Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:227-231. [PMID: 37831963 DOI: 10.1094/mpmi-08-23-0120-fi] [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: 10/15/2023]
Abstract
The multifaceted role of pathogen-encoded effectors in plant-pathogen interactions is complex and not fully understood. Effectors operate within intricate host environments, interacting with host proteins and other effectors to modulate virulence. The complex interplay between effectors raises the concept of metaeffectors, wherein some effectors regulate the activity of others. While previous research has demonstrated the importance of effector repertoires in pathogen virulence, only a limited number of studies have investigated the interactions between these effectors. This study explores the interactions among Phakopsora pachyrhizi effector candidates (PpECs). P. pachyrhizi haustorial transcriptome analysis identified a collection of predicted PpECs. Among these, PpEC23 was found to interact with PpEC48, prompting further exploration into their potential interaction with other effectors. Here, we utilized a yeast two-hybrid screen to explore protein-protein interactions between PpECs. A split-luciferase complementation assay also demonstrated that these interactions could occur within soybean cells. Interestingly, PpEC48 displayed the ability to interact with several small cysteine-rich proteins (SCRPs), suggesting its affinity for this specific class of effectors. We show that these interactions involve a histidine-rich domain within PpEC48, emphasizing the significance of structural motifs in mediating effector interactions. The unique nature of PpEC48, showing no sequence matches in other organisms, suggests its relatively recent evolution and potential orphan gene status. Our work reveals insights into the intricate network of interactions among P. pachyrhizi effector-effector interactions. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Haiyue Yu
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, 100193, Beijing, China
| | - Melissa Bredow
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Aline Sartor Chicowski
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Letícia Dias Fields
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil
| | - Steven A Whitham
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| |
Collapse
|
4
|
Christian N, Perlin MH. Plant-endophyte communication: Scaling from molecular mechanisms to ecological outcomes. Mycologia 2024; 116:227-250. [PMID: 38380970 DOI: 10.1080/00275514.2023.2299658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/22/2023] [Indexed: 02/22/2024]
Abstract
Diverse communities of fungal endophytes reside in plant tissues, where they affect and are affected by plant physiology and ecology. For these intimate interactions to form and persist, endophytes and their host plants engage in intricate systems of communication. The conversation between fungal endophytes and plant hosts ultimately dictates endophyte community composition and function and has cascading effects on plant health and plant interactions. In this review, we synthesize our current knowledge on the mechanisms and strategies of communication used by endophytic fungi and their plant hosts. We discuss the molecular mechanisms of communication that lead to organ specificity of endophytic communities and distinguish endophytes, pathogens, and saprotrophs. We conclude by offering emerging perspectives on the relevance of plant-endophyte communication to microbial community ecology and plant health and function.
Collapse
Affiliation(s)
- Natalie Christian
- Department of Biology, University of Louisville, Louisville, Kentucky 40292
| | - Michael H Perlin
- Department of Biology, University of Louisville, Louisville, Kentucky 40292
| |
Collapse
|
5
|
Khan M, Djamei A. TOPLESS Corepressors as an Emerging Hub of Plant Pathogen Effectors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:190-195. [PMID: 38205771 DOI: 10.1094/mpmi-10-23-0158-fi] [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: 01/12/2024]
Abstract
Transcriptional corepressors form an ancient and essential layer of gene expression control in eukaryotes. TOPLESS and TOPLESS-RELATED (TPL/TPR) proteins constitute a conserved family of Groucho (Gro)/thymidine uptake 1 (Tup1)-type transcriptional corepressors and control diverse growth, developmental, and stress signaling responses in plants. Because of their central and versatile regulatory roles, they act as a signaling hub to integrate various input signaling pathways in the transcriptional responses. Recently, increasing pieces of evidence indicate the roles of TPL/TPR family proteins in the modulation of plant immunity. This is supported by studies on effectors of distantly related pathogens that target TPL/TPR proteins in planta. In this short review, we will summarize the latest findings concerning pathogens targeting plant TPL/TPR proteins to manipulate plant signaling responses for the successful invasion of their hosts. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Mamoona Khan
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Armin Djamei
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| |
Collapse
|
6
|
Zhao H, Huang J, Zhao X, Yu L, Wang X, Zhao C, nasab HR, Tang C, Wang X. Stripe Rust Effector Pst_9302 Inhibits Wheat Immunity to Promote Susceptibility. PLANTS (BASEL, SWITZERLAND) 2023; 13:94. [PMID: 38202402 PMCID: PMC10780974 DOI: 10.3390/plants13010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024]
Abstract
Puccinia striiformis f. sp. tritici is an obligate biotrophic fungus that causes destructive stripe rust disease in wheat. During infection, Pst secretes virulence effectors via a specific infection structure-the haustorium-inside host cells to disturb host immunity and promote fungal colonization and expansion. Hence, the identification and functional analyses of Pst effectors are of great significance in deciphering the Pst pathogenicity mechanism. Here, we identified one candidate Pst effector Pst_9302 that could suppress Bax-triggered cell death in Nicotiana benthamiana. qRT-PCR analyses showed that the transcript levels of Pst_9302 were highly increased during the early infection stages of Pst. The transient expression of Pst_9302 in wheat via the type-three secretion system (T3SS) significantly inhibited the callose deposition induced by Pseudomonas syringae EtHAn. During wheat-Pst interaction, Pst_9302 overexpression suppressed reactive oxygen species (ROS) accumulation and cell death caused by the avirulent Pst race CYR23. The host-induced gene silencing (HIGS) of Pst_9302 resulted in decreased Pst pathogenicity with reduced infection area. The results suggest that Pst_9302 plays a virulence role in suppressing plant immunity and promoting Pst pathogenicity. Moreover, wheat voltage-dependent anion channel 1 protein (TaVDAC1) was identified as candidate Pst_9302-interacting proteins by yeast two-hybrid (Y2H) screening. Pull-down assays using the His-Pst_9302 and GST-TaVDAC1 protein verified their interactions. These results suggest that Pst_9302 may modulate wheat TaVDAC1 to regulate plant immunity.
Collapse
Affiliation(s)
- Haibin Zhao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (H.Z.); (J.H.); (X.Z.); (L.Y.); (X.W.); (C.Z.)
| | - Jiangyu Huang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (H.Z.); (J.H.); (X.Z.); (L.Y.); (X.W.); (C.Z.)
| | - Xiaoyan Zhao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (H.Z.); (J.H.); (X.Z.); (L.Y.); (X.W.); (C.Z.)
| | - Ligang Yu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (H.Z.); (J.H.); (X.Z.); (L.Y.); (X.W.); (C.Z.)
| | - Xiaodong Wang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (H.Z.); (J.H.); (X.Z.); (L.Y.); (X.W.); (C.Z.)
| | - Congcong Zhao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (H.Z.); (J.H.); (X.Z.); (L.Y.); (X.W.); (C.Z.)
| | - Hojjatollah Rabbani nasab
- State Key Laboratory of Crop Stress, Plant Protection Department, Golestan Agricultural and Natural Resource Research and Education Center, Gorgan P.O. Box 49156-77555, Iran;
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (H.Z.); (J.H.); (X.Z.); (L.Y.); (X.W.); (C.Z.)
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (H.Z.); (J.H.); (X.Z.); (L.Y.); (X.W.); (C.Z.)
| |
Collapse
|
7
|
Zheng P, Liu M, Pang L, Sun R, Yao M, Wang X, Kang Z, Liu J. Stripe rust effector Pst21674 compromises wheat resistance by targeting transcription factor TaASR3. PLANT PHYSIOLOGY 2023; 193:2806-2824. [PMID: 37706535 DOI: 10.1093/plphys/kiad497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023]
Abstract
Pathogens compromise host defense responses by strategically secreting effector proteins. However, the molecular mechanisms by which effectors manipulate disease-resistance factors to evade host surveillance remain poorly understood. In this study, we characterized a Puccinia striiformis f. sp. tritici (Pst) effector Pst21674 with a signal peptide. Pst21674 was significantly upregulated during Pst infections in wheat (Triticum aestivum L.) and knocking down Pst21674 by host-induced gene silencing led to reduced Pst pathogenicity and restricted hyphal spread in wheat. Pst21674 interaction with the abscisic acid-, stress-, and ripening-induced protein TaASR3 was validated mainly in the nucleus. Size exclusion chromatography, bimolecular fluorescence complementation, and luciferase complementation imaging assays confirmed that TaASR3 could form a functional tetramer. Virus-induced gene silencing and overexpression demonstrated that TaASR3 contributes to wheat resistance to stripe rust by promoting accumulation of reactive oxygen species and cell death. Additionally, transcriptome analysis revealed that the expression of defense-related genes was regulated in transgenic wheat plants overexpressing TaASR3. Interaction between Pst21674 and TaASR3 interfered with the polymerization of TaASR3 and suppressed TaASR3-mediated transcriptional activation of defense-related genes. These results indicate that Pst21674 serves as an important virulence factor secreted into the host nucleus to impede wheat resistance to Pst, possibly by targeting and preventing polymerization of TaASR3.
Collapse
Affiliation(s)
- Peijing Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Mengxue Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lijing Pang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ruyi Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Mohan Yao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| |
Collapse
|
8
|
Swanepoel S, Visser EA, Shuey LS, Naidoo S. The In Planta Gene Expression of Austropuccinia psidii in Resistant and Susceptible Eucalyptus grandis. PHYTOPATHOLOGY 2023; 113:1066-1076. [PMID: 36611233 DOI: 10.1094/phyto-07-22-0257-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: 06/17/2023]
Abstract
Austropuccinia psidii, commonly known as myrtle rust, is an obligate, biotrophic rust pathogen that causes rust disease in a broad host range of Myrtaceae species. Eucalyptus grandis, a widely cultivated hardwood Myrtaceae species, is susceptible to A. psidii infection, with this pathogen threatening both their natural range and various forest plantations across the world. This study aimed to investigate the A. psidii transcriptomic responses in resistant and susceptible E. grandis at four time points. RNA-seq reads were mapped to the A. psidii reference genome to quantify expressed genes at 12 h postinoculation and 1, 2, and 5 days postinoculation (dpi). A total of eight hundred and ninety expressed genes were found, of which 43 were candidate effector protein genes. These included rust transferred protein 1 (RTP1), expressed in susceptible hosts at 5 dpi, and a hydrolase protein gene expressed in both resistant and susceptible hosts over time. Functional categorization of expressed genes revealed processes enriched in susceptible hosts, including malate metabolic and malate dehydrogenase activity, implicating oxalic acid in disease susceptibility. These results highlight putative virulence or pathogenicity mechanisms employed by A. psidii to cause disease, and they provide the first insight into the molecular responses of A. psidii in E. grandis over time.
Collapse
Affiliation(s)
- Shae Swanepoel
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| | - Erik A Visser
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| | - Louise S Shuey
- Department of Agriculture and Fisheries, Queensland Government, Australia
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| |
Collapse
|
9
|
Magnaporthe oryzae pathotype Triticum (MoT) can act as a heterologous expression system for fungal effectors with high transcript abundance in wheat. Sci Rep 2023; 13:108. [PMID: 36596834 PMCID: PMC9810704 DOI: 10.1038/s41598-022-27030-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
Plant pathogens deliver effector proteins to reprogramme a host plants circuitry, supporting their own growth and development, whilst thwarting defence responses. A subset of these effectors are termed avirulence factors (Avr) and can be recognised by corresponding host resistance (R) proteins, creating a strong evolutionary pressure on pathogen Avr effectors that favours their modification/deletion to evade the immune response. Hence, identifying Avr effectors and tracking their allele frequencies in a population is critical for understanding the loss of host recognition. However, the current systems available to confirm Avr effector function, particularly for obligate biotrophic fungi, remain limited and challenging. Here, we explored the utility of the genetically tractable wheat blast pathogen Magnaporthe oryzae pathotype Triticum (MoT) as a suitable heterologous expression system in wheat. Using the recently confirmed wheat stem rust pathogen (Puccina graminis f. sp. tritici) avirulence effector AvrSr50 as a proof-of-concept, we found that delivery of AvrSr50 via MoT could elicit a visible Sr50-dependant cell death phenotype. However, activation of Sr50-mediated cell death correlated with a high transgene copy number and transcript abundance in MoT transformants. This illustrates that MoT can act as an effective heterologous delivery system for fungal effectors from distantly related fungal species, but only when enough transgene copies and/or transcript abundance is achieved.
Collapse
|
10
|
Cui Z, Wu W, Fan F, Wang F, Liu D, Di D, Wang H. Transcriptome analysis of Lr19-virulent mutants provides clues for the AvrLr19 of Puccinia triticina. Front Microbiol 2023; 14:1062548. [PMID: 37032911 PMCID: PMC10073493 DOI: 10.3389/fmicb.2023.1062548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Wheat leaf rust caused by Puccinia triticina (Pt) remains one of the most destructive diseases of common wheat worldwide. Understanding the pathogenicity mechanisms of Pt is important to control wheat leaf rust. Methods The urediniospores of Pt race PHNT (wheat leaf rust resistance gene Lr19-avirulent isolate) were mutagenized with ethyl methanesulfonate (EMS), and two Lr19-virulent mutants named M1 and M2 were isolated. RNA sequencing was performed on samples collected from wheat cultivars Chinese Spring and TcLr19 infected with wild-type (WT) PHNT, M1, and M2 isolates at 14 days post-inoculation (dpi), respectively. Screening AvrLr19 candidates by quantitative reverse transcription PCR (qPCR) and Agrobacterium-mediated transient assays in Nicotiana benthamiana. Results 560 genes with single nucleotide polymorphisms (SNPs) and insertions or deletions (Indels) from non-differentially expressed genes were identified. Among them, 10 secreted proteins were screened based on their fragments per kilobase of exon model per million mapped reads (FPKM) values in the database. qPCR results showed that the expression profiles of 7 secreted proteins including PTTG_27471, PTTG_12441, PTTG_28324, PTTG_26499, PTTG_06910, PTTG_26516, and PTTG_03570 among 10 secreted proteins in mutants were significantly different with that in wild-type isolate after infection wheat TcLr19 and might be related to the recognition between Lr19 and AvrLr19. In addition, a total of 216 differentially expressed genes (DEGs) were obtained from three different sample comparisons including M1-vs-WT, M2-vs-WT, and M1-vs-M2. Among 216 DEGs, 15 were predicted to be secreted proteins. One secreted protein named PTTG_04779 could inhibit programmed progress of cell death (PCD) induced by apoptosis-controlling genes B-cell lymphoma-2 associated X protein (BAX) on Nicotiana benthamiana, indicating that it might play a virulence function in plant. Taken together, total 8 secreted proteins, PTTG_04779, PTTG_27471, PTTG_12441, PTTG_28324, PTTG_26499, PTTG_06910, PTTG_26516, PTTG_03570 are identified as AvrLr19 candidates. Discussion Our results showed that a large number of genes participate in the interaction between Pt and TcLr19, which will provide valuable resources for the identification of AvrLr19 candidates and pathogenesis-related genes.
Collapse
Affiliation(s)
- Zhongchi Cui
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Wenyue Wu
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Fan Fan
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Fei Wang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Daqun Liu
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
| | - Dianping Di
- Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding, Hebei, China
- *Correspondence: Dianping Di,
| | - Haiyan Wang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, Hebei, China
- Haiyan Wang,
| |
Collapse
|
11
|
Jensen C, Korolev A, Corredor-Moreno P, Minter F, Dodds PN, Saunders DGO. Caveats of Using Bacterial Type Three Secretion Assays for Validating Fungal Avirulence Effectors in Wheat. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1061-1066. [PMID: 36445162 DOI: 10.1094/mpmi-08-22-0167-sc] [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: 06/16/2023]
Abstract
Functional characterization of effector proteins of fungal obligate biotrophic pathogens, especially confirmation of avirulence (Avr) properties, has been notoriously difficult, due to the experimental intractability of many of these organisms. Previous studies in wheat have shown promising data suggesting the type III secretion system (T3SS) of bacteria may be a suitable surrogate for delivery and detection of Avr properties of fungal effectors. However, these delivery systems were tested in the absence of confirmed Avr effectors. Here, we tested two previously described T3SS-mediated delivery systems for their suitability when delivering two confirmed Avr effectors from two fungal pathogens of wheat, Puccinia graminis f. sp. tritici and Magnaporthe oryzae pathotype tritici. We showed that both effectors (AvrSr50 and AvrRmg8) were unable to elicit a hypersensitive response on wheat seedlings with the corresponding resistance gene when expressed by the Pseudomonas fluorescens "Effector to Host Analyser" (EtHAn) system. Furthermore, we found the utility of Burkholderia glumae for screening Avr phenotypes is severely limited, as the wild-type strain elicits nonhost cell death in multiple wheat accessions. These results provide valuable insight into the suitability of these systems for screening fungal effectors for Avr properties that may help guide further development of surrogate bacterial delivery systems in wheat. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Cassandra Jensen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Andrey Korolev
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | | | - Francesca Minter
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Peter N Dodds
- CSIRO Agriculture and Food Australia, GPO Box 1700, Clunies Ross Street, Canberra ACT 2601, Australia
| | - Diane G O Saunders
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| |
Collapse
|
12
|
RoyChowdhury M, Sternhagen J, Xin Y, Lou B, Li X, Li C. Evolution of pathogenicity in obligate fungal pathogens and allied genera. PeerJ 2022; 10:e13794. [PMID: 36042858 PMCID: PMC9420410 DOI: 10.7717/peerj.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 07/06/2022] [Indexed: 01/17/2023] Open
Abstract
Obligate fungal pathogens (ascomycetes and basidiomycetes) and oomycetes are known to cause diseases in cereal crop plants. They feed on living cells and most of them have learned to bypass the host immune machinery. This paper discusses some of the factors that are associated with pathogenicity drawing examples from ascomycetes, basidiomycetes and oomycetes, with respect to their manifestation in crop plants. The comparisons have revealed a striking similarity in the three groups suggesting convergent pathways that have arisen from three lineages independently leading to an obligate lifestyle. This review has been written with the intent, that new information on adaptation strategies of biotrophs, modifications in pathogenicity strategies and population dynamics will improve current strategies for breeding with stable resistance.
Collapse
Affiliation(s)
- Moytri RoyChowdhury
- Infectious Diseases Program, California Department of Public Health, Richmond, California, United States of America
| | - Jake Sternhagen
- Riverside School of Medicine, University of California, Riverside, Riverside, CA, United States of America
| | - Ya Xin
- Hangzhou Academy of Agricultural Sciences, Hangzhou, P.R. China
| | - Binghai Lou
- Guangxi Academy of Specialty Crops, Guilin, Guangxi, P.R. China
| | - Xiaobai Li
- Zhejiang Academy of Agricultural Sciences, Hangzhou, P.R. China
| | - Chunnan Li
- Hangzhou Academy of Agricultural Sciences, Hangzhou, P.R. China
| |
Collapse
|
13
|
Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses. PLANTS 2022; 11:plants11151962. [PMID: 35956440 PMCID: PMC9370660 DOI: 10.3390/plants11151962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
Switchgrass rust caused by Puccinia novopanici (P. novopanici) has the ability to significantly affect the biomass yield of switchgrass, an important biofuel crop in the United States. A comparative genome analysis of P. novopanici with rust pathogen genomes infecting monocot cereal crops wheat, barley, oats, maize and sorghum revealed the presence of larger structural variations contributing to their genome sizes. A comparative alignment of the rust pathogen genomes resulted in the identification of collinear and syntenic relationships between P. novopanici and P. sorghi; P. graminis tritici 21–0 (Pgt 21) and P. graminis tritici Ug99 (Pgt Ug99) and between Pgt 21 and P. triticina (Pt). Repeat element analysis indicated a strong presence of retro elements among different Puccinia genomes, contributing to the genome size variation between ~1 and 3%. A comparative look at the enriched protein families of Puccinia spp. revealed a predominant role of restriction of telomere capping proteins (RTC), disulfide isomerases, polysaccharide deacetylases, glycoside hydrolases, superoxide dismutases and multi-copper oxidases (MCOs). All the proteomes of Puccinia spp. share in common a repertoire of 75 secretory and 24 effector proteins, including glycoside hydrolases cellobiohydrolases, peptidyl-propyl isomerases, polysaccharide deacetylases and protein disulfide-isomerases, that remain central to their pathogenicity. Comparison of the predicted effector proteins from Puccinia spp. genomes to the validated proteins from the Pathogen–Host Interactions database (PHI-base) resulted in the identification of validated effector proteins PgtSR1 (PGTG_09586) from P. graminis and Mlp124478 from Melampsora laricis across all the rust pathogen genomes.
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Bai X, Peng H, Goher F, Islam MA, Xu S, Guo J, Kang Z, Guo J. A candidate effector protein PstCFEM1 contributes to virulence of stripe rust fungus and impairs wheat immunity. STRESS BIOLOGY 2022; 2:21. [PMID: 37676523 PMCID: PMC10441960 DOI: 10.1007/s44154-022-00042-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/28/2022] [Indexed: 09/08/2023]
Abstract
Common in Fungal Extracellular Membrane (CFEM) domain proteins are considered to be unique to fungi and closely related to pathogenicity. However, the Puccinia striiformis f. sp. tritici (Pst) effector containing the CFEM domain has not been reported. Here, we obtained an effector, PstCFEM1, containing a functional N-terminal signal peptide sequence and the CFEM domain from Pst race CYR31. qRT-PCR assay indicated that the transcript levels of PstCFEM1 were highly induced during the early stages of infection. Overexpression of PstCFEM1 suppressed Pst322 (an elicitor-like protein of Pst)-trigged cell death, reactive oxygen species (ROS) accumulation and callose deposition. Host-induced gene silencing (HIGS) experiments showed that knockdown of PstCFEM1 decreased the virulence of Pst, while ROS accumulation in silenced plants increased near the infection site. In addition, wheat containing the PstCFEM1-silenced construct increased resistance to multiple races of Pst. Our data suggest that PstCFEM1 suppresses wheat defense by inhibiting ROS accumulation and contributes to increased virulence of Pst.
Collapse
Affiliation(s)
- Xingxuan Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huan Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Farhan Goher
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Md Ashraful Islam
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Sanding Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, Nancy, France
| | | |
Collapse
|
17
|
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.
Collapse
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;
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Henningsen EC, Omidvar V, Della Coletta R, Michno JM, Gilbert E, Li F, Miller ME, Myers CL, Gordon SP, Vogel JP, Steffenson BJ, Kianian SF, Hirsch CD, Figueroa M. Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:657796. [PMID: 33968112 PMCID: PMC8097158 DOI: 10.3389/fpls.2021.657796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 05/30/2023]
Abstract
Wheat stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is a global threat to wheat production. Fast evolving populations of Pgt limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with Pgt infection in susceptible and resistant Triticum aestivum genotypes as well as the non-host Brachypodium distachyon. We targeted our analysis to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and report several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes.
Collapse
Affiliation(s)
- Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Vahid Omidvar
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Jean-Michel Michno
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
| | - Erin Gilbert
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Chad L. Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | | | - John P. Vogel
- Joint Genome Institute, Walnut Creek, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, United States
| | - Cory D. Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| |
Collapse
|
20
|
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.
Collapse
|
21
|
Miller ME, Nazareno ES, Rottschaefer SM, Riddle J, Dos Santos Pereira D, Li F, Nguyen-Phuc H, Henningsen EC, Persoons A, Saunders DGO, Stukenbrock E, Dodds PN, Kianian SF, Figueroa M. Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci. PLoS Genet 2020; 16:e1009291. [PMID: 33370783 PMCID: PMC7793281 DOI: 10.1371/journal.pgen.1009291] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/08/2021] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations of Puccinia coronata f. sp. avenae (Pca), which causes crown rust disease in oat (Avena sativa) sampled from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified seven Avr loci associated with virulence towards fifteen Pc resistance genes in oat and suggests that some groups of Pc genes recognize the same pathogen effectors. The temporal shift in virulence patterns in the Pca populations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide diversity patterns at a single Avr locus corresponding to Pc38, Pc39, Pc55, Pc63, Pc70, and Pc71 showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.
Collapse
Affiliation(s)
- Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric S. Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Susan M. Rottschaefer
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jakob Riddle
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Danilo Dos Santos Pereira
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Hoa Nguyen-Phuc
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Antoine Persoons
- INRA/Universite de Lorraine Interactions Abres/Microorganismes, Champenoux, France
| | | | - Eva Stukenbrock
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
| |
Collapse
|
22
|
Li J, Fokkens L, Conneely LJ, Rep M. Partial pathogenicity chromosomes in Fusarium oxysporum are sufficient to cause disease and can be horizontally transferred. Environ Microbiol 2020; 22:4985-5004. [PMID: 32452643 PMCID: PMC7818268 DOI: 10.1111/1462-2920.15095] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 01/05/2023]
Abstract
In Fusarium oxysporum f.sp. lycopersici, all effector genes reported so far - also called SIX genes - are located on a single accessory chromosome which is required for pathogenicity and can also be horizontally transferred to another strain. To narrow down the minimal region required for virulence, we selected partial pathogenicity chromosome deletion strains by fluorescence-assisted cell sorting of a strain in which the two arms of the pathogenicity chromosome were labelled with GFP and RFP respectively. By testing the virulence of these deletion mutants, we show that the complete long arm and part of the short arm of the pathogenicity chromosome are not required for virulence. In addition, we demonstrate that smaller versions of the pathogenicity chromosome can also be transferred to a non-pathogenic strain and they are sufficient to turn the non-pathogen into a pathogen. Surprisingly, originally non-pathogenic strains that had received a smaller version of the pathogenicity chromosome were much more aggressive than recipients with a complete pathogenicity chromosome. Whole genome sequencing analysis revealed that partial deletions of the pathogenicity chromosome occurred mainly close to repeats, and that spontaneous duplication of sequences in accessory regions is frequent both in chromosome deletion strains and in horizontal transfer strains.
Collapse
Affiliation(s)
- Jiming Li
- Molecular Plant PathologyUniversity of AmsterdamAmsterdam1098 XHThe Netherlands
| | - Like Fokkens
- Molecular Plant PathologyUniversity of AmsterdamAmsterdam1098 XHThe Netherlands
| | - Lee James Conneely
- Molecular Plant PathologyUniversity of AmsterdamAmsterdam1098 XHThe Netherlands
| | - Martijn Rep
- Molecular Plant PathologyUniversity of AmsterdamAmsterdam1098 XHThe Netherlands
| |
Collapse
|
23
|
Jaswal R, Kiran K, Rajarammohan S, Dubey H, Singh PK, Sharma Y, Deshmukh R, Sonah H, Gupta N, Sharma TR. Effector Biology of Biotrophic Plant Fungal Pathogens: Current Advances and Future Prospects. Microbiol Res 2020; 241:126567. [PMID: 33080488 DOI: 10.1016/j.micres.2020.126567] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022]
Abstract
The interaction of fungal pathogens with their host requires a novel invading mechanism and the presence of various virulence-associated components responsible for promoting the infection. The small secretory proteins, explicitly known as effector proteins, are one of the prime mechanisms of host manipulation utilized by the pathogen to disarm the host. Several effector proteins are known to translocate from fungus to the plant cell for host manipulation. Many fungal effectors have been identified using genomic, transcriptomic, and bioinformatics approaches. Most of the effector proteins are devoid of any conserved signatures, and their prediction based on sequence homology is very challenging, therefore by combining the sequence consensus based upon machine learning features, multiple tools have also been developed for predicting apoplastic and cytoplasmic effectors. Various post-genomics approaches like transcriptomics of virulent isolates have also been utilized for identifying active consortia of effectors. Significant progress has been made in understanding biotrophic effectors; however, most of it is underway due to their complex interaction with host and complicated recognition and signaling networks. This review discusses advances, and challenges in effector identification and highlighted various features of the potential effector proteins and approaches for understanding their genetics and strategies for regulation.
Collapse
Affiliation(s)
- Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India; Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India
| | - Kanti Kiran
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | | | - Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | - Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Yogesh Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Naveen Gupta
- Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India.
| | - T R Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India.
| |
Collapse
|
24
|
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.
Collapse
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.
| |
Collapse
|
25
|
Alternate Hosts of Puccinia striiformis f. sp. tritici and Their Role. Pathogens 2020; 9:pathogens9060434. [PMID: 32498285 PMCID: PMC7350320 DOI: 10.3390/pathogens9060434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 01/06/2023] Open
Abstract
Understanding the interactions between the host and the pathogen is important in developing resistant cultivars and strategies for controlling the disease. Since the discovery of Berberis and Mahonia spp. as alternate hosts of the wheat stripe rust pathogen, Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), their possible role in generating new races of Pst through sexual reproduction has become a hot topic. To date, all the investigations about the role of alternate hosts in the occurrence of the wheat stripe rust epidemics revealed that it depends on alternate host species and environmental conditions. In this review, we summarized the current status of alternate hosts of Pst, their interactions with the pathogen, their importance in genetic diversity and disease epidemics. Most importantly, the recent research progress in understanding the role of alternate hosts of Pst is provided.
Collapse
|
26
|
Derbyshire MC. Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action. Front Microbiol 2020; 11:644. [PMID: 32328056 PMCID: PMC7160247 DOI: 10.3389/fmicb.2020.00644] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/20/2020] [Indexed: 11/13/2022] Open
Abstract
The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.
Collapse
Affiliation(s)
- Mark C. Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Tao SQ, Auer L, Morin E, Liang YM, Duplessis S. Transcriptome Analysis of Apple Leaves Infected by the Rust Fungus Gymnosporangium yamadae at Two Sporulation Stages. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:444-461. [PMID: 31765287 DOI: 10.1094/mpmi-07-19-0208-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Apple rust disease caused by Gymnosporangium yamadae is one of the major threats to apple orchards. In this study, dual RNA-seq analysis was conducted to simultaneously monitor gene expression profiles of G. yamadae and infected apple leaves during the formation of rust spermogonia and aecia. The molecular mechanisms underlying this compatible interaction at 10 and 30 days postinoculation (dpi) indicate a significant reaction from the host plant and comprise detoxication pathways at the earliest stage and the induction of secondary metabolism pathways at 30 dpi. Such host reactions have been previously reported in other rust pathosystems and may represent a general reaction to rust infection. G. yamadae transcript profiling indicates a conserved genetic program in spermogonia and aecia that is shared with other rust fungi, whereas secretome prediction reveals the presence of specific secreted candidate effector proteins expressed during apple infection. Unexpectedly, the survey of fungal unigenes in the transcriptome assemblies of inoculated and mock-inoculated apple leaves reveals that G. yamadae infection may modify the fungal community composition in the apple phyllosphere at 30 dpi. Collectively, our results provide novel insights into the compatible apple-G. yamadae interaction and advance the knowledge of this heteroecious demicyclic rust fungus.
Collapse
Affiliation(s)
- Si-Qi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Université de Lorraine, INRAE, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Lucas Auer
- Université de Lorraine, INRAE, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Ying-Mei Liang
- Museum of Beijing Forestry University, Beijing Forestry University
| | - Sébastien Duplessis
- Université de Lorraine, INRAE, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| |
Collapse
|
29
|
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.
Collapse
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.
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Xu Q, Tang C, Wang X, Sun S, Zhao J, Kang Z, Wang X. An effector protein of the wheat stripe rust fungus targets chloroplasts and suppresses chloroplast function. Nat Commun 2019; 10:5571. [PMID: 31804478 PMCID: PMC6895047 DOI: 10.1038/s41467-019-13487-6] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 11/05/2019] [Indexed: 01/02/2023] Open
Abstract
Chloroplasts are important for photosynthesis and for plant immunity against microbial pathogens. Here we identify a haustorium-specific protein (Pst_12806) from the wheat stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst), that is translocated into chloroplasts and affects chloroplast function. Transient expression of Pst_12806 inhibits BAX-induced cell death in tobacco plants and reduces Pseudomonas-induced hypersensitive response in wheat. It suppresses plant basal immunity by reducing callose deposition and the expression of defense-related genes. Pst_12806 is upregulated during infection, and its knockdown (by host-induced gene silencing) reduces Pst growth and development, likely due to increased ROS accumulation. Pst_12806 interacts with the C-terminal Rieske domain of the wheat TaISP protein (a putative component of the cytochrome b6-f complex). Expression of Pst_12806 in plants reduces electron transport rate, photosynthesis, and production of chloroplast-derived ROS. Silencing TaISP by virus-induced gene silencing in a susceptible wheat cultivar reduces fungal growth and uredinium development, suggesting an increase in resistance against Pst infection.
Collapse
Affiliation(s)
- Qiang Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaodong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shutian Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jinren Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
32
|
de Guillen K, Lorrain C, Tsan P, Barthe P, Petre B, Saveleva N, Rouhier N, Duplessis S, Padilla A, Hecker A. Structural genomics applied to the rust fungus Melampsora larici-populina reveals two candidate effector proteins adopting cystine knot and NTF2-like protein folds. Sci Rep 2019; 9:18084. [PMID: 31792250 PMCID: PMC6889267 DOI: 10.1038/s41598-019-53816-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/31/2019] [Indexed: 12/29/2022] Open
Abstract
Rust fungi are plant pathogens that secrete an arsenal of effector proteins interfering with plant functions and promoting parasitic infection. Effectors are often species-specific, evolve rapidly, and display low sequence similarities with known proteins. How rust fungal effectors function in host cells remains elusive, and biochemical and structural approaches have been scarcely used to tackle this question. In this study, we produced recombinant proteins of eleven candidate effectors of the leaf rust fungus Melampsora larici-populina in Escherichia coli. We successfully purified and solved the three-dimensional structure of two proteins, MLP124266 and MLP124017, using NMR spectroscopy. Although both MLP124266 and MLP124017 show no sequence similarity with known proteins, they exhibit structural similarities to knottins, which are disulfide-rich small proteins characterized by intricate disulfide bridges, and to nuclear transport factor 2-like proteins, which are molecular containers involved in a wide range of functions, respectively. Interestingly, such structural folds have not been reported so far in pathogen effectors, indicating that MLP124266 and MLP124017 may bear novel functions related to pathogenicity. Our findings show that sequence-unrelated effectors can adopt folds similar to known proteins, and encourage the use of biochemical and structural approaches to functionally characterize effector candidates.
Collapse
Affiliation(s)
- Karine de Guillen
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR 5048, Univ Montpellier, F-34090, Montpellier, France
| | - Cécile Lorrain
- Université de Lorraine, INRA, IAM, F-54000, Nancy, France
| | - Pascale Tsan
- Université de Lorraine, CNRS, CRM2, F-54000, Nancy, France
| | - Philippe Barthe
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR 5048, Univ Montpellier, F-34090, Montpellier, France
| | - Benjamin Petre
- Université de Lorraine, INRA, IAM, F-54000, Nancy, France
| | | | | | | | - André Padilla
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR 5048, Univ Montpellier, F-34090, Montpellier, France
| | - Arnaud Hecker
- Université de Lorraine, INRA, IAM, F-54000, Nancy, France.
| |
Collapse
|
33
|
Rampitsch C, Huang M, Djuric-Cignaovic S, Wang X, Fernando U. Temporal Quantitative Changes in the Resistant and Susceptible Wheat Leaf Apoplastic Proteome During Infection by Wheat Leaf Rust ( Puccinia triticina). FRONTIERS IN PLANT SCIENCE 2019; 10:1291. [PMID: 31708941 PMCID: PMC6819374 DOI: 10.3389/fpls.2019.01291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Wheat leaf rust caused by the pathogenic fungus, Puccinia triticina, is a serious threat to bread wheat and durum production in many areas of the world. This plant-pathogen interaction has been studied extensively at the molecular genetics level however, proteomics data are still relatively scarce. The present study investigated temporal changes in the abundance of the apoplastic fluid proteome of resistant and susceptible wheat leaves infected with P. triticina race-1, using a label-free LC-MS-based approach. In general, there was very little difference between inoculated and control apoplastic proteomes in either host, until haustoria had become well established in the susceptible host, although the resistant host responds to pathogen challenge sooner. In the earlier samplings (up to 72 h after inoculation) there were just 46 host proteins with significantly changing abundance, and pathogen proteins were detected only rarely and not reproducibly. This is consistent with the biotrophic lifestyle of P. triticina, where the invading pathogen initially causes little tissue damage or host cell death, which occur only later during the infection cycle. The majority of the host proteins with altered abundance up to 72 h post-inoculation were pathogen-response-related, including peroxidases, chitinases, β-1-3-endo-glucanases, and other PR proteins. Five days after inoculation with the susceptible apoplasm it was possible to detect 150 P. triticina proteins and 117 host proteins which had significantly increased in abundance as well as 33 host proteins which had significantly decreased in abundance. The latter represents potential targets of pathogen effectors and included enzymes which could damage the invader. The pathogen-expressed proteins-seen most abundantly in the incompatible interaction-were mostly uncharacterized proteins however, many of their functions could be inferred through homology-matching with pBLAST. Pathogen proteins also included several candidate effector proteins, some novel, and some which have been reported previously. All MS data have been deposited in the PRIDE archive (www.ebi.ac.uk/pride/archive/) under Project PXD012586.
Collapse
|
34
|
Tao SQ, Cao B, Morin E, Liang YM, Duplessis S. Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle. BMC Genomics 2019; 20:723. [PMID: 31597570 PMCID: PMC6785864 DOI: 10.1186/s12864-019-6099-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we sequenced the transcriptome of G. japonicum teliospores on its host plant Juniperus chinensis and we performed comparison to the transcriptomes of G. yamadae and G. asiaticum at the same life stage, that happens in the same host but on different organs. RESULTS Functional annotation for the three Gymnosporangium species showed the expression of a conserved genetic program with the top abundant cellular categories corresponding to energy, translation and signal transduction processes, indicating that this life stage is particularly active. Moreover, the survey of predicted secretomes in the three Gymnosporangium transcriptomes revealed shared and specific genes encoding carbohydrate active enzymes and secreted proteins of unknown function that could represent candidate pathogenesis effectors. A transcript encoding a hemicellulase of the glycoside hydrolase 26 family, previously identified in other rust fungi, was particularly highly expressed suggesting a general role in rust fungi. The comparison between the transcriptomes of the three Gymnosporangium spp. and selected Pucciniales species in different taxonomical families allowed to identify lineage-specific protein families that may relate to the biology of teliospores in rust fungi. Among clustered gene families, 205, 200 and 152 proteins were specifically identified in G. japonicum, G. yamadae and G. asiaticum, respectively, including candidate effectors expressed in teliospores. CONCLUSIONS This comprehensive comparative transcriptomics study of three Gymnosporangium spp. identified gene functions and metabolic pathways particularly expressed in teliospores, a stage of the life cycle that is mostly overlooked in rust fungi. Secreted protein encoding transcripts expressed in teliospores may reveal new candidate effectors related to pathogenesis. Although this spore stage is not involved in host plant infection but in the production of basidiospores infecting plants in the Amygdaloideae, we speculate that candidate effectors may be expressed as early as the teliospore stage for preparing further infection by basidiospores.
Collapse
Affiliation(s)
- Si-Qi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Bin Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Emmanuelle Morin
- Université de Lorraine, Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, Champenoux, France
| | - Ying-Mei Liang
- Museum of Beijing Forestry University, Beijing Forestry University, Beijing, 100083, China.
| | - Sébastien Duplessis
- Université de Lorraine, Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, Champenoux, France.
| |
Collapse
|
35
|
Prasad P, Savadi S, Bhardwaj SC, Gangwar OP, Kumar S. Rust pathogen effectors: perspectives in resistance breeding. PLANTA 2019; 250:1-22. [PMID: 30980247 DOI: 10.1007/s00425-019-03167-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Identification and functional characterization of plant pathogen effectors promise to ameliorate future research and develop effective and sustainable strategies for controlling or containing crop diseases. Wheat is the second most important food crop of the world after rice. Rust pathogens, one of the major biotic stresses in wheat production, are capable of threatening the world food security. Understanding the molecular basis of plant-pathogen interactions is essential for devising novel strategies for resistance breeding and disease management. Now, it has been established that effectors, the proteins secreted by pathogens, play a key role in plant-pathogen interactions. Therefore, effector biology has emerged as one of the most important research fields in plant biology. Recent advances in genomics and bioinformatics have allowed identification of a large repertoire of candidate effectors, while the evolving high-throughput tools have continued to assist in their functional characterization. The repertoires of effectors have become an important resource for better understanding of effector biology of pathosystems and resistance breeding of crop plants. In recent years, a significant progress has been made in the field of rust effector biology. This review describes the recent advances in effector biology of obligate fungal pathogens, identification and functional analysis of wheat rust pathogens effectors and the potential applications of effectors in molecular plant biology and rust resistance breeding in wheat.
Collapse
Affiliation(s)
- Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Siddanna Savadi
- ICAR-Directorate of Cashew Research, Puttur, Karnataka, 574202, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India.
| | - O P Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Yin C, Ramachandran SR, Zhai Y, Bu C, Pappu HR, Hulbert SH. A novel fungal effector from Puccinia graminis suppressing RNA silencing and plant defense responses. THE NEW PHYTOLOGIST 2019; 222:1561-1572. [PMID: 30623449 DOI: 10.1111/nph.15676] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/03/2019] [Indexed: 05/11/2023]
Abstract
Fungal plant pathogens, like rust-causing biotrophic fungi, secrete hundreds of effectors into plant cells to subvert host immunity and promote pathogenicity on their host plants by manipulating specific physiological processes or signal pathways, but the actual function has been demonstrated for very few of these proteins. Here, we show that the PgtSR1 effector proteins, encoded by two allelic genes (PgtSR1-a and PgtSR1-b), from the wheat stem rust pathogen Puccinia graminis f. sp. tritici (Pgt), suppress RNA silencing in plants and impede plant defenses by altering the abundance of small RNAs that serve as defense regulators. Expression of the PgtSR1s in plants revealed that the PgtSR1s promote susceptibility to multiple pathogens and partially suppress cell death triggered by multiple R proteins. Overall, our study provides the first evidence that the filamentous fungus P. graminis has evolved to produce fungal suppressors of RNA silencing and indicates that PgtSR1s suppress both basal defenses and effector triggered immunity.
Collapse
Affiliation(s)
- Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Sowmya R Ramachandran
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Ying Zhai
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Chunya Bu
- College of Biological Science and Engineering, Beijing University of Agriculture, Beijing, 102206, China
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Scot H Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| |
Collapse
|
38
|
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: 72] [Impact Index Per Article: 14.4] [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.
Collapse
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
| |
Collapse
|
39
|
Qi M, Mei Y, Grayczyk JP, Darben LM, Rieker MEG, Seitz JM, Voegele RT, Whitham SA, Link TI. Candidate Effectors From Uromyces appendiculatus, the Causal Agent of Rust on Common Bean, Can Be Discriminated Based on Suppression of Immune Responses. FRONTIERS IN PLANT SCIENCE 2019; 10:1182. [PMID: 31636645 PMCID: PMC6787271 DOI: 10.3389/fpls.2019.01182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/29/2019] [Indexed: 05/07/2023]
Abstract
Rust fungi are devastating pathogens for several important crop plants. The biotrophic lifestyle of rust fungi requires that they influence their host plants to create a favorable environment for growth and reproduction. Rust fungi secrete a variety of effector proteins that manipulate host target proteins to alter plant metabolism and suppress defense responses. Because of the obligate biotrophic lifestyle of rust fungi, direct evidence for effector function is difficult to obtain, and so suites of experiments utilizing expression in heterologous systems are necessary. Here, we present results from a yeast cell death suppression assay and assays for suppression of PAMP-triggered immunity (PTI) and effector triggered immunity (ETI) based on delivery of effectors through the bacterial type III secretion system. In addition, subcellular localization was tested using transient expression of GFP fusion proteins in Nicotiana benthamiana through Agrobacterium infiltration. We tested 31 representative effector candidates from the devastating common bean rust pathogen Uromyces appendiculatus. These effector candidates were selected based on features of their gene families, most important lineage specificity. We show that several of our effector candidates suppress plant defense. Some of them also belong to families of effector candidates that are present in multiple rust species where their homologs probably also have effector functions. In our analysis of candidate effector mRNA expression, some of those effector candidates that gave positive results in the other assays were not up-regulated during plant infection, indicating that either these proteins have functions at multiple life stages or that strong up-regulation of RNA level in planta may not be as important a criterion for identifying effectors as previously thought. Overall, our pipeline for selecting effector candidates based on sequence features followed by screening assays using heterologous expression systems was successful in discriminating effector candidates. This work lays the foundation for functional characterization of U. appendiculatus effectors, the identification of effector targets, and identification of novel sources for resistance in common bean.
Collapse
Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Yu Mei
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - James P. Grayczyk
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | | | | | - Janina M. Seitz
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Ralf T. Voegele
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Tobias I. Link
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
- *Correspondence: Tobias Link,
| |
Collapse
|
40
|
Martínez-Cruz J, Romero D, De Vicente A, Pérez-García A. Transformation by growth onto agro-infiltrated tissues (TGAT), a simple and efficient alternative for transient transformation of the cucurbit powdery mildew pathogen Podosphaera xanthii. MOLECULAR PLANT PATHOLOGY 2018; 19:2502-2515. [PMID: 30073764 PMCID: PMC6638186 DOI: 10.1111/mpp.12722] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/21/2018] [Accepted: 06/24/2018] [Indexed: 05/30/2023]
Abstract
A major limitation of molecular studies in powdery mildew fungi (Erysiphales) is their genetic intractability. This is because they are obligate biotrophs. In these parasites, biotrophy is determined by the presence of haustoria, which are specialized structures of parasitism that play an essential role in the acquisition of nutrients and the deliverance of effectors. Podosphaera xanthii is the main causal agent of cucurbit powdery mildew and a major limitation for crop productivity. In a previous study using P. xanthii conidia, we showed, for the first time, the transformation of powdery mildew fungi by Agrobacterium tumefaciens. In this work, we hypothesized that the haustorium could also act as a natural route for the acquisition of DNA. To test our hypothesis, melon cotyledons were agro-infiltrated with A. tumefaciens that contained diverse transfer DNA (T-DNA) constructs harbouring different marker genes under the control of fungal promoters and, after elimination of the bacterium, the cotyledons were subsequently inoculated with P. xanthii conidia. Our results conclusively demonstrated the transfer of different T-DNAs from A. tumefaciens to P. xanthii, including two fungicide resistance markers (hph and tub2), a reporter gene (gfp) and a translational fusion (cfp-PxEC2). These results were further supported by the co-localization of translational fluorescent fusions of A. tumefaciens VirD2 and P. xanthii Rab5 proteins into small vesicles of haustorial and hyphal cells, suggesting endocytosis as the mechanism for T-DNA uptake, presumably by the haustorium. From our perspective, transformation by growth onto agro-infiltrated tissues (TGAT) is the easiest and most reliable method for the transient transformation of powdery mildew fungi.
Collapse
Affiliation(s)
- Jesús Martínez-Cruz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, 29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
| | - Diego Romero
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, 29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
| | - Antonio De Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, 29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, 29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, 29071, Spain
| |
Collapse
|
41
|
Xia C, Wang M, Yin C, Cornejo OE, Hulbert SH, Chen X. Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei). BMC Genomics 2018; 19:664. [PMID: 30208837 PMCID: PMC6134786 DOI: 10.1186/s12864-018-5041-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plant fungal pathogens can rapidly evolve and adapt to new environmental conditions in response to sudden changes of host populations in agro-ecosystems. However, the genomic basis of their host adaptation, especially at the forma specialis level, remains unclear. RESULTS We sequenced two isolates each representing Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), different formae speciales of the stripe rust fungus P. striiformis highly adapted to wheat and barley, respectively. The divergence of Pst and Psh, estimated to start 8.12 million years ago, has been driven by high nucleotide mutation rates. The high genomic variation within dikaryotic urediniospores of P. striiformis has provided raw genetic materials for genome evolution. No specific gene families have enriched in either isolate, but extensive gene loss events have occurred in both Pst and Psh after the divergence from their most recent common ancestor. A large number of isolate-specific genes were identified, with unique genomic features compared to the conserved genes, including 1) significantly shorter in length; 2) significantly less expressed; 3) significantly closer to transposable elements; and 4) redundant in pathways. The presence of specific genes in one isolate (or forma specialis) was resulted from the loss of the homologues in the other isolate (or forma specialis) by the replacements of transposable elements or losses of genomic fragments. In addition, different patterns and numbers of telomeric repeats were observed between the isolates. CONCLUSIONS Host adaptation of P. striiformis at the forma specialis level is a complex pathogenic trait, involving not only virulence-related genes but also other genes. Gene loss, which might be adaptive and driven by transposable element activities, provides genomic basis for host adaptation of different formae speciales of P. striiformis.
Collapse
Affiliation(s)
- 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
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA 99164-7520 USA
| | - Scot H. Hulbert
- 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
- Wheat Health, Genetics, and Quality Research Unit, Agriculture Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430 USA
| |
Collapse
|
42
|
Sperschneider J, Dodds PN, Gardiner DM, Singh KB, Taylor JM. Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. MOLECULAR PLANT PATHOLOGY 2018; 19:2094-2110. [PMID: 29569316 PMCID: PMC6638006 DOI: 10.1111/mpp.12682] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 05/14/2023]
Abstract
Plant-pathogenic fungi secrete effector proteins to facilitate infection. We describe extensive improvements to EffectorP, the first machine learning classifier for fungal effector prediction. EffectorP 2.0 is now trained on a larger set of effectors and utilizes a different approach based on an ensemble of classifiers trained on different subsets of negative data, offering different views on classification. EffectorP 2.0 achieves an accuracy of 89%, compared with 82% for EffectorP 1.0 and 59.8% for a small size classifier. Important features for effector prediction appear to be protein size, protein net charge as well as the amino acids serine and cysteine. EffectorP 2.0 decreases the number of predicted effectors in secretomes of fungal plant symbionts and saprophytes by 40% when compared with EffectorP 1.0. However, EffectorP 1.0 retains value, and combining EffectorP 1.0 and 2.0 results in a stringent classifier with a low false positive rate of 9%. EffectorP 2.0 predicts significant enrichments of effectors in 12 of 13 sets of infection-induced proteins from diverse fungal pathogens, whereas a small cysteine-rich classifier detects enrichment in only seven of 13. EffectorP 2.0 will fast track the prioritization of high-confidence effector candidates for functional validation and aid in improving our understanding of effector biology. EffectorP 2.0 is available at http://effectorp.csiro.au.
Collapse
Affiliation(s)
- Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and FoodPerth, WA 6014Australia
| | - Peter N. Dodds
- Black Mountain Laboratories, CSIRO Agriculture and FoodCanberra, ACT 2601Australia
| | - Donald M. Gardiner
- CSIRO Agriculture and FoodQueensland Bioscience PrecinctBrisbane, Qld 4067Australia
| | - Karam B. Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture and FoodPerth, WA 6014Australia
- Department of Environment and Agriculture, Centre for Crop and Disease ManagementCurtin UniversityBentley, WA 6102Australia
| | - Jennifer M. Taylor
- Black Mountain Laboratories, CSIRO Agriculture and FoodCanberra, ACT 2601Australia
| |
Collapse
|
43
|
Hussain M, Iqbal MA, Till BJ, Rahman MU. Identification of induced mutations in hexaploid wheat genome using exome capture assay. PLoS One 2018; 13:e0201918. [PMID: 30102729 PMCID: PMC6089429 DOI: 10.1371/journal.pone.0201918] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/24/2018] [Indexed: 12/02/2022] Open
Abstract
Wheat is a staple food crop of many countries. Improving resilience to biotic and abiotic stresses remain key breeding targets. Among these, rust diseases are the most detrimental in terms of depressing wheat production. In the present study, chemical mutagenesis was used to induce mutations in the wheat variety NN-Gandum-1. This cultivar is moderately resistant to leaf and yellow rust. The aim of mutagenesis was to improve resistance to the disease as well as to study function of genes conferring resistance to the disease. In the present investigation, a 0.8% EMS dose was found optimum for supporting 45-55% germination of NN-Gandum-1. A total of 3,634 M2 fertile plants were produced from each of the M1 plant. Out of these, 33 (0.91%) and 20 plants (0.55%) showed absolute resistance to leaf and yellow rust, respectively. While 126 (3.46%) and 127 plants (3.49%) exhibited high susceptibility to the leaf and yellow rust, respectively. In the M4 generation, a total of 11 M4 lines (nine absolute resistant and two highly susceptible) and one wild type were selected for NGS-based exome capture assay. A total of 104,779 SNPs were identified that were randomly distributed throughout the wheat sub genomes (A, B and D). Induced mutations in intronic sequences predominated. The highest total number of SNPs detected in this assay were mapped to chr.2B (14,273 SNPs), which contains the highest number of targeted base pairs in the assay. The average mutation density across all regions interrogated was estimated to be one mutation per 20.91 Mb. The highest mutation frequency was found in chr.2D (1/11.7 kb) and the lowest in chr.7D (1/353.4 kb). Out of the detected mutations, 101 SNPs were filtered using analysis criteria aimed to enrich for mutations that may affect gene function. Out of these, one putative SNP detected in Lr21 were selected for further analysis. The SNP identified in chimeric allele (Lr21) of a resistant mutant (N1-252) was located in a NBS domain of chr.1BS at 3.4 Mb position. Through computational analysis, it was demonstrated that this identified SNP causes a substitution of glutamic acid with alanine, resulting in a predicted altered protein structure. This mutation, therefore, is a candidate for contributing to the resistance phenotype in the mutant line. Based on this work, we conclude that the wheat mutant resource developed is useful as a source of novel genetic variation for forward-genetic screens and also as a useful tool for gaining insights into the important biological circuits of different traits of complex genomes like wheat.
Collapse
Affiliation(s)
- Momina Hussain
- Plant Genomics & Mol. Breeding Lab, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Atif Iqbal
- Plant Genomics & Mol. Breeding Lab, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Bradley J. Till
- University of Vienna, Department fürChromosomenbiologie, Vienna, Austria
| | - Mehboob-ur- Rahman
- Plant Genomics & Mol. Breeding Lab, National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| |
Collapse
|
44
|
Lorrain C, Marchal C, Hacquard S, Delaruelle C, Pétrowski J, Petre B, Hecker A, Frey P, Duplessis S. The Rust Fungus Melampsora larici-populina Expresses a Conserved Genetic Program and Distinct Sets of Secreted Protein Genes During Infection of Its Two Host Plants, Larch and Poplar. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:695-706. [PMID: 29336199 DOI: 10.1094/mpmi-12-17-0319-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Mechanisms required for broad-spectrum or specific host colonization of plant parasites are poorly understood. As a perfect illustration, heteroecious rust fungi require two alternate host plants to complete their life cycles. Melampsora larici-populina infects two taxonomically unrelated plants, larch, on which sexual reproduction is achieved, and poplar, on which clonal multiplication occurs, leading to severe epidemics in plantations. We applied deep RNA sequencing to three key developmental stages of M. larici-populina infection on larch: basidia, pycnia, and aecia, and we performed comparative transcriptomics of infection on poplar and larch hosts, using available expression data. Secreted protein was the only significantly overrepresented category among differentially expressed M. larici-populina genes between the basidial, the pycnial, and the aecial stages, highlighting their probable involvement in the infection process. Comparison of fungal transcriptomes in larch and poplar revealed a majority of rust genes were commonly expressed on the two hosts and a fraction exhibited host-specific expression. More particularly, gene families encoding small secreted proteins presented striking expression profiles that highlight probable candidate effectors specialized on each host. Our results bring valuable new information about the biological cycle of rust fungi and identify genes that may contribute to host specificity.
Collapse
Affiliation(s)
- Cécile Lorrain
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Clémence Marchal
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Stéphane Hacquard
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Christine Delaruelle
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Jérémy Pétrowski
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Benjamin Petre
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
- 2 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH, Norwich, U.K
| | - Arnaud Hecker
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Pascal Frey
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Sébastien Duplessis
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| |
Collapse
|
45
|
Lorrain C, Petre B, Duplessis S. Show me the way: rust effector targets in heterologous plant systems. Curr Opin Microbiol 2018; 46:19-25. [PMID: 29454191 DOI: 10.1016/j.mib.2018.01.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/14/2018] [Accepted: 01/31/2018] [Indexed: 11/27/2022]
Abstract
For years, the study of rust fungal effectors has been impeded by the lack of molecular genetic tools in rust pathosystems. The recent use of heterologous plants to perform effector screens (effectoromics)-including effector localisation (cellular targets) and protein interactors (molecular targets) in plant cells-has changed the game. These screens revealed that many candidate effectors from various rust fungi target specific plant cell compartments, including chloroplasts, and associate with specific plant protein complexes. Such information represents unparalleled opportunities to understand how effectors sustain extreme parasitic interactions and obligate biotrophy. Despite their limitations, we here portray how the use of heterologous expression systems has been essential for gaining new insight into rust effectors.
Collapse
Affiliation(s)
- Cécile Lorrain
- INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, Champenoux, France
| | - Benjamin Petre
- INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, Champenoux, France
| | - Sébastien Duplessis
- INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, Champenoux, France.
| |
Collapse
|
46
|
Schwessinger B, Sperschneider J, Cuddy WS, Garnica DP, Miller ME, Taylor JM, Dodds PN, Figueroa M, Park RF, Rathjen JP. A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. mBio 2018; 9:e02275-17. [PMID: 29463659 PMCID: PMC5821087 DOI: 10.1128/mbio.02275-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies.IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism's evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
Collapse
Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - William S Cuddy
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Diana P Garnica
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
| | - John P Rathjen
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| |
Collapse
|
47
|
Pitino M, Allen V, Duan Y. LasΔ5315 Effector Induces Extreme Starch Accumulation and Chlorosis as Ca. Liberibacter asiaticus Infection in Nicotiana benthamiana. FRONTIERS IN PLANT SCIENCE 2018; 9:113. [PMID: 29467782 PMCID: PMC5808351 DOI: 10.3389/fpls.2018.00113] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/22/2018] [Indexed: 05/21/2023]
Abstract
Huanglongbing (HLB), a destructive plant bacterial disease, severely impedes worldwide citrus production. HLB is associated with a phloem-limited α-proteobacterium, Candidatus Liberibacter asiaticus (Las). Las infection causes yellow shoots and blotchy mottle on leaves and is associated with excessive starch accumulation. However, the mechanisms underlying the starch accumulation remain unknown. We previously showed that the Las5315mp effector induced callose deposition and cell death in Nicotiana benthamiana. In this study, we demonstrated that Las can experimentally infect N. benthamiana via dodder transmission. Furthermore, we revealed another key function of the Las5315 effector by demonstrating that transient expression of the truncated form of the effector, LasΔ5315, induced excessive starch accumulation by 6 fold after 8 dpi in N. benthamiana after removal of the chloroplast transit peptide from the Las5315mp. The induction mechanisms of LasΔ5315 in N. benthamiana were attributed to the up-regulation of ADP-glucose pyrophosphorylase, granule-bound starch synthase, soluble starch synthase, and starch branching enzyme for increasing starch production, and to the significant down-regulation of the starch degradation enzymes: alpha-glucosidase, alpha-amylase, and glycosyl hydrolase for decreasing starch degradation. This is the first report that Las can infect the model plant N. benthamiana. Using this model plant, we demonstrated that the LasΔ5315 effector caused the most prominent HLB symptoms, starch accumulation and chlorosis as Las infection in N. benthamiana. Altogether the Las 5315 effector is critical for Las pathogenesis, and therefore, an important target for interference.
Collapse
Affiliation(s)
| | | | - Yongping Duan
- US Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL, United States
| |
Collapse
|
48
|
Zhao M, Wang J, Ji S, Chen Z, Xu J, Tang C, Chen S, Kang Z, Wang X. Candidate Effector Pst_8713 Impairs the Plant Immunity and Contributes to Virulence of Puccinia striiformis f. sp. tritici. FRONTIERS IN PLANT SCIENCE 2018; 9:1294. [PMID: 30254653 PMCID: PMC6141802 DOI: 10.3389/fpls.2018.01294] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/17/2018] [Indexed: 05/20/2023]
Abstract
Puccinia striiformis f. sp. tritici (Pst), the causal agent of stripe rust, is an obligate biotrophic pathogen responsible for severe wheat disease epidemics worldwide. Pst and other rust fungi are acknowledged to deliver many effector proteins to the host, but little is known about the effectors' functions. Here, we report a candidate effector Pst_8713 isolated based on the genome data of CY32 and the expression of Pst_8713 is highly induced during the early infection stage. The Pst_8713 gene shows a low level of intra-species polymorphism. It has a functional N-terminal signal peptide and its product was found in the host cytoplasm and nucleus. Co-infiltrations in Nicotiana benthamiana demonsrated that Pst_8713 was capable of suppressing cell death triggered by mouse pro-apoptotic protein-BAX or Phytophthora infestans PAMP-INF1. Overexpression of Pst_8713 in plants suppressed pattern-triggered immunity (PTI) -associated callose deposition and expression of PTI-associated marker genes and promoted bacterial growth in planta. Effector-triggered immunity (ETI) induced by an avirulent Pst isolate was weakened when we overexpressed Pst_8713 in wheat leaves which accompanied by reduction of reactive oxygen species (ROS) accumulation and hypersensitive response (HR). In addition, the host induced gene silencing (HIGS) experiment showed that knockdown of Pst_8713 weakened the virulence of Pst by producing fewer uredinia. These results indicated that candidate effector Pst_8713 is involved in plant defense suppression and contributes to enhancing the Pst virulence.
Collapse
|
49
|
Qi M, Grayczyk JP, Seitz JM, Lee Y, Link TI, Choi D, Pedley KF, Voegele RT, Baum TJ, Whitham SA. Suppression or Activation of Immune Responses by Predicted Secreted Proteins of the Soybean Rust Pathogen Phakopsora pachyrhizi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:163-174. [PMID: 29144203 DOI: 10.1094/mpmi-07-17-0173-fi] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Rust fungi, such as the soybean rust pathogen Phakopsora pachyrhizi, are major threats to crop production. They form specialized haustoria that are hyphal structures intimately associated with host-plant cell membranes. These haustoria have roles in acquiring nutrients and secreting effector proteins that manipulate host immune systems. Functional characterization of effector proteins of rust fungi is important for understanding mechanisms that underlie their virulence and pathogenicity. Hundreds of candidate effector proteins have been predicted for rust pathogens, but it is not clear how to prioritize these effector candidates for further characterization. There is a need for high-throughput approaches for screening effector candidates to obtain experimental evidence for effector-like functions, such as the manipulation of host immune systems. We have focused on identifying effector candidates with immune-related functions in the soybean rust fungus P. pachyrhizi. To facilitate the screening of many P. pachyrhizi effector candidates (named PpECs), we used heterologous expression systems, including the bacterial type III secretion system, Agrobacterium infiltration, a plant virus, and a yeast strain, to establish an experimental pipeline for identifying PpECs with immune-related functions and establishing their subcellular localizations. Several PpECs were identified that could suppress or activate immune responses in nonhost Nicotiana benthamiana, N. tabacum, Arabidopsis, tomato, or pepper plants.
Collapse
Affiliation(s)
- Mingsheng Qi
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
| | - James P Grayczyk
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
| | - Janina M Seitz
- 2 Institut für Phytomedizin, Universität Hohenheim, Otto-Sander-Straße 5, 70599 Stuttgart, Germany
| | - Youngsill Lee
- 3 Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea; and
| | - Tobias I Link
- 2 Institut für Phytomedizin, Universität Hohenheim, Otto-Sander-Straße 5, 70599 Stuttgart, Germany
| | - Doil Choi
- 3 Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea; and
| | - Kerry F Pedley
- 4 Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Ft. Detrick, MD 21702, U.S.A
| | - Ralf T Voegele
- 2 Institut für Phytomedizin, Universität Hohenheim, Otto-Sander-Straße 5, 70599 Stuttgart, Germany
| | - Thomas J Baum
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
| | - Steven A Whitham
- 1 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
| |
Collapse
|
50
|
Germain H, Joly DL, Mireault C, Plourde MB, Letanneur C, Stewart D, Morency M, Petre B, Duplessis S, Séguin A. Infection assays in Arabidopsis reveal candidate effectors from the poplar rust fungus that promote susceptibility to bacteria and oomycete pathogens. MOLECULAR PLANT PATHOLOGY 2018; 19:191-200. [PMID: 27868319 PMCID: PMC6638046 DOI: 10.1111/mpp.12514] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 11/09/2016] [Accepted: 11/14/2016] [Indexed: 05/03/2023]
Abstract
Fungi of the Pucciniales order cause rust diseases which, altogether, affect thousands of plant species worldwide and pose a major threat to several crops. How rust effectors-virulence proteins delivered into infected tissues to modulate host functions-contribute to pathogen virulence remains poorly understood. Melampsora larici-populina is a devastating and widespread rust pathogen of poplar, and its genome encodes 1184 identified small secreted proteins that could potentially act as effectors. Here, following specific criteria, we selected 16 candidate effector proteins and characterized their virulence activities and subcellular localizations in the leaf cells of Arabidopsis thaliana. Infection assays using bacterial (Pseudomonas syringae) and oomycete (Hyaloperonospora arabidopsidis) pathogens revealed subsets of candidate effectors that enhanced or decreased pathogen leaf colonization. Confocal imaging of green fluorescent protein-tagged candidate effectors constitutively expressed in stable transgenic plants revealed that some protein fusions specifically accumulate in nuclei, chloroplasts, plasmodesmata and punctate cytosolic structures. Altogether, our analysis suggests that rust fungal candidate effectors target distinct cellular components in host cells to promote parasitic growth.
Collapse
Affiliation(s)
- Hugo Germain
- Department of Chemistry, Biochemistry and PhysicsUniversité du Québec à Trois‐RivièresTrois‐RivièresQCCanadaG9A 5H7
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaSainte‐FoyQCCanadaG1V 4C7
| | - David L. Joly
- Département de BiologieUniversité de MonctonMonctonNBCanadaE1A 3E9
| | - Caroline Mireault
- Department of Chemistry, Biochemistry and PhysicsUniversité du Québec à Trois‐RivièresTrois‐RivièresQCCanadaG9A 5H7
| | - Mélodie B. Plourde
- Department of Chemistry, Biochemistry and PhysicsUniversité du Québec à Trois‐RivièresTrois‐RivièresQCCanadaG9A 5H7
| | - Claire Letanneur
- Department of Chemistry, Biochemistry and PhysicsUniversité du Québec à Trois‐RivièresTrois‐RivièresQCCanadaG9A 5H7
| | - Donald Stewart
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaSainte‐FoyQCCanadaG1V 4C7
| | - Marie‐Josée Morency
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaSainte‐FoyQCCanadaG1V 4C7
| | - Benjamin Petre
- The Sainsbury LaboratoryNorwich Research ParkNorwichNR4 7UHUK
- Centre INRA Nancy LorraineINRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de LorraineChampenoux54280France
| | - Sébastien Duplessis
- Centre INRA Nancy LorraineINRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de LorraineChampenoux54280France
| | - Armand Séguin
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaSainte‐FoyQCCanadaG1V 4C7
| |
Collapse
|