101
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Phylogenetics and Phylogenomics of Rust Fungi. FUNGAL PHYLOGENETICS AND PHYLOGENOMICS 2017; 100:267-307. [DOI: 10.1016/bs.adgen.2017.09.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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102
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Stirnberg A, Djamei A. Characterization of ApB73, a virulence factor important for colonization of Zea mays by the smut Ustilago maydis. MOLECULAR PLANT PATHOLOGY 2016; 17:1467-1479. [PMID: 27279632 PMCID: PMC5132131 DOI: 10.1111/mpp.12442] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 05/22/2023]
Abstract
The biotrophic fungus Ustilago maydis, the causal agent of corn smut disease, uses numerous small secreted effector proteins to suppress plant defence responses and reshape the host metabolism. However, the role of specific effectors remains poorly understood. Here, we describe the identification of ApB73 (Apathogenic in B73), an as yet uncharacterized protein essential for the successful colonization of maize by U. maydis. We show that apB73 is transcriptionally induced during the biotrophic stages of the fungal life cycle. The deletion of the apB73 gene results in cultivar-specific loss of gall formation in the host. The ApB73 protein is conserved among closely related smut fungi. However, using virulence assays, we show that only the orthologue of the maize-infecting head smut Sporisorium reilianum can complement the mutant phenotype of U. maydis. Although microscopy shows that ApB73 is secreted into the biotrophic interface, it seems to remain associated with fungal cell wall components or the fungal plasma membrane. Taken together, the results show that ApB73 is a conserved and important virulence factor of U. maydis that localizes to the interface between the pathogen and its host Zea mays.
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Affiliation(s)
- Alexandra Stirnberg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
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103
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Rabe F, Bosch J, Stirnberg A, Guse T, Bauer L, Seitner D, Rabanal FA, Czedik-Eysenberg A, Uhse S, Bindics J, Genenncher B, Navarrete F, Kellner R, Ekker H, Kumlehn J, Vogel JP, Gordon SP, Marcel TC, Münsterkötter M, Walter MC, Sieber CMK, Mannhaupt G, Güldener U, Kahmann R, Djamei A. A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem. eLife 2016; 5:e20522. [PMID: 27835569 PMCID: PMC5106213 DOI: 10.7554/elife.20522] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/12/2016] [Indexed: 11/18/2022] Open
Abstract
Due to their economic relevance, the study of plant pathogen interactions is of importance. However, elucidating these interactions and their underlying molecular mechanisms remains challenging since both host and pathogen need to be fully genetically accessible organisms. Here we present milestones in the establishment of a new biotrophic model pathosystem: Ustilago bromivora and Brachypodium sp. We provide a complete toolset, including an annotated fungal genome and methods for genetic manipulation of the fungus and its host plant. This toolset will enable researchers to easily study biotrophic interactions at the molecular level on both the pathogen and the host side. Moreover, our research on the fungal life cycle revealed a mating type bias phenomenon. U. bromivora harbors a haplo-lethal allele that is linked to one mating type region. As a result, the identified mating type bias strongly promotes inbreeding, which we consider to be a potential speciation driver.
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Affiliation(s)
- Franziska Rabe
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jason Bosch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Alexandra Stirnberg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Tilo Guse
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Lisa Bauer
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Denise Seitner
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Fernando A Rabanal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | | | - Simon Uhse
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Janos Bindics
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Bianca Genenncher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Fernando Navarrete
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Ronny Kellner
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Heinz Ekker
- Vienna Biocenter Core Facilities GmbH, Vienna, Austria
| | - Jochen Kumlehn
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
| | - John P Vogel
- DOE Joint Genome Institute, California, United States
| | - Sean P Gordon
- DOE Joint Genome Institute, California, United States
| | - Thierry C Marcel
- INRA UMR BIOGER, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mathias C Walter
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Christian MK Sieber
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gertrud Mannhaupt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ulrich Güldener
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Armin Djamei
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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104
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Toh SS, Perlin MH. Resurgence of Less-Studied Smut Fungi as Models of Phytopathogenesis in the Omics Age. PHYTOPATHOLOGY 2016; 106:1244-1254. [PMID: 27111800 DOI: 10.1094/phyto-02-16-0075-rvw] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The smut fungi form a large, diverse, and nonmonophyletic group of plant pathogens that have long served as both important pests of human agriculture and, also, as fertile organisms of scientific investigation. As modern techniques of molecular genetic analysis became available, many previously studied species that proved refractive to these techniques fell by the wayside and were neglected. Now, as the advent of rapid and affordable next-generation sequencing provides genomic and transcriptomic resources for even these "forgotten" fungi, several species are making a comeback and retaking prominent places in phytopathogenic research. In this review, we highlight several of these smut fungi, with special emphasis on Microbotryum lychnidis-dioicae, an anther smut whose molecular genetic tools have finally begun to catch up with its historical importance in classical genetics and now provide mechanistic insights for ecological studies, evolution of host-pathogen interaction, and investigations of emerging infectious disease.
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Affiliation(s)
- Su San Toh
- First and second authors: Department of Biology and Program on Disease Evolution, University of Louisville, Kentucky; and first author: Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore
| | - Michael H Perlin
- First and second authors: Department of Biology and Program on Disease Evolution, University of Louisville, Kentucky; and first author: Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore
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105
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Gibriel HAY, Thomma BPHJ, Seidl MF. The Age of Effectors: Genome-Based Discovery and Applications. PHYTOPATHOLOGY 2016; 106:1206-1212. [PMID: 27050568 DOI: 10.1094/phyto-02-16-0110-fi] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Microbial pathogens cause devastating diseases on economically and ecologically important plant species, threatening global food security, and causing billions of dollars of losses annually. During the infection process, pathogens secrete so-called effectors that support host colonization, often by deregulating host immune responses. Over the last decades, much of the research on molecular plant-microbe interactions has focused on the identification and functional characterization of such effectors. The increasing availability of sequenced plant pathogen genomes has enabled genomics-based discovery of effector candidates. Nevertheless, identification of full plant pathogen effector repertoires is often hampered by erroneous gene annotation and the localization effector genes in genomic regions that are notoriously difficult to assemble. Here, we argue that recent advances in genome sequencing technologies, genome assembly, gene annotation, as well as effector identification methods hold promise to disclose complete and correct effector repertoires. This allows to exploit complete effector repertoires, and knowledge of their diversity within pathogen populations, to develop durable and sustainable resistance breeding strategies, disease control, and management of plant pathogens.
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Affiliation(s)
- Hesham A Y Gibriel
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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106
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Sesma A. RNA metabolism and regulation of virulence programs in fungi. Semin Cell Dev Biol 2016; 57:120-127. [DOI: 10.1016/j.semcdb.2016.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 01/16/2023]
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107
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Cervantes-Montelongo JA, Aréchiga-Carvajal ET, Ruiz-Herrera J. Adaptation ofUstilago maydisto extreme pH values: A transcriptomic analysis. J Basic Microbiol 2016; 56:1222-1233. [DOI: 10.1002/jobm.201600130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/06/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Juan Antonio Cervantes-Montelongo
- Departamento de Ingeniería Genética, Unidad Irapuato; Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional; Irapuato Gto. México
| | - Elva Teresa Aréchiga-Carvajal
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Biológicas, Laboratorio de Micología y Fitopatología; Unidad de Manipulación Genética, San Nicolás de los Garza; Nuevo León México
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato; Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional; Irapuato Gto. México
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108
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Tollot M, Assmann D, Becker C, Altmüller J, Dutheil JY, Wegner CE, Kahmann R. The WOPR Protein Ros1 Is a Master Regulator of Sporogenesis and Late Effector Gene Expression in the Maize Pathogen Ustilago maydis. PLoS Pathog 2016; 12:e1005697. [PMID: 27332891 PMCID: PMC4917244 DOI: 10.1371/journal.ppat.1005697] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/20/2016] [Indexed: 12/31/2022] Open
Abstract
The biotrophic basidiomycete fungus Ustilago maydis causes smut disease in maize. Hallmarks of the disease are large tumors that develop on all aerial parts of the host in which dark pigmented teliospores are formed. We have identified a member of the WOPR family of transcription factors, Ros1, as major regulator of spore formation in U. maydis. ros1 expression is induced only late during infection and hence Ros1 is neither involved in plant colonization of dikaryotic fungal hyphae nor in plant tumor formation. However, during late stages of infection Ros1 is essential for fungal karyogamy, massive proliferation of diploid fungal cells and spore formation. Premature expression of ros1 revealed that Ros1 counteracts the b-dependent filamentation program and induces morphological alterations resembling the early steps of sporogenesis. Transcriptional profiling and ChIP-seq analyses uncovered that Ros1 remodels expression of about 30% of all U. maydis genes with 40% of these being direct targets. In total the expression of 80 transcription factor genes is controlled by Ros1. Four of the upregulated transcription factor genes were deleted and two of the mutants were affected in spore development. A large number of b-dependent genes were differentially regulated by Ros1, suggesting substantial changes in this regulatory cascade that controls filamentation and pathogenic development. Interestingly, 128 genes encoding secreted effectors involved in the establishment of biotrophic development were downregulated by Ros1 while a set of 70 “late effectors” was upregulated. These results indicate that Ros1 is a master regulator of late development in U. maydis and show that the biotrophic interaction during sporogenesis involves a drastic shift in expression of the fungal effectome including the downregulation of effectors that are essential during early stages of infection. The fungus Ustilago maydis is a pathogen of maize which induces tumor formation in the infected tissue. In these tumors huge amounts of fungal spores develop. As a biotrophic pathogen, U. maydis establishes itself in the plant with the help of a large number of secreted effector proteins. Many effector proteins are important for virulence because they counteract plant defense reactions. In this manuscript we have identified and characterized Ros1, a master regulator for the late stages of U. maydis development. This transcription factor is expressed late during infection and controls nuclear fusion, hyphal aggregation and late proliferation. ros1 mutants are still able to induce tumor formation but these are a dead end because they do not contain any spores. We show that Ros1 interferes with the early regulatory cascade controlled by a complex of two homeodomain proteins. In addition, Ros1 triggers a major switch in the effector repertoire, suggesting that different sets of effectors are needed for different stages of fungal development inside the plant.
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Affiliation(s)
- Marie Tollot
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Daniela Assmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Christian Becker
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Julien Y. Dutheil
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Carl-Eric Wegner
- Max Planck Institute for Terrestrial Microbiology, Deparment of Biogeochemistry, Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
- * E-mail:
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109
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Hwang IS, Ahn IP. Multi-Homologous Recombination-Based Gene Manipulation in the Rice Pathogen Fusarium fujikuroi. THE PLANT PATHOLOGY JOURNAL 2016; 32:173-181. [PMID: 27298592 PMCID: PMC4892813 DOI: 10.5423/ppj.oa.12.2015.0263] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/04/2016] [Accepted: 02/10/2016] [Indexed: 06/06/2023]
Abstract
Gene disruption by homologous recombination is widely used to investigate and analyze the function of genes in Fusarium fujikuroi, a fungus that causes bakanae disease and root rot symptoms in rice. To generate gene deletion constructs, the use of conventional cloning methods, which rely on restriction enzymes and ligases, has had limited success due to a lack of unique restriction enzyme sites. Although strategies that avoid the use of restriction enzymes have been employed to overcome this issue, these methods require complicated PCR steps or are frequently inefficient. Here, we introduce a cloning system that utilizes multi-fragment assembly by In-Fusion to generate a gene disruption construct. This method utilizes DNA fragment fusion and requires only one PCR step and one reaction for construction. Using this strategy, a gene disruption construct for Fusarium cyclin C1 (FCC1 ), which is associated with fumonisin B1 biosynthesis, was successfully created and used for fungal transformation. In vivo and in vitro experiments using confirmed fcc1 mutants suggest that fumonisin production is closely related to disease symptoms exhibited by F. fujikuroi strain B14. Taken together, this multi-fragment assembly method represents a simpler and a more convenient process for targeted gene disruption in fungi.
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Affiliation(s)
| | - Il-Pyung Ahn
- Corresponding author. Phone) +82-63-238-4668, FAX) +82-63-238-4654, E-mail)
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110
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Poloni A, Schirawski J. Host specificity in Sporisorium reilianum is determined by distinct mechanisms in maize and sorghum. MOLECULAR PLANT PATHOLOGY 2016; 17:741-54. [PMID: 26419898 PMCID: PMC6638427 DOI: 10.1111/mpp.12326] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Smut fungi are biotrophic plant pathogens that exhibit a very narrow host range. The smut fungus Sporisorium reilianum exists in two host-adapted formae speciales: S. reilianum f. sp. reilianum (SRS), which causes head smut of sorghum, and S. reilianum f. sp. zeae (SRZ), which induces disease on maize. It is unknown why the two formae speciales cannot form spores on their respective non-favoured hosts. By fungal DNA quantification and fluorescence microscopy of stained plant samples, we followed the colonization behaviour of both SRS and SRZ on sorghum and maize. Both formae speciales were able to penetrate and multiply in the leaves of both hosts. In sorghum, the hyphae of SRS reached the apical meristems, whereas the hyphae of SRZ did not. SRZ strongly induced several defence responses in sorghum, such as the generation of H2 O2 , callose and phytoalexins, whereas the hyphae of SRS did not. In maize, both SRS and SRZ were able to spread through the plant to the apical meristem. Transcriptome analysis of colonized maize leaves revealed more genes induced by SRZ than by SRS, with many of them being involved in defence responses. Amongst the maize genes specifically induced by SRS were 11 pentatricopeptide repeat proteins. Together with the microscopic analysis, these data indicate that SRZ succumbs to plant defence after sorghum penetration, whereas SRS proliferates in a relatively undisturbed manner, but non-efficiently, on maize. This shows that host specificity is determined by distinct mechanisms in sorghum and maize.
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Affiliation(s)
- Alana Poloni
- Albrecht-von-Haller Institute for Plant Sciences, Department for Molecular Biology of Plant-Microbe Interaction, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077, Göttingen, Germany
- Institute of Applied Microbiology, Department of Microbial Genetics, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Jan Schirawski
- Albrecht-von-Haller Institute for Plant Sciences, Department for Molecular Biology of Plant-Microbe Interaction, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077, Göttingen, Germany
- Institute of Applied Microbiology, Department of Microbial Genetics, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
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111
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Zhong Z, Norvienyeku J, Chen M, Bao J, Lin L, Chen L, Lin Y, Wu X, Cai Z, Zhang Q, Lin X, Hong Y, Huang J, Xu L, Zhang H, Chen L, Tang W, Zheng H, Chen X, Wang Y, Lian B, Zhang L, Tang H, Lu G, Ebbole DJ, Wang B, Wang Z. Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species. Sci Rep 2016; 6:25591. [PMID: 27151494 PMCID: PMC4858695 DOI: 10.1038/srep25591] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/20/2016] [Indexed: 02/07/2023] Open
Abstract
One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants.
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Affiliation(s)
- Zhenhui Zhong
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Justice Norvienyeku
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meilian Chen
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiandong Bao
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianyu Lin
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liqiong Chen
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yahong Lin
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoxian Wu
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zena Cai
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qi Zhang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoye Lin
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yonghe Hong
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jun Huang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Linghong Xu
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Honghong Zhang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Long Chen
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Tang
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huakun Zheng
- Haixia Institute of Science and Technology (HIST), Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaofeng Chen
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanli Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Bi Lian
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangsheng Zhang
- Haixia Institute of Science and Technology (HIST), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haibao Tang
- Haixia Institute of Science and Technology (HIST), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guodong Lu
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Daniel J. Ebbole
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Baohua Wang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zonghua Wang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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112
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Selin C, de Kievit TR, Belmonte MF, Fernando WGD. Elucidating the Role of Effectors in Plant-Fungal Interactions: Progress and Challenges. Front Microbiol 2016; 7:600. [PMID: 27199930 PMCID: PMC4846801 DOI: 10.3389/fmicb.2016.00600] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
Pathogenic fungi have diverse growth lifestyles that support fungal colonization on plants. Successful colonization and infection for all lifestyles depends upon the ability to modify living host plants to sequester the necessary nutrients required for growth and reproduction. Secretion of virulence determinants referred to as “effectors” is assumed to be the key governing factor that determines host infection and colonization. Effector proteins are capable of suppressing plant defense responses and alter plant physiology to accommodate fungal invaders. This review focuses on effector molecules of biotrophic and hemibiotrophic plant pathogenic fungi, and the mechanism required for the release and uptake of effector molecules by the fungi and plant cells, respectively. We also place emphasis on the discovery of effectors, difficulties associated with predicting the effector repertoire, and fungal genomic features that have helped promote effector diversity leading to fungal evolution. We discuss the role of specific effectors found in biotrophic and hemibiotrophic fungi and examine how CRISPR/Cas9 technology may provide a new avenue for accelerating our ability in the discovery of fungal effector function.
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Affiliation(s)
- Carrie Selin
- Department of Plant Science, University of Manitoba Winnipeg, MB, Canada
| | | | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba Winnipeg, MB, Canada
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113
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Álvarez-Cervantes J, Díaz-Godínez G, Mercado-Flores Y, Gupta VK, Anducho-Reyes MA. Phylogenetic analysis of β-xylanase SRXL1 of Sporisorium reilianum and its relationship with families (GH10 and GH11) of Ascomycetes and Basidiomycetes. Sci Rep 2016; 6:24010. [PMID: 27040368 PMCID: PMC4819176 DOI: 10.1038/srep24010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/17/2016] [Indexed: 11/10/2022] Open
Abstract
In this paper, the amino acid sequence of the β-xylanase SRXL1 of Sporisorium reilianum, which is a pathogenic fungus of maize was used as a model protein to find its phylogenetic relationship with other xylanases of Ascomycetes and Basidiomycetes and the information obtained allowed to establish a hypothesis of monophyly and of biological role. 84 amino acid sequences of β-xylanase obtained from the GenBank database was used. Groupings analysis of higher-level in the Pfam database allowed to determine that the proteins under study were classified into the GH10 and GH11 families, based on the regions of highly conserved amino acids, 233-318 and 180-193 respectively, where glutamate residues are responsible for the catalysis.
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Affiliation(s)
| | - Gerardo Díaz-Godínez
- Laboratory of Biotechnology, Research Center for Biological Sciences, Universidad Autónoma de Tlaxcala, Tlaxcala, México
| | | | - Vijai Kumar Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
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114
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Dutheil JY, Mannhaupt G, Schweizer G, M K Sieber C, Münsterkötter M, Güldener U, Schirawski J, Kahmann R. A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi. Genome Biol Evol 2016; 8:681-704. [PMID: 26872771 PMCID: PMC4824034 DOI: 10.1093/gbe/evw026] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Smut fungi are plant pathogens mostly parasitizing wild species of grasses as well as domesticated cereal crops. Genome analysis of several smut fungi including Ustilago maydis revealed a singular clustered organization of genes encoding secreted effectors. In U. maydis, many of these clusters have a role in virulence. Reconstructing the evolutionary history of clusters of effector genes is difficult because of their intrinsically fast evolution, which erodes the phylogenetic signal and homology relationships. Here, we describe the use of comparative evolutionary analyses of quality draft assemblies of genomes to study the mechanisms of this evolution. We report the genome sequence of a South African isolate of Sporisorium scitamineum, a smut fungus parasitizing sugar cane with a phylogenetic position intermediate to the two previously sequenced species U. maydis and Sporisorium reilianum. We show that the genome of S. scitamineum contains more and larger gene clusters encoding secreted effectors than any previously described species in this group. We trace back the origin of the clusters and find that their evolution is mainly driven by tandem gene duplication. In addition, transposable elements play a major role in the evolution of the clustered genes. Transposable elements are significantly associated with clusters of genes encoding fast evolving secreted effectors. This suggests that such clusters represent a case of genome compartmentalization that restrains the activity of transposable elements on genes under diversifying selection for which this activity is potentially beneficial, while protecting the rest of the genome from its deleterious effect.
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Affiliation(s)
- Julien Y Dutheil
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gertrud Mannhaupt
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gabriel Schweizer
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Christian M K Sieber
- German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Münsterkötter
- German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ulrich Güldener
- German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jan Schirawski
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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115
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Lyu X, Shen C, Fu Y, Xie J, Jiang D, Li G, Cheng J. A Small Secreted Virulence-Related Protein Is Essential for the Necrotrophic Interactions of Sclerotinia sclerotiorum with Its Host Plants. PLoS Pathog 2016; 12:e1005435. [PMID: 26828434 PMCID: PMC4735494 DOI: 10.1371/journal.ppat.1005435] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/11/2016] [Indexed: 12/28/2022] Open
Abstract
Small, secreted proteins have been found to play crucial roles in interactions between biotrophic/hemi-biotrophic pathogens and plants. However, little is known about the roles of these proteins produced by broad host-range necrotrophic phytopathogens during infection. Here, we report that a cysteine-rich, small protein SsSSVP1 in the necrotrophic phytopathogen Sclerotinia sclerotiorum was experimentally confirmed to be a secreted protein, and the secretion of SsSSVP1 from hyphae was followed by internalization and cell-to-cell movement independent of a pathogen in host cells. SsSSVP1∆SP could induce significant plant cell death and targeted silencing of SsSSVP1 resulted in a significant reduction in virulence. Through yeast two-hybrid (Y2H), coimmunoprecipitation (co-IP) and bimolecular fluorescence complementation (BiFC) assays, we demonstrated that SsSSVP1∆SP interacted with QCR8, a subunit of the cytochrome b-c1 complex of mitochondrial respiratory chain in plants. Double site-directed mutagenesis of two cysteine residues (C38 and C44) in SsSSVP1∆SP had significant effects on its homo-dimer formation, SsSSVP1∆SP-QCR8 interaction and plant cell death induction, indicating that partial cysteine residues surely play crucial roles in maintaining the structure and function of SsSSVP1. Co-localization and BiFC assays showed that SsSSVP1∆SP might hijack QCR8 to cytoplasm before QCR8 targeting into mitochondria, thereby disturbing its subcellular localization in plant cells. Furthermore, virus induced gene silencing (VIGS) of QCR8 in tobacco caused plant abnormal development and cell death, indicating the cell death induced by SsSSVP1∆SP might be caused by the SsSSVP1∆SP-QCR8 interaction, which had disturbed the QCR8 subcellular localization and hence disabled its biological functions. These results suggest that SsSSVP1 is a potential effector which may manipulate plant energy metabolism to facilitate the infection of S. sclerotiorum. Our findings indicate novel roles of small secreted proteins in the interactions between host-non-specific necrotrophic fungi and plants, and highlight the significance to illuminate the pathogenic mechanisms of this type of interaction.
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Affiliation(s)
- Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Cuicui Shen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Jiatao Xie
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
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116
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Lo Presti L, López Díaz C, Turrà D, Di Pietro A, Hampel M, Heimel K, Kahmann R. A conserved co-chaperone is required for virulence in fungal plant pathogens. THE NEW PHYTOLOGIST 2016; 209:1135-1148. [PMID: 26487566 DOI: 10.1111/nph.13703] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/04/2015] [Indexed: 06/05/2023]
Abstract
The maize pathogenic fungus Ustilago maydis experiences endoplasmic reticulum (ER) stress during plant colonization and relies on the unfolded protein response (UPR) to cope with this stress. We identified the U. maydis co-chaperone, designated Dnj1, as part of this conserved cellular response to ER stress. ∆dnj1 cells are sensitive to the ER stressor tunicamycin and display a severe virulence defect in maize infection assays. A dnj1 mutant allele unable to stimulate the ATPase activity of chaperones phenocopies the null allele. A Dnj1-mCherry fusion protein localizes in the ER and interacts with the luminal chaperone Bip1. The Fusarium oxysporum Dnj1 ortholog contributes to the virulence of this fungal pathogen in tomato plants. Unlike the human ortholog, F. oxysporum Dnj1 partially rescues the virulence defect of the Ustilago dnj1 mutant. By enabling the fungus to restore ER homeostasis and maintain a high secretory activity, Dnj1 contributes to the establishment of a compatible interaction with the host. Dnj1 orthologs are present in many filamentous fungi, but are absent in budding and fission yeasts. We postulate a conserved and essential role during virulence for this class of co-chaperones.
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Affiliation(s)
- Libera Lo Presti
- Max Planck Institute for Terrestrial Microbiology, Karl-von Frisch-Strasse 10, 35043, Marburg, Germany
| | - Cristina López Díaz
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071, Cordoba, Spain
| | - David Turrà
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071, Cordoba, Spain
| | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071, Cordoba, Spain
| | - Martin Hampel
- Department of Molecular Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Kai Heimel
- Department of Molecular Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von Frisch-Strasse 10, 35043, Marburg, Germany
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117
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Yan M, Zhu G, Lin S, Xian X, Chang C, Xi P, Shen W, Huang W, Cai E, Jiang Z, Deng YZ, Zhang LH. The mating-type locus b of the sugarcane smut Sporisorium scitamineum is essential for mating, filamentous growth and pathogenicity. Fungal Genet Biol 2016; 86:1-8. [DOI: 10.1016/j.fgb.2015.11.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/07/2015] [Accepted: 11/07/2015] [Indexed: 11/29/2022]
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118
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Kim KT, Jeon J, Choi J, Cheong K, Song H, Choi G, Kang S, Lee YH. Kingdom-Wide Analysis of Fungal Small Secreted Proteins (SSPs) Reveals their Potential Role in Host Association. FRONTIERS IN PLANT SCIENCE 2016; 7:186. [PMID: 26925088 PMCID: PMC4759460 DOI: 10.3389/fpls.2016.00186] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 02/03/2016] [Indexed: 05/18/2023]
Abstract
Fungal secretome consists of various functional groups of proteins, many of which participate in nutrient acquisition, self-protection, or manipulation of the environment and neighboring organisms. The least characterized component of the secretome is small secreted proteins (SSPs). Some SSPs have been reported to function as effectors, but most remain to be characterized. The composition of major secretome components, such as carbohydrate-active enzymes, proteases, lipases, and oxidoreductases, appear to reflect the lifestyle and ecological niche of individual species. We hypothesize that many SSPs participate in manipulating plants as effectors. Obligate biotrophs likely encode more and diverse effector-like SSPs to suppress host defense compared to necrotrophs, which generally use cell wall degrading enzymes and phytotoxins to kill hosts. Because different secretome prediction workflows have been used in different studies, available secretome data are difficult to integrate for comprehensive comparative studies to test this hypothesis. In this study, SSPs encoded by 136 fungal species were identified from data archived in Fungal Secretome Database (FSD) via a refined secretome workflow. Subsequently, compositions of SSPs and other secretome components were compared in light of taxa and lifestyles. Those species that are intimately associated with host cells, such as biotrophs and symbionts, usually have higher proportion of species-specific SSPs (SSSPs) than hemibiotrophs and necrotrophs, but the latter groups displayed higher proportions of secreted enzymes. Results from our study established a foundation for functional studies on SSPs and will also help understand genomic changes potentially underpinning different fungal lifestyles.
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Affiliation(s)
- Ki-Tae Kim
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Department of Agricultural Biotechnology, Seoul National UniversitySeoul, South Korea
| | - Jongbum Jeon
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Jaeyoung Choi
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Kyeongchae Cheong
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Hyeunjeong Song
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Gobong Choi
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State UniversityUniversity Park, PA, USA
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Department of Agricultural Biotechnology, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
- Center for Fungal Genetic Resources, Center for Fungal Pathogenesis, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
- *Correspondence: Yong-Hwan Lee
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119
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Druzhinina IS, Kopchinskiy AG, Kubicek EM, Kubicek CP. A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:75. [PMID: 27030800 PMCID: PMC4812632 DOI: 10.1186/s13068-016-0488-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/15/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Investigations on a few eukaryotic model organisms showed that many genes are non-randomly distributed on chromosomes. In addition, chromosome ends frequently possess genes that are important for the fitness of the organisms. Trichoderma reesei is an industrial producer of enzymes for food, feed and biorefinery production. Its seven chromosomes have recently been assembled, thus making an investigation of its chromosome architecture possible. RESULTS We manually annotated and mapped 9194 ORFs on their respective chromosomes and investigated the clustering of the major gene categories and of genes encoding carbohydrate-active enzymes (CAZymes), and the relationship between clustering and expression. Genes responsible for RNA processing and modification, amino acid metabolism, transcription, translation and ribosomal structure and biogenesis indeed showed loose clustering, but this had no impact on their expression. A third of the genes encoding CAZymes also occurred in loose clusters that also contained a high number of genes encoding small secreted cysteine-rich proteins. Five CAZyme clusters were located less than 50 kb apart from the chromosome ends. These genes exhibited the lowest basal (but not induced) expression level, which correlated with an enrichment of H3K9 methylation in the terminal 50 kb areas indicating gene silencing. No differences were found in the expression of CAZyme genes present in other parts of the chromosomes. The putative subtelomeric areas were also enriched in genes encoding secreted proteases, amino acid permeases, enzyme clusters for polyketide synthases (PKS)-non-ribosomal peptide synthase (NRPS) fusion proteins (PKS-NRPS) and proteins involved in iron scavenging. They were strongly upregulated during conidiation and interaction with other fungi. CONCLUSIONS Our findings suggest that gene clustering on the T. reesei chromosomes occurs but generally has no impact on their expression. CAZyme genes, located in subtelomers, however, exhibited a much lower basal expression level. The gene inventory of the subtelomers suggests a major role of competition for nitrogen and iron supported by antibiosis for the fitness of T. reesei. The availability of fully annotated chromosomes will facilitate the use of genetic crossings in identifying still unknown genes responsible for specific traits of T. reesei.
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Affiliation(s)
- Irina S. Druzhinina
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
| | - Alexey G. Kopchinskiy
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
| | - Eva M. Kubicek
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
- />Steinschötelgasse 7, 1100 Vienna, Austria
| | - Christian P. Kubicek
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
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120
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Qhanya LB, Matowane G, Chen W, Sun Y, Letsimo EM, Parvez M, Yu JH, Mashele SS, Syed K. Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens. PLoS One 2015; 10:e0142100. [PMID: 26536121 PMCID: PMC4633277 DOI: 10.1371/journal.pone.0142100] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022] Open
Abstract
Fungi are an exceptional source of diverse and novel cytochrome P450 monooxygenases (P450s), heme-thiolate proteins, with catalytic versatility. Agaricomycotina saprophytes have yielded most of the available information on basidiomycete P450s. This resulted in observing similar P450 family types in basidiomycetes with few differences in P450 families among Agaricomycotina saprophytes. The present study demonstrated the presence of unique P450 family patterns in basidiomycete biotrophic plant pathogens that could possibly have originated from the adaptation of these species to different ecological niches (host influence). Systematic analysis of P450s in basidiomycete biotrophic plant pathogens belonging to three different orders, Agaricomycotina (Armillaria mellea), Pucciniomycotina (Melampsora laricis-populina, M. lini, Mixia osmundae and Puccinia graminis) and Ustilaginomycotina (Ustilago maydis, Sporisorium reilianum and Tilletiaria anomala), revealed the presence of numerous putative P450s ranging from 267 (A. mellea) to 14 (M. osmundae). Analysis of P450 families revealed the presence of 41 new P450 families and 27 new P450 subfamilies in these biotrophic plant pathogens. Order-level comparison of P450 families between biotrophic plant pathogens revealed the presence of unique P450 family patterns in these organisms, possibly reflecting the characteristics of their order. Further comparison of P450 families with basidiomycete non-pathogens confirmed that biotrophic plant pathogens harbour the unique P450 families in their genomes. The CYP63, CYP5037, CYP5136, CYP5137 and CYP5341 P450 families were expanded in A. mellea when compared to other Agaricomycotina saprophytes and the CYP5221 and CYP5233 P450 families in P. graminis and M. laricis-populina. The present study revealed that expansion of these P450 families is due to paralogous evolution of member P450s. The presence of unique P450 families in these organisms serves as evidence of how a host/ecological niche can influence shaping the P450 content of an organism. The present study initiates our understanding of P450 family patterns in basidiomycete biotrophic plant pathogens.
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Affiliation(s)
- Lehlohonolo Benedict Qhanya
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Godfrey Matowane
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Yuxin Sun
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Elizabeth Mpholoseng Letsimo
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Mohammad Parvez
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI, 53706, United States of America
| | - Samson Sitheni Mashele
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Khajamohiddin Syed
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
- * E-mail:
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121
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Sharma R, Xia X, Riess K, Bauer R, Thines M. Comparative Genomics Including the Early-Diverging Smut Fungus Ceraceosorus bombacis Reveals Signatures of Parallel Evolution within Plant and Animal Pathogens of Fungi and Oomycetes. Genome Biol Evol 2015; 7:2781-98. [PMID: 26314305 PMCID: PMC4607519 DOI: 10.1093/gbe/evv162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, the genome of C. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 Mb encodes for 8,024 proteins, of which 576 are putative-secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in C. bombacis compared with other Ustilaginomycotina genomes. Metabolic pathway analyses revealed the absence of genes encoding for nitrite and nitrate reductase in the genome of the human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, while nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed for obligate biotrophic and hemi-biotrophic fungal and oomycete pathogens. Furthermore, it was found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany Cluster for Integrative Fungal Research (IPF), Frankfurt (Main), Germany
| | - Xiaojuan Xia
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany
| | - Kai Riess
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Robert Bauer
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany Cluster for Integrative Fungal Research (IPF), Frankfurt (Main), Germany
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Schuster M, Schweizer G, Reissmann S, Kahmann R. Genome editing in Ustilago maydis using the CRISPR-Cas system. Fungal Genet Biol 2015; 89:3-9. [PMID: 26365384 DOI: 10.1016/j.fgb.2015.09.001] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/26/2022]
Abstract
This communication describes the establishment of the type II bacterial CRISPR-Cas9 system to efficiently disrupt target genes in the fungal maize pathogen Ustilago maydis. A single step transformation of a self-replicating plasmid constitutively expressing the U. maydis codon-optimized cas9 gene and a suitable sgRNA under control of the U. maydis U6 snRNA promoter was sufficient to induce genome editing. On average 70% of the progeny of a single transformant were disrupted within the respective b gene. Without selection the self-replicating plasmid was lost rapidly allowing transient expression of the CRISPR-Cas9 system to minimize potential long-term negative effects of Cas9. This technology will be an important advance for the simultaneous disruption of functionally redundant genes and gene families to investigate their contribution to virulence of U. maydis.
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Affiliation(s)
- Mariana Schuster
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Gabriel Schweizer
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Stefanie Reissmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany.
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Experimental approaches to investigate effector translocation into host cells in the Ustilago maydis/maize pathosystem. Eur J Cell Biol 2015; 94:349-58. [PMID: 26118724 DOI: 10.1016/j.ejcb.2015.06.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The fungus Ustilago maydis is a pathogen that establishes a biotrophic interaction with Zea mays. The interaction with the plant host is largely governed by more than 300 novel, secreted protein effectors, of which only four have been functionally characterized. Prerequisite to examine effector function is to know where effectors reside after secretion. Effectors can remain in the extracellular space, i.e. the plant apoplast (apoplastic effectors), or can cross the plant plasma membrane and exert their function inside the host cell (cytoplasmic effectors). The U. maydis effectors lack conserved motifs in their primary sequences that could allow a classification of the effectome into apoplastic/cytoplasmic effectors. This represents a significant obstacle in functional effector characterization. Here we describe our attempts to establish a system for effector classification into apoplastic and cytoplasmic members, using U. maydis for effector delivery.
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Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane. PLoS One 2015; 10:e0129318. [PMID: 26065709 PMCID: PMC4466345 DOI: 10.1371/journal.pone.0129318] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/08/2015] [Indexed: 12/21/2022] Open
Abstract
Sporisorium scitamineum is a biotrophic fungus responsible for the sugarcane smut, a worldwide spread disease. This study provides the complete sequence of individual chromosomes of S. scitamineum from telomere to telomere achieved by a combination of PacBio long reads and Illumina short reads sequence data, as well as a draft sequence of a second fungal strain. Comparative analysis to previous available sequences of another strain detected few polymorphisms among the three genomes. The novel complete sequence described herein allowed us to identify and annotate extended subtelomeric regions, repetitive elements and the mitochondrial DNA sequence. The genome comprises 19,979,571 bases, 6,677 genes encoding proteins, 111 tRNAs and 3 assembled copies of rDNA, out of our estimated number of copies as 130. Chromosomal reorganizations were detected when comparing to sequences of S. reilianum, the closest smut relative, potentially influenced by repeats of transposable elements. Repetitive elements may have also directed the linkage of the two mating-type loci. The fungal transcriptome profiling from in vitro and from interaction with sugarcane at two time points (early infection and whip emergence) revealed that 13.5% of the genes were differentially expressed in planta and particular to each developmental stage. Among them are plant cell wall degrading enzymes, proteases, lipases, chitin modification and lignin degradation enzymes, sugar transporters and transcriptional factors. The fungus also modulates transcription of genes related to surviving against reactive oxygen species and other toxic metabolites produced by the plant. Previously described effectors in smut/plant interactions were detected but some new candidates are proposed. Ten genomic islands harboring some of the candidate genes unique to S. scitamineum were expressed only in planta. RNAseq data was also used to reassure gene predictions.
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125
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Kemen AC, Agler MT, Kemen E. Host-microbe and microbe-microbe interactions in the evolution of obligate plant parasitism. THE NEW PHYTOLOGIST 2015; 206:1207-28. [PMID: 25622918 DOI: 10.1111/nph.13284] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/12/2014] [Indexed: 05/03/2023]
Abstract
Research on obligate biotrophic plant parasites, which reproduce only on living hosts, has revealed a broad diversity of filamentous microbes that have independently acquired complex morphological structures, such as haustoria. Genome studies have also demonstrated a concerted loss of genes for metabolism and lytic enzymes, and gain of diversity of genes coding for effectors involved in host defense suppression. So far, these traits converge in all known obligate biotrophic parasites, but unexpected genome plasticity remains. This plasticity is manifested as transposable element (TE)-driven increases in genome size, observed to be associated with the diversification of virulence genes under selection pressure. Genome expansion could result from the governing of the pathogen response to ecological selection pressures, such as host or nutrient availability, or to microbial interactions, such as competition, hyperparasitism and beneficial cooperations. Expansion is balanced by alternating sexual and asexual cycles, as well as selfing and outcrossing, which operate to control transposon activity in populations. In turn, the prevalence of these balancing mechanisms seems to be correlated with external biotic factors, suggesting a complex, interconnected evolutionary network in host-pathogen-microbe interactions. Therefore, the next phase of obligate biotrophic pathogen research will need to uncover how this network, including multitrophic interactions, shapes the evolution and diversity of pathogens.
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Affiliation(s)
- Ariane C Kemen
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany
| | - Matthew T Agler
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany
| | - Eric Kemen
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany
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126
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Ludwig-Müller J, Jülke S, Geiß K, Richter F, Mithöfer A, Šola I, Rusak G, Keenan S, Bulman S. A novel methyltransferase from the intracellular pathogen Plasmodiophora brassicae methylates salicylic acid. MOLECULAR PLANT PATHOLOGY 2015; 16:349-64. [PMID: 25135243 PMCID: PMC6638400 DOI: 10.1111/mpp.12185] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The obligate biotrophic pathogen Plasmodiophora brassicae causes clubroot disease in Arabidopsis thaliana, which is characterized by large root galls. Salicylic acid (SA) production is a defence response in plants, and its methyl ester is involved in systemic signalling. Plasmodiophora brassicae seems to suppress plant defence reactions, but information on how this is achieved is scarce. Here, we profile the changes in SA metabolism during Arabidopsis clubroot disease. The accumulation of SA and the emission of methylated SA (methyl salicylate, MeSA) were observed in P. brassicae-infected Arabidopsis 28 days after inoculation. There is evidence that MeSA is transported from infected roots to the upper plant. Analysis of the mutant Atbsmt1, deficient in the methylation of SA, indicated that the Arabidopsis SA methyltransferase was not responsible for alterations in clubroot symptoms. We found that P. brassicae possesses a methyltransferase (PbBSMT) with homology to plant methyltransferases. The PbBSMT gene is maximally transcribed when SA production is highest. By heterologous expression and enzymatic analyses, we showed that PbBSMT can methylate SA, benzoic and anthranilic acids.
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Affiliation(s)
- Jutta Ludwig-Müller
- Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany
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127
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Hemetsberger C, Mueller AN, Matei A, Herrberger C, Hensel G, Kumlehn J, Mishra B, Sharma R, Thines M, Hückelhoven R, Doehlemann G. The fungal core effector Pep1 is conserved across smuts of dicots and monocots. THE NEW PHYTOLOGIST 2015; 206:1116-1126. [PMID: 25628012 DOI: 10.1111/nph.13304] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/16/2014] [Indexed: 05/03/2023]
Abstract
The secreted fungal effector Pep1 is essential for penetration of the host epidermis and establishment of biotrophy in the Ustilago maydis-maize pathosystem. Previously, Pep1 was found to be an inhibitor of apoplastic plant peroxidases, which suppresses the oxidative burst, a primary immune response of the host plant and enables fungal colonization. To investigate the conservation of Pep1 in other pathogens, genomes of related smut species were screened for pep1 orthologues. Pep1 proteins were produced in Escherichia coli for functional assays. The biological function of Pep1 was tested by heterologous expression in U. maydis and Hordeum vulgare. Pep1 orthologues revealed a remarkable degree of sequence conservation, indicating that this effector might play a fundamental role in virulence of biotrophic smut fungi. Pep1 function and its role in virulence are conserved in different pathogenic fungi, even across the monocot-dicot border of host plants. The findings described in this study classify Pep1 as a phylogenetically conserved fungal core effector. Furthermore, we documented the influence of Pep1 on the disease caused by Blumeria graminis f. sp. hordei which is a non-smut-related pathosystem.
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Affiliation(s)
- Christoph Hemetsberger
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, D-35043, Marburg, Germany
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Str. 2, D-85350, Freising-Weihenstephan, Germany
| | - André N Mueller
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, D-35043, Marburg, Germany
| | - Alexandra Matei
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, D-35043, Marburg, Germany
| | - Christian Herrberger
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, D-35043, Marburg, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Plant Reproductive Biology, D-06466, Stadt Seeland/OT Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Plant Reproductive Biology, D-06466, Stadt Seeland/OT Gatersleben, Germany
| | - Bagdevi Mishra
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, D-60438, Frankfurt am Main, Germany
| | - Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, D-60438, Frankfurt am Main, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, D-60438, Frankfurt am Main, Germany
| | - Ralph Hückelhoven
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Str. 2, D-85350, Freising-Weihenstephan, Germany
| | - Gunther Doehlemann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, D-35043, Marburg, Germany
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Biocenter, Zuelpicher Str. 47a, 50674 Cologne, Germany
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128
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Redkar A, Hoser R, Schilling L, Zechmann B, Krzymowska M, Walbot V, Doehlemann G. A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors. THE PLANT CELL 2015; 27:1332-51. [PMID: 25888589 PMCID: PMC4558682 DOI: 10.1105/tpc.114.131086] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 03/31/2015] [Indexed: 05/15/2023]
Abstract
The biotrophic smut fungus Ustilago maydis infects all aerial organs of maize (Zea mays) and induces tumors in the plant tissues. U. maydis deploys many effector proteins to manipulate its host. Previously, deletion analysis demonstrated that several effectors have important functions in inducing tumor expansion specifically in maize leaves. Here, we present the functional characterization of the effector See1 (Seedling efficient effector1). See1 is required for the reactivation of plant DNA synthesis, which is crucial for tumor progression in leaf cells. By contrast, See1 does not affect tumor formation in immature tassel floral tissues, where maize cell proliferation occurs independent of fungal infection. See1 interacts with a maize homolog of SGT1 (Suppressor of G2 allele of skp1), a factor acting in cell cycle progression in yeast (Saccharomyces cerevisiae) and an important component of plant and human innate immunity. See1 interferes with the MAPK-triggered phosphorylation of maize SGT1 at a monocot-specific phosphorylation site. We propose that See1 interferes with SGT1 activity, resulting in both modulation of immune responses and reactivation of DNA synthesis in leaf cells. This identifies See1 as a fungal effector that directly and specifically contributes to the formation of leaf tumors in maize.
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Affiliation(s)
- Amey Redkar
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, D-35043 Marburg, Germany
| | - Rafal Hoser
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Lena Schilling
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, D-35043 Marburg, Germany
| | - Bernd Zechmann
- Baylor University, Center for Microscopy and Imaging, Waco, Texas 76798
| | - Magdalena Krzymowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, California 94305
| | - Gunther Doehlemann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, D-35043 Marburg, Germany Botanical Institute and Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
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129
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Zhao C, Escalante L, Chen H, Benatti T, Qu J, Chellapilla S, Waterhouse R, Wheeler D, Andersson M, Bao R, Batterton M, Behura S, Blankenburg K, Caragea D, Carolan J, Coyle M, El-Bouhssini M, Francisco L, Friedrich M, Gill N, Grace T, Grimmelikhuijzen C, Han Y, Hauser F, Herndon N, Holder M, Ioannidis P, Jackson L, Javaid M, Jhangiani S, Johnson A, Kalra D, Korchina V, Kovar C, Lara F, Lee S, Liu X, Löfstedt C, Mata R, Mathew T, Muzny D, Nagar S, Nazareth L, Okwuonu G, Ongeri F, Perales L, Peterson B, Pu LL, Robertson H, Schemerhorn B, Scherer S, Shreve J, Simmons D, Subramanyam S, Thornton R, Xue K, Weissenberger G, Williams C, Worley K, Zhu D, Zhu Y, Harris M, Shukle R, Werren J, Zdobnov E, Chen MS, Brown S, Stuart J, Richards S. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor. Curr Biol 2015; 25:613-20. [DOI: 10.1016/j.cub.2014.12.057] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/07/2014] [Accepted: 12/23/2014] [Indexed: 01/27/2023]
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130
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Tsai IJ, Tanaka E, Masuya H, Tanaka R, Hirooka Y, Endoh R, Sahashi N, Kikuchi T. Comparative genomics of Taphrina fungi causing varying degrees of tumorous deformity in plants. Genome Biol Evol 2015; 6:861-72. [PMID: 24682155 PMCID: PMC4007546 DOI: 10.1093/gbe/evu067] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Taphrina fungi are biotrophic plant pathogens that cause plant deformity diseases. We sequenced the genomes of four Taphrina species—Taphrina wiesneri, T. deformans, T. flavorubra, and T. populina—which parasitize Prunus, Cerasus, and Populus hosts with varying severity of disease symptoms. High levels of gene synteny within Taphrina species were observed, and our comparative analysis further revealed that these fungi may utilize multiple strategies in coping with the host environment that are also found in some specialized dimorphic species. These include species-specific aneuploidy and clusters of highly diverged secreted proteins located at subtelomeres. We also identified species differences in plant hormone biosynthesis pathways, which may contribute to varying degree of disease symptoms. The genomes provide a rich resource for investigation into Taphrina biology and evolutionary studies across the basal ascomycetes clade.
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Affiliation(s)
- Isheng J Tsai
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Japan
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131
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Lo Presti L, Lanver D, Schweizer G, Tanaka S, Liang L, Tollot M, Zuccaro A, Reissmann S, Kahmann R. Fungal effectors and plant susceptibility. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:513-45. [PMID: 25923844 DOI: 10.1146/annurev-arplant-043014-114623] [Citation(s) in RCA: 625] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants can be colonized by fungi that have adopted highly diverse lifestyles, ranging from symbiotic to necrotrophic. Colonization is governed in all systems by hundreds of secreted fungal effector molecules. These effectors suppress plant defense responses and modulate plant physiology to accommodate fungal invaders and provide them with nutrients. Fungal effectors either function in the interaction zone between the fungal hyphae and host or are transferred to plant cells. This review describes the effector repertoires of 84 plant-colonizing fungi. We focus on the mechanisms that allow these fungal effectors to promote virulence or compatibility, discuss common plant nodes that are targeted by effectors, and provide recent insights into effector evolution. In addition, we address the issue of effector uptake in plant cells and highlight open questions and future challenges.
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Affiliation(s)
- Libera Lo Presti
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; , , , , , , , ,
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132
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A maize wall-associated kinase confers quantitative resistance to head smut. Nat Genet 2014; 47:151-7. [PMID: 25531751 DOI: 10.1038/ng.3170] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 12/01/2014] [Indexed: 11/08/2022]
Abstract
Head smut is a systemic disease in maize caused by the soil-borne fungus Sporisorium reilianum that poses a grave threat to maize production worldwide. A major head smut quantitative resistance locus, qHSR1, has been detected on maize chromosome bin2.09. Here we report the map-based cloning of qHSR1 and the molecular mechanism of qHSR1-mediated resistance. Sequential fine mapping and transgenic complementation demonstrated that ZmWAK is the gene within qHSR1 conferring quantitative resistance to maize head smut. ZmWAK spans the plasma membrane, potentially serving as a receptor-like kinase to perceive and transduce extracellular signals. ZmWAK was highly expressed in the mesocotyl of seedlings where it arrested biotrophic growth of the endophytic S. reilianum. Impaired expression in the mesocotyl compromised ZmWAK-mediated resistance. Deletion of the ZmWAK locus appears to have occurred after domestication and spread among maize germplasm, and the ZmWAK kinase domain underwent functional constraints during maize evolution.
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133
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Sun PF, Fang WT, Shin LY, Wei JY, Fu SF, Chou JY. Indole-3-acetic acid-producing yeasts in the phyllosphere of the carnivorous plant Drosera indica L. PLoS One 2014; 9:e114196. [PMID: 25464336 PMCID: PMC4252105 DOI: 10.1371/journal.pone.0114196] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 11/03/2014] [Indexed: 11/18/2022] Open
Abstract
Yeasts are widely distributed in nature and exist in association with other microorganisms as normal inhabitants of soil, vegetation, and aqueous environments. In this study, 12 yeast strains were enriched and isolated from leaf samples of the carnivorous plant Drosera indica L., which is currently threatened because of restricted habitats and use in herbal industries. According to similarities in large subunit and small subunit ribosomal RNA gene sequences, we identified 2 yeast species in 2 genera of the phylum Ascomycota, and 5 yeast species in 5 genera of the phylum Basidiomycota. All of the isolated yeasts produced indole-3-acetic acid (IAA) when cultivated in YPD broth supplemented with 0.1% L-tryptophan. Growth conditions, such as the pH and temperature of the medium, influenced yeast IAA production. Our results also suggested the existence of a tryptophan-independent IAA biosynthetic pathway. We evaluated the effects of various concentrations of exogenous IAA on yeast growth and observed that IAA produced by wild yeasts modifies auxin-inducible gene expression in Arabidopsis. Our data suggest that yeasts can promote plant growth and support ongoing prospecting of yeast strains for inclusion into biofertilizer for sustainable agriculture.
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Affiliation(s)
- Pei-Feng Sun
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan, R.O.C
| | - Wei-Ta Fang
- Graduate Institute of Environmental Education, National Taiwan Normal University, Taipei 116, Taiwan, R.O.C
| | - Li-Ying Shin
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan, R.O.C
| | - Jyuan-Yu Wei
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan, R.O.C
| | - Shih-Feng Fu
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan, R.O.C
| | - Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan, R.O.C
- * E-mail:
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134
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Genome sequencing of Sporisorium scitamineum provides insights into the pathogenic mechanisms of sugarcane smut. BMC Genomics 2014; 15:996. [PMID: 25406499 PMCID: PMC4246466 DOI: 10.1186/1471-2164-15-996] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 11/04/2014] [Indexed: 11/10/2022] Open
Abstract
Background Sugarcane smut can cause losses in cane yield and sugar content that range from 30% to total crop failure. Losses tend to increase with the passage of years. Sporisorium scitamineum is the fungus that causes sugarcane smut. This fungus has the potential to infect all sugarcane species unless a species is resistant to biotrophic fungal pathogens. However, it remains unclear how the fungus breaks through the cell walls of sugarcane and causes the formation of black or gray whip-like structures on the sugarcane plants. Results Here, we report the first high-quality genome sequence of S. scitamineum assembled de novo with a contig N50 of 41 kb, a scaffold N50 of 884 kb and genome size 19.8 Mb, containing an estimated 6,636 genes. This phytopathogen can utilize a wide range of carbon and nitrogen sources. A reduced set of genes encoding plant cell wall hydrolytic enzymes leads to its biotrophic lifestyle, in which damage to the host should be minimized. As a bipolar mating fungus, a and b loci are linked and the mating-type locus segregates as a single locus. The S. scitamineum genome has only 6 G protein-coupled receptors (GPCRs) grouped into five classes, which are responsible for transducing extracellular signals into intracellular responses, however, the genome is without any PTH11-like GPCR. There are 192 virulence associated genes in the genome of S. scitamineum, among which 31 expressed in all the stages, which mainly encode for energy metabolism and redox of short-chain compound related enzymes. Sixty-eight candidates for secreted effector proteins (CSEPs) were found in the genome of S. scitamineum, and 32 of them expressed in the different stages of sugarcane infection, which are probably involved in infection and/or triggering defense responses. There are two non-ribosomal peptide synthetase (NRPS) gene clusters that are involved in the generation of ferrichrome and ferrichrome A, while the terpenes gene cluster is composed of three unknown function genes and seven biosynthesis related genes. Conclusions As a destructive pathogen to sugar industry, the S. scitamineum genome will facilitate future research on the genomic basis and the pathogenic mechanisms of sugarcane smut. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-996) contains supplementary material, which is available to authorized users.
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135
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Vollmeister E, Schipper K, Feldbrügge M. Microtubule-dependent mRNA transport in the model microorganismUstilago maydis. RNA Biol 2014; 9:261-8. [DOI: 10.4161/rna.19432] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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136
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Bautista-España D, Anastacio-Marcelino E, Horta-Valerdi G, Celestino-Montes A, Kojic M, Negrete-Abascal E, Reyes-Cervantes H, Vázquez-Cruz C, Guzmán P, Sánchez-Alonso P. The telomerase reverse transcriptase subunit from the dimorphic fungus Ustilago maydis. PLoS One 2014; 9:e109981. [PMID: 25299159 PMCID: PMC4192592 DOI: 10.1371/journal.pone.0109981] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 09/15/2014] [Indexed: 01/11/2023] Open
Abstract
In this study, we investigated the reverse transcriptase subunit of telomerase in the dimorphic fungus Ustilago maydis. This protein (Trt1) contains 1371 amino acids and all of the characteristic TERT motifs. Mutants created by disrupting trt1 had senescent traits, such as delayed growth, low replicative potential, and reduced survival, that were reminiscent of the traits observed in est2 budding yeast mutants. Telomerase activity was observed in wild-type fungus sporidia but not those of the disruption mutant. The introduction of a self-replicating plasmid expressing Trt1 into the mutant strain restored growth proficiency and replicative potential. Analyses of trt1 crosses in planta suggested that Trt1 is necessary for teliospore formation in homozygous disrupted diploids and that telomerase is haploinsufficient in heterozygous diploids. Additionally, terminal restriction fragment analysis in the progeny hinted at alternative survival mechanisms similar to those of budding yeast.
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Affiliation(s)
- Dolores Bautista-España
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla, Mexico
| | - Estela Anastacio-Marcelino
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla, Mexico
| | - Guillermo Horta-Valerdi
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla, Mexico
| | - Antonio Celestino-Montes
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla, Mexico
| | - Milorad Kojic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Erasmo Negrete-Abascal
- Facultad de Estudios Superiores Iztacala, UNAM, Los Reyes Iztacala, Tlalnepantla, Estado de Mexico, Mexico
| | - Hortensia Reyes-Cervantes
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla, Mexico
| | - Candelario Vázquez-Cruz
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla, Mexico
| | - Plinio Guzmán
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, Guanajuato, Mexico
| | - Patricia Sánchez-Alonso
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla, Mexico
- * E-mail:
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137
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Schilling L, Matei A, Redkar A, Walbot V, Doehlemann G. Virulence of the maize smut Ustilago maydis is shaped by organ-specific effectors. MOLECULAR PLANT PATHOLOGY 2014; 15:780-9. [PMID: 25346968 PMCID: PMC6638905 DOI: 10.1111/mpp.12133] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
With the exception of Ustilago maydis, smut fungi infecting monocotyledonous hosts systemically colonize infected plants and cause symptoms exclusively in the inflorescences. Ustilago may disinfects primordia of all aerial organs of maize (Zea mays L.) and results in the formation of large plant tumours. Previously, we have found that U. maydis infection of seedling leaves, adult leaves and tassels causes organ-specific transcriptional changes in both the pathogen and the host. Of particular interest, U. may disgenes encoding secreted proteins are differentially expressed depending on the colonized maize organ. Therefore, we hypothesized that the fungus secretes virulence-related proteins (effectors)that act in an organ-specific manner. Here, we present the identification and functional characterization of 20 presumptive organ-specific U. maydis effector genes. Ustilago maydis deletion strains for these genes were generated and tested for infectivity of maize seedling leaves and tassels. This approach identified 11 effector genes required for the full virulence of U. maydis. In nine cases, virulence was only affected in one of the tested plant organs. These results demonstrate that individual fungal effector proteins contribute to fungal virulence in an organ-specific manner.
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138
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Microbial genome-enabled insights into plant–microorganism interactions. Nat Rev Genet 2014; 15:797-813. [DOI: 10.1038/nrg3748] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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139
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Morgenstern I, Powlowski J, Tsang A. Fungal cellulose degradation by oxidative enzymes: from dysfunctional GH61 family to powerful lytic polysaccharide monooxygenase family. Brief Funct Genomics 2014; 13:471-81. [PMID: 25217478 PMCID: PMC4239789 DOI: 10.1093/bfgp/elu032] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our understanding of fungal cellulose degradation has shifted dramatically in the past few years with the characterization of a new class of secreted enzymes, the lytic polysaccharide monooxygenases (LPMO). After a period of intense research covering structural, biochemical, theoretical and evolutionary aspects, we have a picture of them as wedge-like copper-dependent metalloenzymes that on reduction generate a radical copper-oxyl species, which cleaves mainly crystalline cellulose. The main biological function lies in the synergism of fungal LPMOs with canonical hydrolytic cellulases in achieving efficient cellulose degradation. Their important role in cellulose degradation is highlighted by the wide distribution and often numerous occurrences in the genomes of almost all plant cell-wall degrading fungi. In this review, we provide an overview of the latest achievements in LPMO research and consider the open questions and challenges that undoubtedly will continue to stimulate interest in this new and exciting group of enzymes.
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140
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Perez-Nadales E, Nogueira MFA, Baldin C, Castanheira S, El Ghalid M, Grund E, Lengeler K, Marchegiani E, Mehrotra PV, Moretti M, Naik V, Oses-Ruiz M, Oskarsson T, Schäfer K, Wasserstrom L, Brakhage AA, Gow NAR, Kahmann R, Lebrun MH, Perez-Martin J, Di Pietro A, Talbot NJ, Toquin V, Walther A, Wendland J. Fungal model systems and the elucidation of pathogenicity determinants. Fungal Genet Biol 2014; 70:42-67. [PMID: 25011008 PMCID: PMC4161391 DOI: 10.1016/j.fgb.2014.06.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 12/05/2022]
Abstract
Fungi have the capacity to cause devastating diseases of both plants and animals, causing significant harvest losses that threaten food security and human mycoses with high mortality rates. As a consequence, there is a critical need to promote development of new antifungal drugs, which requires a comprehensive molecular knowledge of fungal pathogenesis. In this review, we critically evaluate current knowledge of seven fungal organisms used as major research models for fungal pathogenesis. These include pathogens of both animals and plants; Ashbya gossypii, Aspergillus fumigatus, Candida albicans, Fusarium oxysporum, Magnaporthe oryzae, Ustilago maydis and Zymoseptoria tritici. We present key insights into the virulence mechanisms deployed by each species and a comparative overview of key insights obtained from genomic analysis. We then consider current trends and future challenges associated with the study of fungal pathogenicity.
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Affiliation(s)
- Elena Perez-Nadales
- Department of Genetics, Edificio Gregor Mendel, Planta 1. Campus de Rabanales, University of Cordoba, 14071 Cordoba, Spain.
| | | | - Clara Baldin
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutembergstr. 11a, 07745 Jena, Germany; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Sónia Castanheira
- Instituto de Biología Funcional y GenómicaCSIC, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Mennat El Ghalid
- Department of Genetics, Edificio Gregor Mendel, Planta 1. Campus de Rabanales, University of Cordoba, 14071 Cordoba, Spain
| | - Elisabeth Grund
- Functional Genomics of Plant Pathogenic Fungi, UMR 5240 CNRS-UCB-INSA-Bayer SAS, Bayer CropScience, 69263 Lyon, France
| | - Klaus Lengeler
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
| | - Elisabetta Marchegiani
- Evolution and Genomics of Plant Pathogen Interactions, UR 1290 INRA, BIOGER-CPP, Campus AgroParisTech, 78850 Thiverval-Grignon, France
| | - Pankaj Vinod Mehrotra
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Marino Moretti
- Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Vikram Naik
- Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Miriam Oses-Ruiz
- School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK
| | - Therese Oskarsson
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
| | - Katja Schäfer
- Department of Genetics, Edificio Gregor Mendel, Planta 1. Campus de Rabanales, University of Cordoba, 14071 Cordoba, Spain
| | - Lisa Wasserstrom
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutembergstr. 11a, 07745 Jena, Germany; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Neil A R Gow
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Regine Kahmann
- Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Marc-Henri Lebrun
- Evolution and Genomics of Plant Pathogen Interactions, UR 1290 INRA, BIOGER-CPP, Campus AgroParisTech, 78850 Thiverval-Grignon, France
| | - José Perez-Martin
- Instituto de Biología Funcional y GenómicaCSIC, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Antonio Di Pietro
- Department of Genetics, Edificio Gregor Mendel, Planta 1. Campus de Rabanales, University of Cordoba, 14071 Cordoba, Spain
| | - Nicholas J Talbot
- School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK
| | - Valerie Toquin
- Biochemistry Department, Bayer SAS, Bayer CropScience, CRLD, 69263 Lyon, France
| | - Andrea Walther
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
| | - Jürgen Wendland
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
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141
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Rutter WB, Hewezi T, Abubucker S, Maier TR, Huang G, Mitreva M, Hussey RS, Baum TJ. Mining novel effector proteins from the esophageal gland cells of Meloidogyne incognita. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:965-74. [PMID: 24875667 PMCID: PMC4249689 DOI: 10.1094/mpmi-03-14-0076-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Meloidogyne incognita is one of the most economically damaging plant pathogens in agriculture and horticulture. Identifying and characterizing the effector proteins which M. incognita secretes into its host plants during infection is an important step toward finding new ways to manage this pest. In this study, we have identified the cDNAs for 18 putative effectors (i.e., proteins that have the potential to facilitate M. incognita parasitism of host plants). These putative effectors are secretory proteins that do not contain transmembrane domains and whose genes are specifically expressed in the secretory gland cells of the nematode, indicating that they are likely secreted from the nematode through its stylet. We have determined that, in the plant cells, these putative effectors are likely to localize to the cytoplasm. Furthermore, the transcripts of many of these novel effectors are specifically upregulated during different stages of the nematode's life cycle, indicating that they function at specific stages during M. incognita parasitism. The predicted proteins showed little to no homology to known proteins from free-living nematode species, suggesting that they evolved recently to support the parasitic lifestyle. On the other hand, several of the effectors are part of gene families within the M. incognita genome as well as that of M. hapla, which points to an important role that these putative effectors are playing in both parasites. With the discovery of these putative effectors, we have increased our knowledge of the effector repertoire utilized by root-knot nematodes to infect, feed on, and reproduce on their host plants. Future studies investigating the roles that these proteins play in planta will help mitigate the effects of this damaging pest.
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Affiliation(s)
- William B. Rutter
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Tarek Hewezi
- University of Tennessee, Department of Plant Sciences, Knoxville, TN 37996-4561
| | - Sahar Abubucker
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108
| | - Tom R. Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Guozhong Huang
- Department of Plant Pathology, University of Georgia, Athens 30602-7274
| | - Makedonka Mitreva
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108
| | - Richard S. Hussey
- Department of Plant Pathology, University of Georgia, Athens 30602-7274
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
- Address correspondence to 351 Bessey Hall, , phone: 515-294-2398, Fax: 515-294-9420
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142
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Sharma R, Mishra B, Runge F, Thines M. Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the Smut Fungus Melanopsichium pennsylvanicum. Genome Biol Evol 2014; 6:2034-49. [PMID: 25062916 PMCID: PMC4159001 DOI: 10.1093/gbe/evu148] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Smut fungi are well-suited to investigate the ecology and evolution of plant pathogens, as they are strictly biotrophic, yet cultivable on media. Here we report the genome sequence of Melanopsichium pennsylvanicum, closely related to Ustilago maydis and other Poaceae-infecting smuts, but parasitic to a dicot plant. To explore the evolutionary patterns resulting from host adaptation after this huge host jump, the genome of Me. pennsylvanicum was sequenced and compared with the genomes of U. maydis, Sporisorium reilianum, and U. hordei. Although all four genomes had a similar completeness in CEGMA (Core Eukaryotic Genes Mapping Approach) analysis, gene absence was highest in Me. pennsylvanicum, and most pronounced in putative secreted proteins, which are often considered as effector candidates. In contrast, the amount of private genes was similar among the species, highlighting that gene loss rather than gene gain is the hallmark of adaptation after the host jump to the dicot host. Our analyses revealed a trend of putative effectors to be next to another putative effector, but the majority of these are not in clusters and thus the focus on pathogenicity clusters might not be appropriate for all smut genomes. Positive selection studies revealed that Me. pennsylvanicum has the highest number and proportion of genes under positive selection. In general, putative effectors showed a higher proportion of positively selected genes than noneffector candidates. The 248 putative secreted effectors found in all four smut genomes might constitute a core set needed for pathogenicity, whereas those 92 that are found in all grass-parasitic smuts but have no ortholog in Me. pennsylvanicum might constitute a set of effectors important for successful colonization of grass hosts.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyInstitute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, GermanySenckenberg Gesellschaft für Naturforschung, Frankfurt am Main, GermanyCluster for Integrative Fungal Research (IPF), Frankfurt am Main, Germany
| | - Bagdevi Mishra
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyInstitute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, GermanySenckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Fabian Runge
- Institute of Botany 210, University of Hohenheim, Stuttgart, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyInstitute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, GermanySenckenberg Gesellschaft für Naturforschung, Frankfurt am Main, GermanyCluster for Integrative Fungal Research (IPF), Frankfurt am Main, Germany
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143
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Lanver D, Berndt P, Tollot M, Naik V, Vranes M, Warmann T, Münch K, Rössel N, Kahmann R. Plant surface cues prime Ustilago maydis for biotrophic development. PLoS Pathog 2014; 10:e1004272. [PMID: 25033195 PMCID: PMC4102580 DOI: 10.1371/journal.ppat.1004272] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 06/12/2014] [Indexed: 11/19/2022] Open
Abstract
Infection-related development of phytopathogenic fungi is initiated by sensing and responding to plant surface cues. This response can result in the formation of specialized infection structures, so-called appressoria. To unravel the program inducing filaments and appressoria in the biotrophic smut fungus Ustilago maydis, we exposed cells to a hydrophobic surface and the cutin monomer 16-hydroxy hexadecanoic acid. Genome-wide transcriptional profiling at the pre-penetration stage documented dramatic transcriptional changes in almost 20% of the genes. Comparisons with the U. maydis sho1 msb2 double mutant, lacking two putative sensors for plant surface cues, revealed that these plasma membrane receptors regulate a small subset of the surface cue-induced genes comprising mainly secreted proteins including potential plant cell wall degrading enzymes. Targeted gene deletion analysis ascribed a role to up-regulated GH51 and GH62 arabinofuranosidases during plant penetration. Among the sho1/msb2-dependently expressed genes were several secreted effectors that are essential for virulence. Our data also demonstrate specific effects on two transcription factors that redirect the transcriptional regulatory network towards appressorium formation and plant penetration. This shows that plant surface cues prime U. maydis for biotrophic development. A basic requirement for pathogens to infect their hosts and to cause disease is to detect that they are in contact with the host surface. Plant pathogenic fungi typically respond to leaf surface contact with the development of specialized infection structures enabling the fungus to penetrate the leaf cuticle and to enter the plant tissue. In this study we analyzed the response of the corn smut fungus Ustilago maydis to two plant surface cues, such as hydrophobic surface and cutin monomers. Based on genome-wide gene expression analysis we found that these cues trigger the production of secreted plant cell wall degrading enzymes helping the fungus to penetrate the plant surface. In addition, genes were activated that code for a group of secreted proteins, so-called effectors, that affect virulence after penetration. These results demonstrate that plant surface cues trigger fungal penetration of the plant surface and also prime the fungus for later development inside plant tissue. These specific responses required two cell surface proteins that likely function as plant surface sensors.
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Affiliation(s)
- Daniel Lanver
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Patrick Berndt
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Marie Tollot
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Vikram Naik
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Miroslav Vranes
- Karlsruhe Institute of Technology (KIT), Institute for Applied Biosciences, Department of Genetics, Karlsruhe, Germany
| | - Tobias Warmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Karin Münch
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Nicole Rössel
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
- * E-mail:
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144
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Wollenberg T, Schirawski J. Comparative genomics of plant fungal pathogens: the Ustilago-Sporisorium paradigm. PLoS Pathog 2014; 10:e1004218. [PMID: 24992444 PMCID: PMC4081819 DOI: 10.1371/journal.ppat.1004218] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Theresa Wollenberg
- RWTH Aachen University, Microbial Genetics, Institute of Applied Microbiology, Aachen Biology and Biotechnology, Aachen, Germany
| | - Jan Schirawski
- RWTH Aachen University, Microbial Genetics, Institute of Applied Microbiology, Aachen Biology and Biotechnology, Aachen, Germany
- * E-mail:
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145
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An immunity-triggering effector from the Barley smut fungus Ustilago hordei resides in an Ustilaginaceae-specific cluster bearing signs of transposable element-assisted evolution. PLoS Pathog 2014; 10:e1004223. [PMID: 24992661 PMCID: PMC4081816 DOI: 10.1371/journal.ppat.1004223] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 05/15/2014] [Indexed: 11/19/2022] Open
Abstract
The basidiomycete smut fungus Ustilago hordei was previously shown to comprise isolates that are avirulent on various barley host cultivars. Through genetic crosses we had revealed that a dominant avirulence locus UhAvr1 which triggers immunity in barley cultivar Hannchen harboring resistance gene Ruh1, resided within an 80-kb region. DNA sequence analysis of this genetically delimited region uncovered the presence of 7 candidate secreted effector proteins. Sequence comparison of their coding sequences among virulent and avirulent parental and field isolates could not distinguish UhAvr1 candidates. Systematic deletion and complementation analyses revealed that UhAvr1 is UHOR_10022 which codes for a small effector protein of 171 amino acids with a predicted 19 amino acid signal peptide. Virulence in the parental isolate is caused by the insertion of a fragment of 5.5 kb with similarity to a common U. hordei transposable element (TE), interrupting the promoter of UhAvr1 and thereby changing expression and hence recognition of UhAVR1p. This rearrangement is likely caused by activities of TEs and variation is seen among isolates. Using GFP-chimeric constructs we show that UhAvr1 is induced only in mated dikaryotic hyphae upon sensing and infecting barley coleoptile cells. When infecting Hannchen, UhAVR1p causes local callose deposition and the production of reactive oxygen species and necrosis indicative of the immune response. UhAvr1 does not contribute significantly to overall virulence. UhAvr1 is located in a cluster of ten effectors with several paralogs and over 50% of TEs. This cluster is syntenous with clusters in closely-related U. maydis and Sporisorium reilianum. In these corn-infecting species, these clusters harbor however more and further diversified homologous effector families but very few TEs. This increased variability may have resulted from past selection pressure by resistance genes since U. maydis is not known to trigger immunity in its corn host.
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146
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Brefort T, Tanaka S, Neidig N, Doehlemann G, Vincon V, Kahmann R. Characterization of the largest effector gene cluster of Ustilago maydis. PLoS Pathog 2014; 10:e1003866. [PMID: 24992561 PMCID: PMC4081774 DOI: 10.1371/journal.ppat.1003866] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 11/20/2013] [Indexed: 12/21/2022] Open
Abstract
In the genome of the biotrophic plant pathogen Ustilago maydis, many of the genes coding for secreted protein effectors modulating virulence are arranged in gene clusters. The vast majority of these genes encode novel proteins whose expression is coupled to plant colonization. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. Here we present the functional analysis of this genomic region. We show that a 19A deletion mutant behaves like an endophyte, i.e. is still able to colonize plants and complete the infection cycle. However, tumors, the most conspicuous symptoms of maize smut disease, are only rarely formed and fungal biomass in infected tissue is significantly reduced. The generation and analysis of strains carrying sub-deletions identified several genes significantly contributing to tumor formation after seedling infection. Another of the effectors could be linked specifically to anthocyanin induction in the infected tissue. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. We propose that the analysis of plant responses to effector mutant strains that lack a strong virulence phenotype may be a general way to visualize differences in effector function.
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Affiliation(s)
- Thomas Brefort
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Shigeyuki Tanaka
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Nina Neidig
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Gunther Doehlemann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Volker Vincon
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
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147
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Kellner R, Hanschke C, Begerow D. Patterns of variation at Ustilago maydis virulence clusters 2A and 19A largely reflect the demographic history of its populations. PLoS One 2014; 9:e98837. [PMID: 24887029 PMCID: PMC4041787 DOI: 10.1371/journal.pone.0098837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/07/2014] [Indexed: 12/18/2022] Open
Abstract
The maintenance of an intimate interaction between plant-biotrophic fungi and their hosts over evolutionary times involves strong selection and adaptative evolution of virulence-related genes. The highly specialised maize pathogen Ustilago maydis is assigned with a high evolutionary capability to overcome host resistances due to its high rates of sexual recombination, large population sizes and long distance dispersal. Unlike most studied fungus-plant interactions, the U. maydis – Zea mays pathosystem lacks a typical gene-for-gene interaction. It exerts a large set of secreted fungal virulence factors that are mostly organised in gene clusters. Their contribution to virulence has been experimentally demonstrated but their genetic diversity within U. maydis remains poorly understood. Here, we report on the intraspecific diversity of 34 potential virulence factor genes of U. maydis. We analysed their sequence polymorphisms in 17 isolates of U. maydis from Europe, North and Latin America. We focused on gene cluster 2A, associated with virulence attenuation, cluster 19A that is crucial for virulence, and the cluster-independent effector gene pep1. Although higher compared to four house-keeping genes, the overall levels of intraspecific genetic variation of virulence clusters 2A and 19A, and pep1 are remarkably low and commensurate to the levels of 14 studied non-virulence genes. In addition, each gene is present in all studied isolates and synteny in cluster 2A is conserved. Furthermore, 7 out of 34 virulence genes contain either no polymorphisms or only synonymous substitutions among all isolates. However, genetic variation of clusters 2A and 19A each resolve the large scale population structure of U. maydis indicating subpopulations with decreased gene flow. Hence, the genetic diversity of these virulence-related genes largely reflect the demographic history of U. maydis populations.
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Affiliation(s)
- Ronny Kellner
- MPRG Fungal Biodiversity, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Geobotany, Ruhr-Universität Bochum, Bochum, Germany
- * E-mail:
| | | | - Dominik Begerow
- Department of Geobotany, Ruhr-Universität Bochum, Bochum, Germany
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Link TI, Lang P, Scheffler BE, Duke MV, Graham MA, Cooper B, Tucker ML, van de Mortel M, Voegele RT, Mendgen K, Baum TJ, Whitham SA. The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families. MOLECULAR PLANT PATHOLOGY 2014; 15:379-93. [PMID: 24341524 PMCID: PMC6638672 DOI: 10.1111/mpp.12099] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Haustoria of biotrophic rust fungi are responsible for the uptake of nutrients from their hosts and for the production of secreted proteins, known as effectors, which modulate the host immune system. The identification of the transcriptome of haustoria and an understanding of the functions of expressed genes therefore hold essential keys for the elucidation of fungus-plant interactions and the development of novel fungal control strategies. Here, we purified haustoria from infected leaves and used 454 sequencing to examine the haustorial transcriptomes of Phakopsora pachyrhizi and Uromyces appendiculatus, the causal agents of soybean rust and common bean rust, respectively. These pathogens cause extensive yield losses in their respective legume crop hosts. A series of analyses were used to annotate expressed sequences, including transposable elements and viruses, to predict secreted proteins from the assembled sequences and to identify families of candidate effectors. This work provides a foundation for the comparative analysis of haustorial gene expression with further insights into physiology and effector evolution.
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Affiliation(s)
- Tobias I Link
- Institut für Phytomedizin, FG Phytopathologie, Universität Hohenheim, Otto-Sander-Straße 5, 70599, Stuttgart, Germany
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149
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Hane JK, Anderson JP, Williams AH, Sperschneider J, Singh KB. Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8. PLoS Genet 2014; 10:e1004281. [PMID: 24810276 PMCID: PMC4014442 DOI: 10.1371/journal.pgen.1004281] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 02/20/2014] [Indexed: 11/30/2022] Open
Abstract
Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA. We also observed SNP-level "hypermutation" of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens.
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Affiliation(s)
- James K. Hane
- Molecular Plant Pathology and Crop Genomics Laboratory, Centre for Environment and Life Sciences, Division of Plant Industry, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia
| | - Jonathan P. Anderson
- Molecular Plant Pathology and Crop Genomics Laboratory, Centre for Environment and Life Sciences, Division of Plant Industry, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia
- The University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| | - Angela H. Williams
- Molecular Plant Pathology and Crop Genomics Laboratory, Centre for Environment and Life Sciences, Division of Plant Industry, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia
| | - Jana Sperschneider
- Molecular Plant Pathology and Crop Genomics Laboratory, Centre for Environment and Life Sciences, Division of Plant Industry, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia
| | - Karam B. Singh
- Molecular Plant Pathology and Crop Genomics Laboratory, Centre for Environment and Life Sciences, Division of Plant Industry, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia
- The University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
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150
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Toome M, Ohm RA, Riley RW, James TY, Lazarus KL, Henrissat B, Albu S, Boyd A, Chow J, Clum A, Heller G, Lipzen A, Nolan M, Sandor L, Zvenigorodsky N, Grigoriev IV, Spatafora JW, Aime MC. Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae. THE NEW PHYTOLOGIST 2014; 202:554-564. [PMID: 24372469 DOI: 10.1111/nph.12653] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 11/19/2013] [Indexed: 05/06/2023]
Abstract
Mixia osmundae (Basidiomycota, Pucciniomycotina) represents a monotypic class containing an unusual fern pathogen with incompletely understood biology. We sequenced and analyzed the genome of M. osmundae, focusing on genes that may provide some insight into its mode of pathogenicity and reproductive biology. Mixia osmundae has the smallest plant pathogenic basidiomycete genome sequenced to date, at 13.6 Mb, with very few repeats, high gene density, and relatively few significant gene family gains. The genome shows that the yeast state of M. osmundae is haploid and the lack of segregation of mating genes suggests that the spores produced on Osmunda spp. fronds are probably asexual. However, our finding of a complete complement of mating and meiosis genes suggests the capacity to undergo sexual reproduction. Analyses of carbohydrate active enzymes suggest that this fungus is a biotroph with the ability to break down several plant cell wall components. Analyses of publicly available sequence data show that other Mixia members may exist on other plant hosts and with a broader distribution than previously known.
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Affiliation(s)
- Merje Toome
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Robin A Ohm
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Robert W Riley
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Katherine L Lazarus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University, CNRS UMR 7257, 13288, Marseille, France
| | - Sebastian Albu
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Alexander Boyd
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Julianna Chow
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Gregory Heller
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Matt Nolan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
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