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Mukhopadhyay S, Garvetto A, Neuhauser S, Pérez-López E. Decoding the Arsenal: Protist Effectors and Their Impact on Photosynthetic Hosts. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:498-506. [PMID: 38551366 DOI: 10.1094/mpmi-11-23-0196-cr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Interactions between various microbial pathogens including viruses, bacteria, fungi, oomycetes, and their plant hosts have traditionally been the focus of phytopathology. In recent years, a significant and growing interest in the study of eukaryotic microorganisms not classified among fungi or oomycetes has emerged. Many of these protists establish complex interactions with photosynthetic hosts, and understanding these interactions is crucial in understanding the dynamics of these parasites within traditional and emerging types of farming, including marine aquaculture. Many phytopathogenic protists are biotrophs with complex polyphasic life cycles, which makes them difficult or impossible to culture, a fact reflected in a wide gap in the availability of comprehensive genomic data when compared to fungal and oomycete plant pathogens. Furthermore, our ability to use available genomic resources for these protists is limited by the broad taxonomic distance that these organisms span, which makes comparisons with other genomic datasets difficult. The current rapid progress in genomics and computational tools for the prediction of protein functions and interactions is revolutionizing the landscape in plant pathology. This is also opening novel possibilities, specifically for a deeper understanding of protist effectors. Tools like AlphaFold2 enable structure-based function prediction of effector candidates with divergent protein sequences. In turn, this allows us to ask better biological questions and, coupled with innovative experimental strategies, will lead into a new era of effector research, especially for protists, to expand our knowledge on these elusive pathogens and their interactions with photosynthetic hosts. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Soham Mukhopadhyay
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Institute de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- L'Institute EDS, Université Laval, Quebec City, Quebec, Canada
| | - Andrea Garvetto
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Sigrid Neuhauser
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Edel Pérez-López
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Institute de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- L'Institute EDS, Université Laval, Quebec City, Quebec, Canada
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Sasaki T, Naito R, Ohara T, Sakane K, Tanaka S, Sasaki K, Osato A, Nomura Y, Ito SI. Effects of flusulfamide on spore germination of Plasmodiophora brassicae. JOURNAL OF PESTICIDE SCIENCE 2024; 49:52-57. [PMID: 38450088 PMCID: PMC10912929 DOI: 10.1584/jpestics.d23-031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/12/2023] [Indexed: 03/08/2024]
Abstract
Flusulfamide inhibits germination of Plasmodiophora brassicae resting spores to suppress clubroot disease, but its mechanism of action on the germination of P. brassicae resting spores remains unclear. In this study, P. brassicae resting spores were treated with flusulfamide and visualized using transmission electron microscopy (TEM). The gene expression of P. brassicae resting spores was analyzed using RT-PCR, followed by immunoblotting analysis. TEM results revealed that flusulfamide suppressed the primary zoosporogenesis of P. brassicae resting spores during the early phase, and RT-PCR results revealed that flusulfamide affected the gene expression during the germination of the resting spores. Immunoblot and RT-qPCR analyses revealed that PbCyp3, an immunophilin (peptidyl-prolyl-isomerase) gene, was highly expressed, resulting in the unusual accumulation of PbCYP3 protein in P. brassicae resting spores immediately after treatment with flusulfamide. This suggests that flusulfamide may cause aberrant folding of proteins involved in primary zoosporogenesis, thereby inhibiting germination.
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Affiliation(s)
- Taito Sasaki
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University
| | - Ryohei Naito
- Agrochemicals Research Center, Mitsui Chemicals Crop & Life Solutions, Inc
| | - Toshiaki Ohara
- Agrochemicals Research Center, Mitsui Chemicals Crop & Life Solutions, Inc
| | - Kosei Sakane
- The United Graduate School of Agricultural Sciences, Tottori University
| | - Shuhei Tanaka
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University
| | - Kazunori Sasaki
- Research Center for Thermotolerant Microbial Resources, Advanced Science and Innovational Research Center, Yamaguchi University
| | - Aoi Osato
- Faculty of Agriculture, Yamaguchi University
| | - Yuki Nomura
- Faculty of Agriculture, Yamaguchi University
| | - Shin-ichi Ito
- Research Center for Thermotolerant Microbial Resources, Advanced Science and Innovational Research Center, Yamaguchi University
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3
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Advances in molecular interactions on the Rhizoctonia solani-sugar beet pathosystem. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ludwig-Müller J. What Can We Learn from -Omics Approaches to Understand Clubroot Disease? Int J Mol Sci 2022; 23:ijms23116293. [PMID: 35682976 PMCID: PMC9180986 DOI: 10.3390/ijms23116293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023] Open
Abstract
Clubroot is one of the most economically significant diseases worldwide. As a result, many investigations focus on both curing the disease and in-depth molecular studies. Although the first transcriptome dataset for the clubroot disease describing the clubroot disease was published in 2006, many different pathogen-host plant combinations have only recently been investigated and published. Articles presenting -omics data and the clubroot pathogen Plasmodiophora brassicae as well as different host plants were analyzed to summarize the findings in the richness of these datasets. Although genome data for the protist have only recently become available, many effector candidates have been identified, but their functional characterization is incomplete. A better understanding of the life cycle is clearly required to comprehend its function. While only a few proteome studies and metabolome analyses were performed, the majority of studies used microarrays and RNAseq approaches to study transcriptomes. Metabolites, comprising chemical groups like hormones were generally studied in a more targeted manner. Furthermore, functional approaches based on such datasets have been carried out employing mutants, transgenic lines, or ecotypes/cultivars of either Arabidopsis thaliana or other economically important host plants of the Brassica family. This has led to new discoveries of potential genes involved in disease development or in (partial) resistance or tolerance to P. brassicae. The overall contribution of individual experimental setups to a larger picture will be discussed in this review.
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Balotf S, Tegg RS, Nichols DS, Wilson CR. Spore Germination of the Obligate Biotroph Spongospora subterranea: Transcriptome Analysis Reveals Germination Associated Genes. Front Microbiol 2021; 12:691877. [PMID: 34234764 PMCID: PMC8256667 DOI: 10.3389/fmicb.2021.691877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/20/2021] [Indexed: 11/22/2022] Open
Abstract
For soilborne pathogens, germination of the resting or dormant propagule that enables persistence within the soil environment is a key point in pathogenesis. Spongospora subterranea is an obligate soilborne protozoan that infects the roots and tubers of potato causing root and powdery scab disease for which there are currently no effective controls. A better understanding of the molecular basis of resting spore germination of S. subterranea could be important for development of novel disease interventions. However, as an obligate biotroph and soil dwelling organism, the application of new omics techniques for the study of the pre-infection process in S. subterranea has been problematic. Here, RNA sequencing was used to analyse the reprogramming of S. subterranea resting spores during the transition to zoospores in an in-vitro model. More than 63 million mean high-quality reads per sample were generated from the resting and germinating spores. By using a combination of reference-based and de novo transcriptome assembly, 6,664 unigenes were identified. The identified unigenes were subsequently annotated based on known proteins using BLAST search. Of 5,448 annotated genes, 570 genes were identified to be differentially expressed during the germination of S. subterranea resting spores, with most of the significant genes belonging to transcription and translation, amino acids biosynthesis, transport, energy metabolic processes, fatty acid metabolism, stress response and DNA repair. The datasets generated in this study provide a basic knowledge of the physiological processes associated with spore germination and will facilitate functional predictions of novel genes in S. subterranea and other plasmodiophorids. We introduce several candidate genes related to the germination of an obligate biotrophic soilborne pathogen which could be applied to the development of antimicrobial agents for soil inoculum management.
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Affiliation(s)
- Sadegh Balotf
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, TAS, Australia
| | - Robert S Tegg
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, TAS, Australia
| | - David S Nichols
- Central Science Laboratory, University of Tasmania, Hobart, TAS, Australia
| | - Calum R Wilson
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, TAS, Australia
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González-García M, Pérez-López E. Looking for a Cultured Surrogate for Effectome Studies of the Clubroot Pathogen. Front Microbiol 2021; 12:650307. [PMID: 34122364 PMCID: PMC8193517 DOI: 10.3389/fmicb.2021.650307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/05/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Melaine González-García
- Department of Plant Sciences, Faculté des Sciences de l'agriculture et de l'alimentation (FSAA), Université Laval, Québec, QC, Canada
| | - Edel Pérez-López
- Department of Plant Sciences, Faculté des Sciences de l'agriculture et de l'alimentation (FSAA), Université Laval, Québec, QC, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec, QC, Canada
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
- Centre de recherche en sciences du végétal (Centre SÈVE), Fonds de recherche du Québec - Nature et technologies (FRQNT), Québec, QC, Canada
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Schwelm A, Ludwig-Müller J. Molecular Pathotyping of Plasmodiophora brassicae-Genomes, Marker Genes, and Obstacles. Pathogens 2021; 10:pathogens10030259. [PMID: 33668372 PMCID: PMC7996130 DOI: 10.3390/pathogens10030259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/16/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022] Open
Abstract
Here we review the usefulness of the currently available genomic information for the molecular identification of pathotypes. We focused on effector candidates and genes implied to be pathotype specific and tried to connect reported marker genes to Plasmodiophora brassicae genome information. The potentials for practical applications, current obstacles and future perspectives are discussed.
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Singh H, Kaur K, Singh M, Kaur G, Singh P. Plant Cyclophilins: Multifaceted Proteins With Versatile Roles. FRONTIERS IN PLANT SCIENCE 2020; 11:585212. [PMID: 33193535 PMCID: PMC7641896 DOI: 10.3389/fpls.2020.585212] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 05/03/2023]
Abstract
Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.
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Affiliation(s)
- Harpreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Kirandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Mangaljeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- William Harvey Heart Centre, Queen Mary University of London, London, United Kingdom
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
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Badstöber J, Gachon CMM, Ludwig-Müller J, Sandbichler AM, Neuhauser S. Demystifying biotrophs: FISHing for mRNAs to decipher plant and algal pathogen-host interaction at the single cell level. Sci Rep 2020; 10:14269. [PMID: 32868853 PMCID: PMC7459097 DOI: 10.1038/s41598-020-70884-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 08/05/2020] [Indexed: 12/18/2022] Open
Abstract
Plant-pathogen interactions follow spatial and temporal developmental dynamics where gene expression in pathogen and host undergo crucial changes. Therefore, it is of great interest to detect, quantify and localise where and when key genes are active to understand these processes. Many pathosystems are not accessible for genetic amendments or other spatially-resolved gene expression monitoring methods. Here, we adapt single molecule FISH techniques to demonstrate the presence and activity of mRNAs at the single-cell level using phytomyxids in their plant and algal host in lab and field material. This allowed us to monitor and quantify the expression of genes from the clubroot pathogen Plasmodiophora brassicae, several species of its Brassica hosts, and of several brown algae, including the genome model Ectocarpus siliculosus, infected with the phytomyxid Maullinia ectocarpii. We show that mRNAs are localised along a spatiotemporal gradient, thus providing a proof-of-concept of the usefulness of single-molecule FISH to increase knowledge about the interactions between plants, algae and phytomyxids. The methods used are easily applicable to any interaction between microbes and their algal or plant host, and have therefore the potential to rapidly increase our understanding of key, spatially- and temporally-resolved processes underpinning complex plant-microbe interactions.
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Affiliation(s)
- Julia Badstöber
- Institute of Microbiology, University of Innsbruck, 6020, Innsbruck, Austria
| | - Claire M M Gachon
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA, UK
- UMR 7245 - Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, Paris, 75005, France
| | - Jutta Ludwig-Müller
- Institute of Botany, Technische Universität Dresden, 01217, Dresden, Germany
| | | | - Sigrid Neuhauser
- Institute of Microbiology, University of Innsbruck, 6020, Innsbruck, Austria.
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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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Search for Partner Proteins of A. thaliana Immunophilins Involved in the Control of Plant Immunity. Molecules 2018; 23:molecules23040953. [PMID: 29671793 PMCID: PMC6017422 DOI: 10.3390/molecules23040953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 12/04/2022] Open
Abstract
The involvement of plant immunophilins in multiple essential processes such as development, various ways of adapting to biotic and abiotic stresses, and photosynthesis has already been established. Previously, research has demonstrated the involvement of three immunophilin genes (AtCYP19-1/ROC3, AtFKBP65/ROF2, and AtCYP57) in the control of plant response to invasion by various pathogens. Current research attempts to identify host target proteins for each of the selected immunophilins. As a result, candidate interactors have been determined and confirmed using a yeast 2-hybrid (Y2H) system for protein–protein interaction assays. The generation of mutant isoforms of ROC3 and AtCYP57 harboring substituted amino acids in the in silico-predicted active sites became essential to achieving significant binding to its target partners. This data shows that ROF2 targets calcium-dependent lipid-binding domain-containing protein (At1g70790; AT1) and putative protein phosphatase (At2g30020; АТ2), whereas ROC3 interacts with GTP-binding protein (At1g30580; ENGD-1) and RmlC-like cupin (At5g39120). The immunophilin AtCYP57 binds to putative pyruvate decarboxylase-1 (Pdc1) and clathrin adaptor complex-related protein (At5g05010). Identified interactors confirm our previous findings that immunophilins ROC3, ROF2, and AtCYP57 are directly involved with stress response control. Further, these findings extend our understanding of the molecular functional pathways of these immunophilins.
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