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Letanneur C, Brisson A, Bisaillon M, Devèze T, Plourde MB, Schattat M, Duplessis S, Germain H. Host-Specific and Homologous Pairs of Melampsora larici-populina Effectors Unveil Novel Nicotiana benthamiana Stromule Induction Factors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:277-289. [PMID: 38148279 DOI: 10.1094/mpmi-09-23-0148-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: 12/28/2023]
Abstract
The poplar rust fungus Melampsora larici-populina is part of one of the most devastating group of fungi (Pucciniales) and causes important economic losses to the poplar industry. Because M. larici-populina is a heteroecious obligate biotroph, its spread depends on its ability to carry out its reproductive cycle through larch and then poplar parasitism. Genomic approaches have identified more than 1,000 candidate secreted effector proteins (CSEPs) from the predicted secretome of M. larici-populina that are potentially implicated in the infection process. In this study, we selected CSEP pairs (and one triplet) among CSEP gene families that share high sequence homology but display specific gene expression profiles among the two distinct hosts. We determined their subcellular localization by confocal microscopy through expression in the heterologous plant system Nicotiana benthamiana. Five out of nine showed partial or complete chloroplastic localization. We also screened for potential protein interactors from larch and poplar by yeast two-hybrid assays. One pair of CSEPs and the triplet shared common interactors, whereas the members of the two other pairs did not have common targets from either host. Finally, stromule induction quantification revealed that two pairs and the triplet of CSEPs induced stromules when transiently expressed in N. benthamiana. The use of N. benthamiana eds1 and nrg1 knockout lines showed that CSEPs can induce stromules through an eds1-independent mechanism. However, CSEP homologs shared the same impact on stromule induction and contributed to discovering a new stromule induction cascade that can be partially and/or fully independent of eds1. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Claire Letanneur
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Alexandre Brisson
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Mathias Bisaillon
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Théo Devèze
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Mélodie B Plourde
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Martin Schattat
- Plant Physiology Department, Martin Luther University, 06120 Halle, Germany
| | | | - Hugo Germain
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
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2
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Hayashibara CADA, Lopes MDS, Tobias PA, dos Santos IB, Figueredo EF, Ferrarezi JA, Marques JPR, Marcon J, Park RF, Teixeira PJPL, Quecine MC. In Planta Study Localizes an Effector Candidate from Austropuccinia psidii Strain MF-1 to the Nucleus and Demonstrates In Vitro Cuticular Wax-Dependent Differential Expression. J Fungi (Basel) 2023; 9:848. [PMID: 37623619 PMCID: PMC10455828 DOI: 10.3390/jof9080848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Austropuccinia psidii is a biotrophic fungus that causes myrtle rust. First described in Brazil, it has since spread to become a globally important pathogen that infects more than 480 myrtaceous species. One of the most important commercial crops affected by A. psidii is eucalypt, a widely grown forestry tree. The A. psidii-Eucalyptus spp. interaction is poorly understood, but pathogenesis is likely driven by pathogen-secreted effector molecules. Here, we identified and characterized a total of 255 virulence effector candidates using a genome assembly of A. psidii strain MF-1, which was recovered from Eucalyptus grandis in Brazil. We show that the expression of seven effector candidate genes is modulated by cell wax from leaves sourced from resistant and susceptible hosts. Two effector candidates with different subcellular localization predictions, and with specific gene expression profiles, were transiently expressed with GFP-fusions in Nicotiana benthamiana leaves. Interestingly, we observed the accumulation of an effector candidate, Ap28303, which was upregulated under cell wax from rust susceptible E. grandis and described as a peptidase inhibitor I9 domain-containing protein in the nucleus. This was in accordance with in silico analyses. Few studies have characterized nuclear effectors. Our findings open new perspectives on the study of A. psidii-Eucalyptus interactions by providing a potential entry point to understand how the pathogen manipulates its hosts in modulating physiology, structure, or function with effector proteins.
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Affiliation(s)
- Carolina Alessandra de Almeida Hayashibara
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | - Mariana da Silva Lopes
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | - Peri A. Tobias
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Isaneli Batista dos Santos
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | | | - Jessica Aparecida Ferrarezi
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | - João Paulo Rodrigues Marques
- Department of Basic Sciences, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil;
| | - Joelma Marcon
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
| | - Robert F. Park
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW 2570, Australia;
| | - Paulo José Pereira Lima Teixeira
- Department of Biological Sciences, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil;
| | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (C.A.d.A.H.); (M.d.S.L.); (I.B.d.S.); (J.A.F.); (J.M.)
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Guo J, Mou Y, Li Y, Yang Q, Wang X, Lin H, Kang Z, Guo J. Silencing a Chitinase Gene, PstChia1, Reduces Virulence of Puccinia striiformis f. sp. tritici. Int J Mol Sci 2023; 24:ijms24098215. [PMID: 37175921 PMCID: PMC10179651 DOI: 10.3390/ijms24098215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Chitin is the main component of fungal cell walls, which can be recognized by pattern recognition receptors (PRRs) as pathogen-associated molecular patterns (PAMP). Chitinase in filamentous fungi has been reported to degrade immunogenic chitin oligomers, thereby preventing chitin-induced immune activation. In this study, we identified the chitinase families in 10 fungal genomes. A total of 131 chitinase genes were identified. Among the chitinase families, 16 chitinase genes from Puccinia striiformis f. sp. tritici (Pst) were identified, and the expression of PstChia1 was the highest during Pst infection. Further studies indicated that PstChia1 is highly induced during the early stages of the interaction of wheat and Pst and has chitinase enzyme activity. The silencing of PstChia1 revealed that PstChia1 limited the growth and reduced the virulence of Pst. The expression level of TaPR1 and TaPR2 was induced in PstChia1 knockdown plants, suggesting that PstChia1 is involved in regulating wheat resistance to Pst. Our data suggest that PstChia1 contributes to pathogenicity by interfering with plant immunity and regulating the growth of Pst.
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Affiliation(s)
- Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Ying Mou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Yuanxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Qing Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Xue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Haocheng Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
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Wang Y, Liu C, Du Y, Cai K, Wang Y, Guo J, Bai X, Kang Z, Guo J. A stripe rust fungal effector PstSIE1 targets TaSGT1 to facilitate pathogen infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1413-1428. [PMID: 36308427 DOI: 10.1111/tpj.16019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Puccinia striiformis f. sp. tritici (Pst), the causal agent of stripe rust, is a destructive pathogen of Triticum aestivum (wheat), threatening wheat production worldwide. Pst delivers hundreds of effectors to manipulate processes in its hosts during infection. The SGT1 (suppressor of the G2 allele of skp1), RAR1 (required for Mla12 resistance) and HSP90 (heat-shock protein 90) proteins form a chaperone complex that acts as a core modulator in plant immunity. However, little is known about how Pst effectors target this immune component to suppress plant immunity. Here, we identified a Pst effector PstSIE1 that interacts with TaSGT1 in wheat and is upregulated during the early infection stage. Transient expression of PstSIE1 suppressed cell death in Nicotiana benthamiana induced by VmE02 and PcNLP2. Transgenic expression of PstSIE1-RNAi constructs in wheat significantly reduced the virulence of Pst. Overexpression of PstSIE1 in wheat increased the number of rust pustules and reduced the accumulation of reactive oxygen species (ROS), indicating that PstSIE1 functions as an important pathogenicity factor in Pst. PstSIE1 was found to compete with TaRAR1 to bind TaSGT1, thus disrupting the formation of the TaRAR1-TaSGT1 subcomplex. Taken together, PstSIE1 is an important Pst effector targeting the immune component TaSGT1 and involved in suppressing wheat defense.
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Affiliation(s)
- Yunqian Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuanyuan Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Kunyan Cai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xingxuan Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Helm M, Singh R, Hiles R, Jaiswal N, Myers A, Iyer-Pascuzzi AS, Goodwin SB. Candidate Effector Proteins from the Maize Tar Spot Pathogen Phyllachora maydis Localize to Diverse Plant Cell Compartments. PHYTOPATHOLOGY 2022; 112:2538-2548. [PMID: 35815936 DOI: 10.1094/phyto-05-22-0181-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Most fungal pathogens secrete effector proteins into host cells to modulate their immune responses, thereby promoting pathogenesis and fungal growth. One such fungal pathogen is the ascomycete Phyllachora maydis, which causes tar spot disease on leaves of maize (Zea mays). Sequencing of the P. maydis genome revealed 462 putatively secreted proteins, of which 40 contain expected effector-like sequence characteristics. However, the subcellular compartments targeted by P. maydis effector candidate (PmEC) proteins remain unknown, and it will be important to prioritize them for further functional characterization. To test the hypothesis that PmECs target diverse subcellular compartments, cellular locations of super yellow fluorescent protein-tagged PmEC proteins were identified using a Nicotiana benthamiana-based heterologous expression system. Immunoblot analyses showed that most of the PmEC-fluorescent protein fusions accumulated protein in N. benthamiana, indicating that the candidate effectors could be expressed in dicot leaf cells. Laser-scanning confocal microscopy of N. benthamiana epidermal cells revealed that most of the P. maydis putative effectors localized to the nucleus and cytosol. One candidate effector, PmEC01597, localized to multiple subcellular compartments including the nucleus, nucleolus, and plasma membrane, whereas an additional putative effector, PmEC03792, preferentially labelled both the nucleus and nucleolus. Intriguingly, one candidate effector, PmEC04573, consistently localized to the stroma of chloroplasts as well as stroma-containing tubules (stromules). Collectively, these data suggest that effector candidate proteins from P. maydis target diverse cellular organelles and could thus provide valuable insights into their putative functions, as well as host processes potentially manipulated by this fungal pathogen.
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Affiliation(s)
- Matthew Helm
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
| | - Raksha Singh
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
| | - Rachel Hiles
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Namrata Jaiswal
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
| | - Ariana Myers
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
| | | | - Stephen B Goodwin
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
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Petre B, Duplessis S. A decade after the first Pucciniales genomes: A bibliometric snapshot of (post) genomics studies in three model rust fungi. Front Microbiol 2022; 13:989580. [PMID: 36187960 PMCID: PMC9515648 DOI: 10.3389/fmicb.2022.989580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Pucciniales (rust fungi) are one of the largest fungal order of plant pathogens. They collectively infect key crops such as wheat and soybean, and threaten global food security. In the early 2010s, the genome sequences of three rust fungi were released: Melampsora larici-populina (the poplar leaf rust fungus), Puccinia graminis f. sp. tritici (the wheat stem rust fungus), and Puccinia striiformis f. sp. triciti (the wheat stripe rust or wheat yellow rust fungus). The availability of those genomes has forwarded rust biology into the post-genomic era, sparking a series of genomics, transcriptomics, in silico, and functional studies. Here, we snapshot the last 10 years of post-genomics studies addressing M. larici-populina, P. graminis f. sp. tritici, and/or P. striiformis f. sp. tritici. This mini-review notably reveals the model species-centered structure of the research community, and highlights the drastic increase of the number of functional studies focused on effectors since 2014, which notably revealed chloroplasts as a central host compartment targeted by rust fungi. This mini-review also discusses genomics-facilitated studies in other rust species, and emerging post-genomic research trends related to fully-phased rust genomes.
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Exploiting breakdown in nonhost effector-target interactions to boost host disease resistance. Proc Natl Acad Sci U S A 2022; 119:e2114064119. [PMID: 35994659 PMCID: PMC9436328 DOI: 10.1073/pnas.2114064119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Plant nonhost resistance (NHR) prevents infection by all members of most microbial species, but its molecular mechanisms are not well understood. We found that effector proteins from the potato blight pathogen Phytophthora infestans, which enhance infection in host plants, fail to enhance susceptibility in nonhost Arabidopsis. These P. infestans effectors often failed to interact with Arabidopsis orthologs of their potato target proteins, whereas many interactions were detected between these Arabidopsis orthologs and effectors from its adapted pathogen Hyaloperonospora arabidopsidis. Thus, breakdown in effector–target interactions in distantly related nonhost plants is likely a key component of NHR. Importantly, we demonstrate that exploiting this breakdown and expressing nonhost target orthologs in host plants provide a strategy to prevent crop disease. Plants are resistant to most microbial species due to nonhost resistance (NHR), providing broad-spectrum and durable immunity. However, the molecular components contributing to NHR are poorly characterised. We address the question of whether failure of pathogen effectors to manipulate nonhost plants plays a critical role in NHR. RxLR (Arg-any amino acid-Leu-Arg) effectors from two oomycete pathogens, Phytophthora infestans and Hyaloperonospora arabidopsidis, enhanced pathogen infection when expressed in host plants (Nicotiana benthamiana and Arabidopsis, respectively) but the same effectors performed poorly in distantly related nonhost pathosystems. Putative target proteins in the host plant potato were identified for 64 P. infestans RxLR effectors using yeast 2-hybrid (Y2H) screens. Candidate orthologues of these target proteins in the distantly related non-host plant Arabidopsis were identified and screened using matrix Y2H for interaction with RxLR effectors from both P. infestans and H. arabidopsidis. Few P. infestans effector-target protein interactions were conserved from potato to candidate Arabidopsis target orthologues (cAtOrths). However, there was an enrichment of H. arabidopsidis RxLR effectors interacting with cAtOrths. We expressed the cAtOrth AtPUB33, which unlike its potato orthologue did not interact with P. infestans effector PiSFI3, in potato and Nicotiana benthamiana. Expression of AtPUB33 significantly reduced P. infestans colonization in both host plants. Our results provide evidence that failure of pathogen effectors to interact with and/or correctly manipulate target proteins in distantly related non-host plants contributes to NHR. Moreover, exploiting this breakdown in effector-nonhost target interaction, transferring effector target orthologues from non-host to host plants is a strategy to reduce disease.
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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.
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9
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Louet C, Blot C, Shelest E, Guerillot P, Zannini F, Pétrowski J, Frey P, Duplessis S. Annotation survey and life-cycle transcriptomics of transcription factors in rust fungi (Pucciniales) identify a possible role for cold shock proteins in dormancy exit. Fungal Genet Biol 2022; 161:103698. [PMID: 35483517 DOI: 10.1016/j.fgb.2022.103698] [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: 10/19/2021] [Revised: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Fungi of the order Pucciniales are obligate plant biotrophs causing rust diseases. They exhibit a complex life cycle with the production of up to five spore types, infection of two unrelated hosts and an overwintering stage. Transcription factors (TFs) are key regulators of gene expression in eukaryote cells. In order to better understand genetic programs expressed during major transitions of the rust life cycle, we surveyed the complement of TFs in fungal genomes with an emphasis on Pucciniales. We found that despite their large gene numbers, rust genomes have a reduced repertoire of TFs compared to other fungi. The proportions of C2H2 and Zinc cluster -two of the most represented TF families in fungi- indicate differences in their evolutionary relationships in Pucciniales and other fungal taxa. The regulatory gene family encoding cold shock protein (CSP) showed a striking expansion in Pucciniomycotina with specific duplications in the order Pucciniales. The survey of expression profiles collected by transcriptomics along the life cycle of the poplar rust fungus revealed TF genes related to major biological transitions, e.g. response to environmental cues and host infection. Particularly, poplar rust CSPs were strongly expressed in basidia produced after the overwintering stage suggesting a possible role in dormancy exit. Expression during transition from dormant telia to basidia confirmed the specific expression of the three poplar rust CSP genes. Their heterologous expression in yeast improved cell growth after cold stress exposure, suggesting a probable regulatory function when the poplar rust fungus exits dormancy. This study addresses for the first time TF and regulatory genes involved in developmental transition in the rust life cycle opening perspectives to further explore molecular regulation in the biology of the Pucciniales.
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Affiliation(s)
| | - Carla Blot
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | - Ekaterina Shelest
- School of biological Sciences, University of Portsmouth, King Henry 1 Street, PO1 D2Y, Portsmouth, United Kingdom
| | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
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Zhang D, Tang J, Wei K, Jia S, Jiang Y, Cai H, Mao P, Li M. Physiological and Molecular Responses of Zoysia japonica to Rust Infection. Int J Mol Sci 2022; 23:ijms23084185. [PMID: 35457004 PMCID: PMC9026483 DOI: 10.3390/ijms23084185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
Zoysiagrass (Zoysia japonica) is a popular turfgrass species and is widely used for sport turf and urban landscape. Zoysiagrass is often infected by Puccinia zoysiae, which causes a loss in turf quality. The physiological and molecular mechanisms of rust resistance are poorly understood in this species. In this study, the rust-resistant and susceptible lines of zoysiagrass were inoculated with P. zoysiae, and alterations of leaf cell structure, physiological indicators and transcriptomic response were investigated at the various stages of inoculation. After inoculation, the cell membranes, nucleus, mitochondria, and chloroplast were all impaired, followed by abnormal physiological metabolism. The damage occurred earlier and more severely in the susceptible line. Changes in electrolyte leakage and chlorophyll content varied with the genotype and the inoculation stages. The transcriptome analysis showed that plant hormones, MAPK signal transduction pathway, photosynthesis and energy generation pathways were significantly enriched in the early response, in both the resistant and susceptible lines. The results provided insights into the physiological and molecular mechanisms of rust disease resistance and would benefit the breeding of rust-resistant varieties in zoysiagrass and related turfgrass species.
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Affiliation(s)
- Di Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (D.Z.); (J.T.); (K.W.); (S.J.); (H.C.); (P.M.)
| | - Jun Tang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (D.Z.); (J.T.); (K.W.); (S.J.); (H.C.); (P.M.)
| | - Kai Wei
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (D.Z.); (J.T.); (K.W.); (S.J.); (H.C.); (P.M.)
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (D.Z.); (J.T.); (K.W.); (S.J.); (H.C.); (P.M.)
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA;
| | - Hongwei Cai
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (D.Z.); (J.T.); (K.W.); (S.J.); (H.C.); (P.M.)
| | - Peisheng Mao
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (D.Z.); (J.T.); (K.W.); (S.J.); (H.C.); (P.M.)
| | - Manli Li
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (D.Z.); (J.T.); (K.W.); (S.J.); (H.C.); (P.M.)
- Correspondence:
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11
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Persoons A, Maupetit A, Louet C, Andrieux A, Lipzen A, Barry KW, Na H, Adam C, Grigoriev IV, Segura V, Duplessis S, Frey P, Halkett F, De Mita S. Genomic signatures of a major adaptive event in the pathogenic fungus Melampsora larici-populina. Genome Biol Evol 2021; 14:6468622. [PMID: 34919678 PMCID: PMC8755504 DOI: 10.1093/gbe/evab279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in nonmodel organisms. Host–pathogen interactions constitute good models due to the strong selective pressures that they entail. We focused on an adaptive event which affected the poplar rust fungus Melampsora larici-populina when it overcame a resistance gene borne by its host, cultivated poplar. Based on 76 virulent and avirulent isolates framing narrowly the estimated date of the adaptive event, we examined the molecular signatures of selection. Using an array of genome scan methods based on different features of nucleotide diversity, we detected a single locus exhibiting a consistent pattern suggestive of a selective sweep in virulent individuals (excess of differentiation between virulent and avirulent samples, linkage disequilibrium, genotype–phenotype statistical association, and long-range haplotypes). Our study pinpoints a single gene and further a single amino acid replacement which may have allowed the adaptive event. Although our samples are nearly contemporary to the selective sweep, it does not seem to have affected genome diversity further than the immediate vicinity of the causal locus, which can be explained by a soft selective sweep (where selection acts on standing variation) and by the impact of recombination in mitigating the impact of selection. Therefore, it seems that properties of the life cycle of M. larici-populina, which entails both high genetic diversity and outbreeding, has facilitated its adaptation.
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Affiliation(s)
| | - Agathe Maupetit
- Université de Lorraine,INRAE, IAM, Nancy, France.,Physiology and Biotechnology of Algae Laboratory,IFREMER, Nantes, France
| | | | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kerrie W Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Catherine Adam
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Vincent Segura
- BioForA,INRAE, ONF, Orléans, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | | | - Pascal Frey
- Université de Lorraine,INRAE, IAM, Nancy, France
| | | | - Stéphane De Mita
- Université de Lorraine,INRAE, IAM, Nancy, France.,PHIM, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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12
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Duplessis S, Lorrain C, Petre B, Figueroa M, Dodds PN, Aime MC. Host Adaptation and Virulence in Heteroecious Rust Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:403-422. [PMID: 34077239 DOI: 10.1146/annurev-phyto-020620-121149] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rust fungi (Pucciniales, Basidiomycota) are obligate biotrophic pathogens that cause rust diseases in plants, inflicting severe damage to agricultural crops. Pucciniales possess the most complex life cycles known in fungi. These include an alternation of generations, the development of up to five different sporulating stages, and, for many species, the requirement of infecting two unrelated host plants during different parts of their life cycle, termed heteroecism. These fungi have been extensively studied in the past century through microscopy and inoculation studies, providing precise descriptions of their infection processes, although the molecular mechanisms underlying their unique biology are poorly understood. In this review, we cover recent genomic and life cycle transcriptomic studies in several heteroecious rust species, which provide insights into the genetic tool kits associated with host adaptation and virulence, opening new avenues for unraveling their unique evolution.
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Affiliation(s)
- Sebastien Duplessis
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Cecile Lorrain
- Plant Pathology Group, ETH Zurich, 8092 Zurich, Switzerland;
| | - Benjamin Petre
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Melania Figueroa
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA;
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13
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Figueroa M, Ortiz D, Henningsen EC. Tactics of host manipulation by intracellular effectors from plant pathogenic fungi. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102054. [PMID: 33992840 DOI: 10.1016/j.pbi.2021.102054] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Fungal pathogens can secrete hundreds of effectors, some of which are known to promote host susceptibility. This biological complexity, together with the lack of genetic tools in some fungi, presents a substantial challenge to develop a broad picture of the mechanisms these pathogens use for host manipulation. Nevertheless, recent advances in understanding individual effector functions are beginning to flesh out our view of fungal pathogenesis. This review discusses some of the latest findings that illustrate how effectors from diverse species use similar strategies to modulate plant physiology to their advantage. We also summarize recent breakthroughs in the identification of effectors from challenging systems, like obligate biotrophs, and emerging concepts such as the 'iceberg model' to explain how the activation of plant immunity can be turned off by effectors with suppressive activity.
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Affiliation(s)
- Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Diana Ortiz
- National Research Institute for Agriculture, Food and Environment, Unit of Genetics and Breeding of Fruit and Vegetables, Domaine St Maurice, CS 60094, F-84143 Montfavet, France
| | - Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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14
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Singh Y, Nair AM, Verma PK. Surviving the odds: From perception to survival of fungal phytopathogens under host-generated oxidative burst. PLANT COMMUNICATIONS 2021; 2:100142. [PMID: 34027389 PMCID: PMC8132124 DOI: 10.1016/j.xplc.2021.100142] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/04/2020] [Accepted: 01/01/2021] [Indexed: 05/04/2023]
Abstract
Fungal phytopathogens pose a serious threat to global crop production. Only a handful of strategies are available to combat these fungal infections, and the increasing incidence of fungicide resistance is making the situation worse. Hence, the molecular understanding of plant-fungus interactions remains a primary focus of plant pathology. One of the hallmarks of host-pathogen interactions is the overproduction of reactive oxygen species (ROS) as a plant defense mechanism, collectively termed the oxidative burst. In general, high accumulation of ROS restricts the growth of pathogenic organisms by causing localized cell death around the site of infection. To survive the oxidative burst and achieve successful host colonization, fungal phytopathogens employ intricate mechanisms for ROS perception, ROS neutralization, and protection from ROS-mediated damage. Together, these countermeasures maintain the physiological redox homeostasis that is essential for cell viability. In addition to intracellular antioxidant systems, phytopathogenic fungi also deploy interesting effector-mediated mechanisms for extracellular ROS modulation. This aspect of plant-pathogen interactions is significantly under-studied and provides enormous scope for future research. These adaptive responses, broadly categorized into "escape" and "exploitation" mechanisms, are poorly understood. In this review, we discuss the oxidative stress response of filamentous fungi, their perception signaling, and recent insights that provide a comprehensive understanding of the distinct survival mechanisms of fungal pathogens in response to the host-generated oxidative burst.
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Affiliation(s)
- Yeshveer Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Athira Mohandas Nair
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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15
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dos Santos KCG, Pelletier G, Séguin A, Guillemette F, Hawkes J, Desgagné-Penix I, Germain H. Unrelated Fungal Rust Candidate Effectors Act on Overlapping Plant Functions. Microorganisms 2021; 9:microorganisms9050996. [PMID: 34063040 PMCID: PMC8148019 DOI: 10.3390/microorganisms9050996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/30/2021] [Indexed: 11/21/2022] Open
Abstract
Rust fungi cause epidemics that threaten the production of important plant species, such as wheat and soy. Melampsora larici-populina (Mlp) causes the poplar rust and encodes at least 1184 candidate effectors (CEs) whose functions are poorly known. In this study, we sequenced the transcriptome and used mass spectrometry to analyze the metabolome of Arabidopsis plants constitutively expressing 14 Mlp CEs and of a control line to discover alterations leading to plant susceptibility. We found 2299 deregulated genes across the experiment. Genes involved in pattern-triggered immunity, such as FRK1, PR1, RBOHD, and WRKY33, as well as AUX/IAA genes were down-regulated. We further observed that 680 metabolites were deregulated in at least one CE-expressing transgenic line, with “highly unsaturated and phenolic compounds” and “peptides” enriched among down- and up-regulated metabolites. Interestingly, transgenic lines expressing unrelated CEs had correlated patterns of gene and metabolite deregulation, while expression of CEs belonging to the same family deregulated different genes and metabolites. Thus, our results uncouple effector sequence similarity and function. This supports that effector functional investigation in the context of their virulence activity and effect on plant susceptibility requires the investigation of the individual effector and precludes generalization based on sequence similarity.
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Affiliation(s)
- Karen Cristine Goncalves dos Santos
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada; (K.C.G.d.S.); (I.D.-P.)
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada
| | - Gervais Pelletier
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC G1V 4C7, Canada; (G.P.); (A.S.)
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC G1V 4C7, Canada; (G.P.); (A.S.)
| | - François Guillemette
- Centre for Research on Aquatic Ecosystem Interactions (RIVE), Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada;
| | - Jeffrey Hawkes
- Department of Chemistry—BMC, Analytical Chemistry, Uppsala University, VJ2J+92 Uppsala, Sweden;
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada; (K.C.G.d.S.); (I.D.-P.)
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H9, Canada; (K.C.G.d.S.); (I.D.-P.)
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 1V3, Canada
- Correspondence:
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16
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Fabre F, Urbach S, Roche S, Langin T, Bonhomme L. Proteomics-Based Data Integration of Wheat Cultivars Facing Fusarium graminearum Strains Revealed a Core-Responsive Pattern Controlling Fusarium Head Blight. FRONTIERS IN PLANT SCIENCE 2021; 12:644810. [PMID: 34135919 PMCID: PMC8201412 DOI: 10.3389/fpls.2021.644810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Fusarium head blight (FHB), mainly occurring upon Fusarium graminearum infection in a wide variety of small-grain cereals, is supposed to be controlled by a range of processes diverted by the fungal pathogen, the so-called susceptibility factors. As a mean to provide relevant information about the molecular events involved in FHB susceptibility in bread wheat, we studied an extensive proteome of more than 7,900 identified wheat proteins in three cultivars of contrasting susceptibilities during their interaction with three F. graminearum strains of different aggressiveness. No cultivar-specific proteins discriminated the three wheat genotypes, demonstrating the establishment of a core proteome regardless of unequivocal FHB susceptibility differences. Quantitative protein analysis revealed that most of the FHB-induced molecular adjustments were shared by wheat cultivars and occurred independently of the F. graminearum strain aggressiveness. Although subtle abundance changes evidenced genotype-dependent responses to FHB, cultivar distinction was found to be mainly due to basal abundance differences, especially regarding the chloroplast functions. Integrating these data with previous proteome mapping of the three F. graminearum strains facing the three same wheat cultivars, we demonstrated strong correlations between the wheat protein abundance changes and the adjustments of fungal proteins supposed to interfere with host molecular functions. Together, these results provide a resourceful dataset that expands our understanding of the specific molecular events taking place during the wheat-F. graminearum interaction.
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Affiliation(s)
- Francis Fabre
- Université Clermont Auvergne, INRAE, UMR 1095 Génétique Diversité Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Sylvie Roche
- INRAE, Unité Experimentale 1375, Phénotypage au Champ des Céréales (PHACC), Clermont-Ferrand, France
| | - Thierry Langin
- Université Clermont Auvergne, INRAE, UMR 1095 Génétique Diversité Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Ludovic Bonhomme
- Université Clermont Auvergne, INRAE, UMR 1095 Génétique Diversité Ecophysiologie des Céréales, Clermont-Ferrand, France
- *Correspondence: Ludovic Bonhomme,
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17
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Leaping into the Unknown World of Sporisorium scitamineum Candidate Effectors. J Fungi (Basel) 2020; 6:jof6040339. [PMID: 33291820 PMCID: PMC7762069 DOI: 10.3390/jof6040339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Sporisorium scitamineum is a biotrophic fungus causing sugarcane smut disease. In this study, we set up a pipeline and used genomic and dual transcriptomic data previously obtained by our group to identify candidate effectors of S. scitamineum and their expression profiles in infected smut-resistant and susceptible sugarcane plants. The expression profile of different genes after infection in contrasting sugarcane genotypes assessed by RT-qPCR depended on the plant genotypes and disease progression. Three candidate effector genes expressed earlier only in resistant plants, four expressed in both genotypes, and three later in susceptible plants. Ten genes were cloned and transiently expressed in N. benthamiana leaves to determine their subcellular location, while four localized in more than one compartment. Two candidates, g3890 having a nucleoplasmic and mitochondrial location and g5159 targeting the plant cell wall, were selected to obtain their possible corresponding host targets using co-immunoprecipitation (CoIP) experiments and mass spectrometry. Various potential interactors were identified, including subunits of the protein phosphatase 2A and an endochitinase. We investigated the presence of orthologs in sugarcane and using transcriptome data present their expression profiles. Orthologs of sugarcane shared around 70% similarity. Identifying a set of putative fungal effectors and their plant targets provides a valuable resource for functional characterization of the molecular events leading to smut resistance in sugarcane plants and uncovers further opportunities for investigation.
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18
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Lacaze A, Joly DL. Structural specificity in plant-filamentous pathogen interactions. MOLECULAR PLANT PATHOLOGY 2020; 21:1513-1525. [PMID: 32889752 PMCID: PMC7548998 DOI: 10.1111/mpp.12983] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/06/2020] [Accepted: 07/26/2020] [Indexed: 05/07/2023]
Abstract
Plant diseases bear names such as leaf blights, root rots, sheath blights, tuber scabs, and stem cankers, indicating that symptoms occur preferentially on specific parts of host plants. Accordingly, many plant pathogens are specialized to infect and cause disease in specific tissues and organs. Conversely, others are able to infect a range of tissues, albeit often disease symptoms fluctuate in different organs infected by the same pathogen. The structural specificity of a pathogen defines the degree to which it is reliant on a given tissue, organ, or host developmental stage. It is influenced by both the microbe and the host but the processes shaping it are not well established. Here we review the current status on structural specificity of plant-filamentous pathogen interactions and highlight important research questions. Notably, this review addresses how constitutive defence and induced immunity as well as virulence processes vary across plant organs, tissues, and even cells. A better understanding of the mechanisms underlying structural specificity will aid targeted approaches for plant health, for instance by considering the variation in the nature and the amplitude of defence responses across distinct plant organs and tissues when performing selective breeding.
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Affiliation(s)
- Aline Lacaze
- Department of BiologyUniversité de MonctonMonctonCanada
| | - David L. Joly
- Department of BiologyUniversité de MonctonMonctonCanada
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19
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Jaswal R, Rajarammohan S, Dubey H, Sharma TR. Smut fungi as a stratagem to characterize rust effectors: opportunities and challenges. World J Microbiol Biotechnol 2020; 36:150. [PMID: 32924088 DOI: 10.1007/s11274-020-02927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/05/2020] [Indexed: 11/30/2022]
Abstract
The rust pathogens are one of the most complex fungi in the Basidiomycetes. The development of genomic resources for rust and other plant pathogens has opened the opportunities for functional genomics of fungal genes. Despite significant progress in the field of fungal genomics, functional characterization of the genome components has lacked, especially for the rust pathogens. Their obligate nature and lack of standard stable transformation protocol are the primary reasons for rusts to be one of the least explored genera despite its significance. In the recently sequenced rust genomes, a vast catalogue of predicted effectors and pathogenicity genes have been reported. However, most of these candidate genes remained unexplored due to the lack of suitable characterization methods. The heterologous expression of putative effectors in Nicotiana benthamiana and Arabidopsis thaliana has proved to be a rapid screening method for identifying the role of these effectors in virulence. However, no fungal system has been used for the functional validation of these candidate genes. The smuts, from the evolutionary point of view, are closely related to the rust pathogens. Moreover, they have been widely studied and hence could be a suitable model system for expressing rust fungal genes heterologously. The genetic manipulation methods for smuts are also well standardized. Complementation assays can be used for functional validation of the homologous genes present in rust and smut fungal pathogens, while the species-specific proteins can be expressed in the mutant strains of smut pathogens having reduced or no virulence for virulence analysis. We propose that smuts, especially Ustilago maydis, may prove to be a good model system to characterize rust effector proteins in the absence of methods to manipulate the rust genomes directly.
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Affiliation(s)
- Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), PO Manauli, S.A.S. Nagar, Mohali, Punjab, 140306, India
| | - Sivasubramanian Rajarammohan
- National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), PO Manauli, S.A.S. Nagar, Mohali, Punjab, 140306, India
| | - Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - T R Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), PO Manauli, S.A.S. Nagar, Mohali, Punjab, 140306, India.
- Crop Science Division, Indian Council of Agricultural Research, New Delhi, 110001, India.
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20
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Christian RW, Hewitt SL, Nelson G, Roalson EH, Dhingra A. Plastid transit peptides-where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution. PeerJ 2020; 8:e9772. [PMID: 32913678 PMCID: PMC7456531 DOI: 10.7717/peerj.9772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/30/2020] [Indexed: 01/22/2023] Open
Abstract
Subcellular relocalization of proteins determines an organism's metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.
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Affiliation(s)
- Ryan W. Christian
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Seanna L. Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Grant Nelson
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Eric H. Roalson
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
- Department of Horticulture, Washington State University, Pullman, WA, USA
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21
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Feurtey A, Lorrain C, Croll D, Eschenbrenner C, Freitag M, Habig M, Haueisen J, Möller M, Schotanus K, Stukenbrock EH. Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria. BMC Genomics 2020; 21:588. [PMID: 32842972 PMCID: PMC7448473 DOI: 10.1186/s12864-020-06871-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/26/2020] [Indexed: 11/25/2022] Open
Abstract
Background Antagonistic co-evolution can drive rapid adaptation in pathogens and shape genome architecture. Comparative genome analyses of several fungal pathogens revealed highly variable genomes, for many species characterized by specific repeat-rich genome compartments with exceptionally high sequence variability. Dynamic genome structure may enable fast adaptation to host genetics. The wheat pathogen Zymoseptoria tritici with its highly variable genome, has emerged as a model organism to study genome evolution of plant pathogens. Here, we compared genomes of Z. tritici isolates and of sister species infecting wild grasses to address the evolution of genome composition and structure. Results Using long-read technology, we sequenced and assembled genomes of Z. ardabiliae, Z. brevis, Z. pseudotritici and Z. passerinii, together with two isolates of Z. tritici. We report a high extent of genome collinearity among Zymoseptoria species and high conservation of genomic, transcriptomic and epigenomic signatures of compartmentalization. We identify high gene content variability both within and between species. In addition, such variability is mainly limited to the accessory chromosomes and accessory compartments. Despite strong host specificity and non-overlapping host-range between species, predicted effectors are mainly shared among Zymoseptoria species, yet exhibiting a high level of presence-absence polymorphism within Z. tritici. Using in planta transcriptomic data from Z. tritici, we suggest different roles for the shared orthologs and for the accessory genes during infection of their hosts. Conclusion Despite previous reports of high genomic plasticity in Z. tritici, we describe here a high level of conservation in genomic, epigenomic and transcriptomic composition and structure across the genus Zymoseptoria. The compartmentalized genome allows the maintenance of a functional core genome co-occurring with a highly variable accessory genome.
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Affiliation(s)
- Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
| | - Cécile Lorrain
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany. .,Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany. .,INRA Centre Grand Est - Nancy, UMR 1136 INRA/Universite de Lorraine Interactions Arbres/Microorganismes, 54280, Champenoux, France.
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland
| | - Christoph Eschenbrenner
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Habig
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
| | - Janine Haueisen
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
| | - Mareike Möller
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Klaas Schotanus
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany.,Department of Molecular Genetics and Microbiology, Duke University, Duke University Medical Center, Durham, NC, 27710, USA
| | - Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
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22
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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.
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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.
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Zhao S, Shang X, Bi W, Yu X, Liu D, Kang Z, Wang X, Wang X. Genome-Wide Identification of Effector Candidates With Conserved Motifs From the Wheat Leaf Rust Fungus Puccinia triticina. Front Microbiol 2020; 11:1188. [PMID: 32582112 PMCID: PMC7283542 DOI: 10.3389/fmicb.2020.01188] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
Rust fungi secrete various specialized effectors into host cells to manipulate the plant defense response. Conserved motifs, including RXLR, LFLAK-HVLVxxP (CRN), Y/F/WxC, CFEM, LysM, EAR, [SG]-P-C-[KR]-P, DPBB_1 (PNPi), and ToxA, have been identified in various oomycete and fungal effectors and are reported to be crucial for effector translocation or function. However, little is known about potential effectors containing any of these conserved motifs in the wheat leaf rust fungus (Puccinia triticina, Pt). In this study, sequencing was performed on RNA samples collected from the germ tubes (GT) of uredospores of an epidemic Pt pathotype PHTT(P) and Pt-infected leaves of a susceptible wheat cultivar "Chinese Spring" at 4, 6, and 8 days post-inoculation (dpi). The assembled transcriptome data were compared to the reference genome of "Pt 1-1 BBBD Race 1." A total of 17,976 genes, including 2,284 "novel" transcripts, were annotated. Among all these genes, we identified 3,149 upregulated genes upon Pt infection at all time points compared to GT, whereas 1,613 genes were more highly expressed in GT. A total of 464 secreted proteins were encoded by those upregulated genes, with 79 of them also predicted as possible effectors by EffectorP. Using hmmsearch and Regex, we identified 719 RXLR-like, 19 PNPi-like, 19 CRN-like, 138 Y/F/WxC, and 9 CFEM effector candidates from the deduced protein database including data based on the "Pt 1-1 BBBD Race 1" genome and the transcriptome data collected here. Four of the PNPi-like effector candidates with DPBB_1 conserved domain showed physical interactions with wheat NPR1 protein in yeast two-hybrid assay. Nine Y/F/WxC and seven CFEM effector candidates were transiently expressed in Nicotiana benthamiana. None of these effector candidates showed induction or suppression of cell death triggered by BAX protein, but the expression of one CFEM effector candidate, PTTG_08198, accelerated the progress of cell death and promoted the accumulation of reactive oxygen species (ROS). In conclusion, we profiled genes associated with the infection process of the Pt pathotype PHTT(P). The identified effector candidates with conserved motifs will help guide the investigation of virulent mechanisms of leaf rust fungus.
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Affiliation(s)
- Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Xiaofeng Shang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Weishuai Bi
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Xiumei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Daqun Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
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24
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Abstract
Among the thousands of rust species described, many are known for their devastating effects on their hosts, which include major agriculture crops and trees. Hence, for over a century, these basidiomycete pathogenic fungi have been researched and experimented with. However, due to their biotrophic nature, they are challenging organisms to work with and, needing their hosts for propagation, represent pathosystems that are not easily experimentally accessible. Indeed, efforts to perform genetics have been few and far apart for the rust fungi, though one study performed in the 1940s was famously instrumental in formulating the gene-for-gene hypothesis describing pathogen-host interactions. By taking full advantage of the molecular genetic tools developed in the 1980s, research on many plant pathogenic microbes thrived, yet similar work on the rusts remained very challenging though not without some successes. However, the genomics era brought real breakthrough research for the biotrophic fungi and with innovative experimentation and the use of heterologous systems, molecular genetic analyses over the last 2 decades have significantly advanced our insight into the function of many rust fungus genes and their role in the interaction with their hosts. This has allowed optimizing efforts for resistance breeding and the design and testing of various novel strategies to reduce the devastating diseases they cause.
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Affiliation(s)
- Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research & Development Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0
| | - Les J Szabo
- U.S. Department of Agriculture-Agriculture Research Service, Cereal Disease Laboratory and University of Minnesota, 1551 Lindig Street, St. Paul, MN 55108, U.S.A
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25
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Prasad P, Savadi S, Bhardwaj SC, Gupta PK. The progress of leaf rust research in wheat. Fungal Biol 2020; 124:537-550. [PMID: 32448445 DOI: 10.1016/j.funbio.2020.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/25/2023]
Abstract
Leaf rust (also called brown rust) in wheat, caused by fungal pathogen Puccinia triticina Erikss. (Pt) is one of the major constraints in wheat production worldwide. Pt is widespread with diverse population structure and undergoes rapid evolution to produce new virulent races against resistant cultivars that are regularly developed to provide resistance against the prevailing races of the pathogen. Occasionally, the disease may also take the shape of an epidemic in some wheat-growing areas causing major economic losses. In the recent past, substantial progress has been made in characterizing the sources of leaf rust resistance including non-host resistance (NHR). Progress has also been made in elucidating the population biology of Pt and the mechanisms of wheat-Pt interaction. So far, ∼80 leaf rust resistance genes (Lr genes) have been identified and characterized; some of them have also been used for the development of resistant wheat cultivars. It has also been shown that a gene-for-gene relationship exists between individual wheat Lr genes and the corresponding Pt Avr genes so that no Lr gene can provide resistance unless the prevailing race of the pathogen carries the corresponding Avr gene. Several Lr genes have also been cloned and their products characterized, although no Avr gene corresponding a specific Lr gene has so far been identified. However, several candidate effectors for Pt have been identified and functionally characterized using genome-wide analyses, transcriptomics, RNA sequencing, bimolecular fluorescence complementation (BiFC), virus-induced gene silencing (VIGS), transient expression and other approaches. This review summarizes available information on different aspects of the pathogen Pt, genetics/genomics of leaf rust resistance in wheat including cloning and characterization of Lr genes and epigenetic regulation of disease resistance.
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Affiliation(s)
- Pramod Prasad
- 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
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
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26
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Kretschmer M, Damoo D, Djamei A, Kronstad J. Chloroplasts and Plant Immunity: Where Are the Fungal Effectors? Pathogens 2019; 9:E19. [PMID: 31878153 PMCID: PMC7168614 DOI: 10.3390/pathogens9010019] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 12/12/2022] Open
Abstract
Chloroplasts play a central role in plant immunity through the synthesis of secondary metabolites and defense compounds, as well as phytohormones, such as jasmonic acid and salicylic acid. Additionally, chloroplast metabolism results in the production of reactive oxygen species and nitric oxide as defense molecules. The impact of viral and bacterial infections on plastids and chloroplasts has been well documented. In particular, bacterial pathogens are known to introduce effectors specifically into chloroplasts, and many viral proteins interact with chloroplast proteins to influence viral replication and movement, and plant defense. By contrast, clear examples are just now emerging for chloroplast-targeted effectors from fungal and oomycete pathogens. In this review, we first present a brief overview of chloroplast contributions to plant defense and then discuss examples of connections between fungal interactions with plants and chloroplast function. We then briefly consider well-characterized bacterial effectors that target chloroplasts as a prelude to discussing the evidence for fungal effectors that impact chloroplast activities.
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Affiliation(s)
- Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (M.K.); (D.D.)
| | - Djihane Damoo
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (M.K.); (D.D.)
| | - Armin Djamei
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany;
| | - James Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (M.K.); (D.D.)
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27
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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.
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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.
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28
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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.
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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.
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29
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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.
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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.
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30
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Yu F, Wang S, Zhang W, Tang J, Wang H, Yu L, Zhang X, Fei Z, Li J. Genome-wide identification of genes encoding putative secreted E3 ubiquitin ligases and functional characterization of PbRING1 in the biotrophic protist Plasmodiophora brassicae. Curr Genet 2019; 65:1355-1365. [PMID: 31087129 DOI: 10.1007/s00294-019-00989-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/24/2019] [Accepted: 05/03/2019] [Indexed: 10/26/2022]
Abstract
The E3 ubiquitin ligases are key regulators of protein ubiquitination, which have been shown to be involved in a variety of cellular responses to both biotic and abiotic stresses in eukaryotes. However, the E3 ubiquitin ligase homologues in the soil-borne plant pathogen Plasmodiophora brassicae, the causal agent of clubroot disease of crucifer crops worldwide, remain largely unknown. In this study, we characterized secreted E3 ubiquitin ligases, a group of proteins known to be involved in virulence in many pathogens, in a plasmodiophorid P. brassicae. Genome-wide search in the P. brassicae genome retrieved 139 putative E3 ubiquitin ligases, comprising of 115 RING, 15 HECT, 1 HECT-like, and 8 U-box E3 ubiquitin ligases. Among these E3 ubiquitin ligases, 11 RING, 1 U-box, and 3 HECT were found to harbor signal peptide. Based on published RNA-seq data (Schwelm et al. in Sci Rep 5:11153, 2015), we found that these genes were differentially expressed in distinct life stages including germinating spores, maturing spores, and plasmodia. We characterized one potential secreted E3 ubiquitin ligase, PbRING1 (PBRA_000499). Yeast invertase assay showed that PbRING1 harbors a functional N-terminal signal peptide. PbRING1 also harbors a really interested new gene (RING) domain at its C terminus, which was found to display the E3 ligase activity in vitro. Collectively, this study provides a comprehensive insight into the reservoir of putative secreted E3 ligases in P. brassicae.
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Affiliation(s)
- Fangwei Yu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shenyun Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jun Tang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Hong Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Li Yu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xin Zhang
- Tianjin Gengyun Seed Co. Ltd, Tianjin, 300400, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.
| | - Jianbin Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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31
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Lorrain C, Gonçalves Dos Santos KC, Germain H, Hecker A, Duplessis S. Advances in understanding obligate biotrophy in rust fungi. THE NEW PHYTOLOGIST 2019; 222:1190-1206. [PMID: 30554421 DOI: 10.1111/nph.15641] [Citation(s) in RCA: 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.
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Affiliation(s)
- Cécile Lorrain
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | | | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Quebec à Trois-Rivières, Trois-Rivières, QC, G9A 5H7, Canada
| | - Arnaud Hecker
- Université de Lorraine, UMR 1136 Université de Lorraine/INRA Interactions Arbres/Microorganismes, Vandoeuvre-lès-Nancy, France
| | - Sébastien Duplessis
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
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Fudal I, Balesdent MH, Rouxel T. Effector Biology in Fungal Pathogens of Nonmodel Crop Plants. TRENDS IN PLANT SCIENCE 2018; 23:753-755. [PMID: 30041914 DOI: 10.1016/j.tplants.2018.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
The recent finding of a novel fungal strategy to manipulate salicylic acid (SA) in a nonmodel plant pathogen interaction not only establishes the universality of the strategy to ensure the success of biotrophs and hemibiotrophs, but also illustrates current limitations and challenges to identify targets of fungal effector in crop plants.
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Affiliation(s)
- Isabelle Fudal
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France
| | | | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France.
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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.
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