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Schuster M, Schweizer G, Reißmann S, Happel P, Aßmann D, Rössel N, Güldener U, Mannhaupt G, Ludwig N, Winterberg S, Pellegrin C, Tanaka S, Vincon V, Presti LL, Wang L, Bender L, Gonzalez C, Vranes M, Kämper J, Seong K, Krasileva K, Kahmann R. Novel Secreted Effectors Conserved Among Smut Fungi Contribute to the Virulence of Ustilago maydis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:250-263. [PMID: 38416124 DOI: 10.1094/mpmi-09-23-0139-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Fungal pathogens deploy a set of molecules (proteins, specialized metabolites, and sRNAs), so-called effectors, to aid the infection process. In comparison to other plant pathogens, smut fungi have small genomes and secretomes of 20 Mb and around 500 proteins, respectively. Previous comparative genomic studies have shown that many secreted effector proteins without known domains, i.e., novel, are conserved only in the Ustilaginaceae family. By analyzing the secretomes of 11 species within Ustilaginaceae, we identified 53 core homologous groups commonly present in this lineage. By collecting existing mutants and generating additional ones, we gathered 44 Ustilago maydis strains lacking single core effectors as well as 9 strains containing multiple deletions of core effector gene families. Pathogenicity assays revealed that 20 of these 53 mutant strains were affected in virulence. Among the 33 mutants that had no obvious phenotypic changes, 13 carried additional, sequence-divergent, structurally similar paralogs. We report a virulence contribution of seven previously uncharacterized single core effectors and of one effector family. Our results help to prioritize effectors for understanding U. maydis virulence and provide genetic resources for further characterization. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mariana Schuster
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Gabriel Schweizer
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Independent Data Lab UG, 80937 Munich, Germany
| | - Stefanie Reißmann
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Petra Happel
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Daniela Aßmann
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Nicole Rössel
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Ulrich Güldener
- Deutsches Herzzentrum München, Technische Universität München, 80636 München, Germany
| | - Gertrud Mannhaupt
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Nicole Ludwig
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Research & Development, Weed Control Bayer AG, Crop Science Division, 65926 Frankfurt am Main, Germany
| | - Sarah Winterberg
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Clément Pellegrin
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Shigeyuki Tanaka
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Volker Vincon
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Libera Lo Presti
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lei Wang
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lena Bender
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Department of Pharmaceutics and Biopharmaceutics, Phillips-University Marburg, 35037 Marburg, Germany
| | - Carla Gonzalez
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Miroslav Vranes
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, 76131 Karlsruhe, Germany
| | - Jörg Kämper
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, 76131 Karlsruhe, Germany
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Ksenia Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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Jiang S, Chen Y, Han S, Lv L, Li L. Next-Generation Sequencing Applications for the Study of Fungal Pathogens. Microorganisms 2022; 10:microorganisms10101882. [PMID: 36296159 PMCID: PMC9609632 DOI: 10.3390/microorganisms10101882] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) has become a widely used technology in biological research. NGS applications for clinical pathogen detection have become vital technologies. It is increasingly common to perform fast, accurate, and specific detection of clinical specimens using NGS. Pathogenic fungi with high virulence and drug resistance cause life-threatening clinical infections. NGS has had a significant biotechnological impact on detecting bacteria and viruses but is not equally applicable to fungi. There is a particularly urgent clinical need to use NGS to help identify fungi causing infections and prevent negative impacts. This review summarizes current research on NGS applications for fungi and offers a visual method of fungal detection. With the development of NGS and solutions for overcoming sequencing limitations, we suggest clinicians test specimens as soon as possible when encountering infections of unknown cause, suspected infections in vital organs, or rapidly progressive disease.
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Affiliation(s)
- Shiman Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Shengyi Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Correspondence: ; Tel.: +86-0571-8723-6458
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Saado I, Chia KS, Betz R, Alcântara A, Pettkó-Szandtner A, Navarrete F, D'Auria JC, Kolomiets MV, Melzer M, Feussner I, Djamei A. Effector-mediated relocalization of a maize lipoxygenase protein triggers susceptibility to Ustilago maydis. THE PLANT CELL 2022; 34:2785-2805. [PMID: 35512341 PMCID: PMC9252493 DOI: 10.1093/plcell/koac105] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/17/2022] [Indexed: 05/07/2023]
Abstract
As the gall-inducing smut fungus Ustilago maydis colonizes maize (Zea mays) plants, it secretes a complex effector blend that suppresses host defense responses, including production of reactive oxygen species (ROS) and redirects host metabolism to facilitate colonization. We show that the U. maydis effector ROS burst interfering protein 1 (Rip1), which is involved in pathogen-associated molecular pattern (PAMP)-triggered suppression of host immunity, is functionally conserved in several other monocot-infecting smut fungi. We also have identified a conserved C-terminal motif essential for Rip1-mediated PAMP-triggered suppression of the ROS burst. The maize susceptibility factor lipoxygenase 3 (Zmlox3) bound by Rip1 was relocalized to the nucleus, leading to partial suppression of the ROS burst. Relocalization was independent of its enzymatic activity, revealing a distinct function for ZmLox3. Most importantly, whereas Zmlox3 maize mutant plants showed increased resistance to U. maydis wild-type strains, rip1 deletion strains infecting the Zmlox3 mutant overcame this effect. This could indicate that Rip1-triggered host resistance depends on ZmLox3 to be suppressed and that lox3 mutation-based resistance of maize to U. maydis requires functional Rip1. Together, our results reveal that Rip1 acts in several cellular compartments to suppress immunity and that targeting of ZmLox3 by Rip1 is responsible for the suppression of Rip1-dependent reduced susceptibility of maize to U. maydis.
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Affiliation(s)
- Indira Saado
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | - Khong-Sam Chia
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | - Ruben Betz
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | - André Alcântara
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
| | | | - Fernando Navarrete
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
| | - John C D'Auria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | | | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences and Goettingen Center for Molecular Biosciences (GZMB), Göttingen 37077, Germany
| | - Armin Djamei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences (OEAW), Vienna BioCenter 7(VBC),Vienna 1030, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland D-06466, Germany
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Schneider M, Shrestha A, Ballvora A, Léon J. High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing. PLANT METHODS 2022; 18:34. [PMID: 35313910 PMCID: PMC8935755 DOI: 10.1186/s13007-022-00852-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In addition to heterogeneity and artificial selection, natural selection is one of the forces used to combat climate change and improve agrobiodiversity in evolutionary plant breeding. Accurate identification of the specific genomic effects of natural selection will likely accelerate transfer between populations. Thus, insights into changes in allele frequency, adequate population size, gene flow and drift are essential. However, observing such effects often involves a trade-off between costs and resolution when a large sample of genotypes for many loci is analysed. Pool genotyping approaches achieve high resolution and precision in estimating allele frequency when sequence coverage is high. Nevertheless, high-coverage pool sequencing of large genomes is expensive. RESULTS Three pool samples (n = 300, 300, 288) from a barley backcross population were generated to assess the population's allele frequency. The tested population (BC2F21) has undergone 18 generations of natural adaption to conventional farming practice. The accuracies of estimated pool-based allele frequencies and genome coverage yields were compared using three next-generation sequencing genotyping methods. To achieve accurate allele frequency estimates with low sequence coverage, we employed a haplotyping approach. Low coverage allele frequencies of closely located single polymorphisms were aggregated into a single haplotype allele frequency, yielding 2-to-271-times higher depth and increased precision. When we combined different haplotyping tactics, we found that gene and chip marker-based haplotype analyses performed equivalently or better compared with simple contig haplotype windows. Comparing multiple pool samples and referencing against an individual sequencing approach revealed that whole-genome pool re-sequencing (WGS) achieved the highest correlation with individual genotyping (≥ 0.97). In contrast, transcriptome-based genotyping (MACE) and genotyping by sequencing (GBS) pool replicates were significantly associated with higher error rates and lower correlations, but are still valuable to detect large allele frequency variations. CONCLUSIONS The proposed strategy identified the allele frequency of populations with high accuracy at low cost. This is particularly relevant to evolutionary plant breeding of crops with very large genomes, such as barley. Whole-genome low coverage re-sequencing at 0.03 × coverage per genotype accurately estimated the allele frequency when a loci-based haplotyping approach was applied. The implementation of annotated haplotypes capitalises on the biological background and statistical robustness.
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Affiliation(s)
- Michael Schneider
- Institute of Crop Science and Resource Conservation, University of Bonn, Plant Breeding, Katzenburgweg 5, 53115, Bonn, Germany
- Institute for Quantitative Genetics and Genomics of Plants, University Duesseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Asis Shrestha
- Institute of Crop Science and Resource Conservation, University of Bonn, Plant Breeding, Katzenburgweg 5, 53115, Bonn, Germany
- Institute for Quantitative Genetics and Genomics of Plants, University Duesseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation, University of Bonn, Plant Breeding, Katzenburgweg 5, 53115, Bonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation, University of Bonn, Plant Breeding, Katzenburgweg 5, 53115, Bonn, Germany.
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5
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Developing Functional Genomics Platforms for Fungi. mSystems 2021; 6:e0073021. [PMID: 34427501 PMCID: PMC8407244 DOI: 10.1128/msystems.00730-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungi are responsible for diseases that result in the deaths of over a million individuals each year and devastating crop infestations that threaten global food supplies. However, outside of a select few model organisms, the majority of fungal genes are uncharacterized. The roles of these genes in the biology of the organism, pathogenesis, and mediating interactions with the environment and other microbes are unknown. Historically, fungal gene characterization has primarily relied on classical genetic screens. However, advances in sequencing technology have enabled more rapid methods of gene functional characterization. Large-scale transcriptional profiling projects are one solution to generating hypotheses about fungal gene function. Together with other 'omics techniques and newer tools that enable massively parallel mutant screens, knowledge of fungal gene function will be substantially improved. Understanding the function of fungal genes will be instrumental in increasing global food security, protecting ecosystems, and improving health outcomes.
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The Pleiades are a cluster of fungal effectors that inhibit host defenses. PLoS Pathog 2021; 17:e1009641. [PMID: 34166468 PMCID: PMC8224859 DOI: 10.1371/journal.ppat.1009641] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/13/2021] [Indexed: 01/07/2023] Open
Abstract
Biotrophic plant pathogens secrete effector proteins to manipulate the host physiology. Effectors suppress defenses and induce an environment favorable to disease development. Sequence-based prediction of effector function is impeded by their rapid evolution rate. In the maize pathogen Ustilago maydis, effector-coding genes frequently organize in clusters. Here we describe the functional characterization of the pleiades, a cluster of ten effector genes, by analyzing the micro- and macroscopic phenotype of the cluster deletion and expressing these proteins in planta. Deletion of the pleiades leads to strongly impaired virulence and accumulation of reactive oxygen species (ROS) in infected tissue. Eight of the Pleiades suppress the production of ROS upon perception of pathogen associated molecular patterns (PAMPs). Although functionally redundant, the Pleiades target different host components. The paralogs Taygeta1 and Merope1 suppress ROS production in either the cytoplasm or nucleus, respectively. Merope1 targets and promotes the auto-ubiquitination activity of RFI2, a conserved family of E3 ligases that regulates the production of PAMP-triggered ROS burst in plants.
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7
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Weiland P, Altegoer F. Identification and Characterization of Two Transmembrane Proteins Required for Virulence of Ustilago maydis. FRONTIERS IN PLANT SCIENCE 2021; 12:669835. [PMID: 34093627 PMCID: PMC8176221 DOI: 10.3389/fpls.2021.669835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Smut fungi comprise a large group of biotrophic phytopathogens infecting important crops such as wheat and corn. Through the secretion of effector proteins, the fungus actively suppresses plant immune reactions and modulates its host's metabolism. Consequently, how soluble effector proteins contribute to virulence is already characterized in a range of phytopathogens. However, membrane-associated virulence factors have been much less studied to date. Here, we investigated six transmembrane (TM) proteins that show elevated gene expression during biotrophic development of the maize pathogen Ustilago maydis. We show that two of the six proteins, named Vmp1 and Vmp2 (virulence-associated membrane protein), are essential for the full virulence of U. maydis. The deletion of the corresponding genes leads to a substantial attenuation in the virulence of U. maydis. Furthermore, both are conserved in various related smuts and contain no domains of known function. Our biochemical analysis clearly shows that Vmp1 and Vmp2 are membrane-associated proteins, potentially localizing to the U. maydis plasma membrane. Mass photometry and light scattering suggest that Vmp1 mainly occurs as a monomer, while Vmp2 is dimeric. Notably, the large and partially unstructured C-terminal domain of Vmp2 is crucial for virulence while not contributing to dimerization. Taken together, we here provide an initial characterization of two membrane proteins as virulence factors of U. maydis.
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Affiliation(s)
- Paul Weiland
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
- Department of Organismic Interactions, Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
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8
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Lim CS, Weinstein BN, Roy SW, Brown CM. Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species. Mol Biol Evol 2021; 38:4166-4186. [PMID: 33772558 PMCID: PMC8476143 DOI: 10.1093/molbev/msab094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Brooke N Weinstein
- Quantitative & Systems Biology, School of Natural Sciences, University of California-Merced, Merced, CA, USA.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Scott W Roy
- Quantitative & Systems Biology, School of Natural Sciences, University of California-Merced, Merced, CA, USA.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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Bosch J, Czedik-Eysenberg A, Hastreiter M, Khan M, Güldener U, Djamei A. Two Is Better Than One: Studying Ustilago bromivora- Brachypodium Compatibility by Using a Hybrid Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1623-1634. [PMID: 31657673 DOI: 10.1094/mpmi-05-19-0148-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pathogenic fungi can have devastating effects on agriculture and health. One potential challenge in dealing with pathogens is the possibility of a host jump (i.e., when a pathogen infects a new host species). This can lead to the emergence of new diseases or complicate the management of existing threats. We studied host specificity by using a hybrid fungus formed by mating two closely related fungi: Ustilago bromivora, which normally infects Brachypodium spp., and U. hordei, which normally infects barley. Although U. hordei was unable to infect Brachypodium spp., the hybrid could. These hybrids also displayed the same mating-type bias that had been observed in U. bromivora and provide evidence of a dominant spore-killer-like system on the sex chromosome of U. bromivora. By analyzing the genomic composition of 109 hybrid strains, backcrossed with U. hordei over four generations, we identified three regions associated with infection on Brachypodium spp. and 75 potential virulence candidates. The most strongly associated region was located on chromosome 8, where seven genes encoding predicted secreted proteins were identified. The fact that we identified several regions relevant for pathogenicity on Brachypodium spp. but that none were essential suggests that host specificity, in the case of U. bromivora, is a multifactorial trait which can be achieved through different subsets of virulence factors.
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Affiliation(s)
- Jason Bosch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Angelika Czedik-Eysenberg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Maximilian Hastreiter
- TUM School of Life Sciences, Technical University of Munich, Department of Bioinformatics, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Mamoona Khan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Ulrich Güldener
- TUM School of Life Sciences, Technical University of Munich, Department of Bioinformatics, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Armin Djamei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
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10
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Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei M, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. Systematic Y2H Screening Reveals Extensive Effector-Complex Formation. FRONTIERS IN PLANT SCIENCE 2019; 10:1437. [PMID: 31803201 PMCID: PMC6872519 DOI: 10.3389/fpls.2019.01437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/16/2019] [Indexed: 05/22/2023]
Abstract
During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host's immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant's responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.
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Affiliation(s)
- André Alcântara
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Jason Bosch
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Fahimeh Nazari
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Iranian Research Institute of Plant Protection, Tehran, Iran
| | - Gesa Hoffmann
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michelle Gallei
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Simon Uhse
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Martin A. Darino
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Toluwase Olukayode
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Reumann
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Institute of Molecular Biotechnology, Vienna, Austria
| | - Laura Baggaley
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Biotic Interactions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Armin Djamei
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Department of Breeding Research, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Gatersleben, Germany
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11
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Uhse S, Pflug FG, von Haeseler A, Djamei A. Insertion Pool Sequencing for Insertional Mutant Analysis in Complex Host-Microbe Interactions. ACTA ACUST UNITED AC 2019; 4:e20097. [PMID: 31479207 PMCID: PMC9285383 DOI: 10.1002/cppb.20097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Insertional mutant libraries of microorganisms can be applied in negative depletion screens to decipher gene functions. Because of underrepresentation in colonized tissue, one major bottleneck is analysis of species that colonize hosts. To overcome this, we developed insertion pool sequencing (iPool‐Seq). iPool‐Seq allows direct analysis of colonized tissue due to high specificity for insertional mutant cassettes. Here, we describe detailed protocols for infection as well as genomic DNA extraction to study the interaction between the corn smut fungus Ustilago maydis and its host maize. In addition, we provide protocols for library preparation and bioinformatic data analysis that are applicable to any host‐microbe interaction system. © 2019 The Authors. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Affiliation(s)
- Simon Uhse
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Florian G Pflug
- Center for Integrative Bioinformatics Vienna (CIBIV), Joint Institute of the University of Vienna and Medical University of Vienna, Max F. Perutz Laboratories (MFPL), Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna (CIBIV), Joint Institute of the University of Vienna and Medical University of Vienna, Max F. Perutz Laboratories (MFPL), Vienna, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Armin Djamei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.,Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Elías-Villalobos A, Barrales RR, Ibeas JI. Chromatin modification factors in plant pathogenic fungi: Insights from Ustilago maydis. Fungal Genet Biol 2019; 129:52-64. [PMID: 30980908 DOI: 10.1016/j.fgb.2019.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 01/10/2023]
Abstract
Adaptation to the environment is a requirement for the survival of every organism. For pathogenic fungi this also implies coping with the different conditions that occur during the infection cycle. After detecting changes to external media, organisms must modify their gene expression patterns in order to accommodate the new circumstances. Control of gene expression is a complex process that involves the coordinated action of multiple regulatory elements. Chromatin modification is a well-known mechanism for controlling gene expression in response to environmental changes in all eukaryotes. In pathogenic fungi, chromatin modifications are known to play crucial roles in controlling host interactions and their virulence capacity, yet little is known about the specific genes they directly target and to which signals they respond. The smut fungus Ustilago maydis is an excellent model system in which multiple molecular and cellular approaches are available to study biotrophic interactions. Many target genes regulated during the infection process have been well studied, however, how they are controlled and specifically how chromatin modifications affect gene regulation in the context of infection is not well known in this organism. Here, we analyse the presence of chromatin modifying enzymes and complexes in U. maydis and discuss their putative roles in this plant pathogen in the context of findings from other organisms, including other plant pathogens such as Magnaporthe oryzae and Fusarium graminearum. We propose U. maydis as a remarkable organism with interesting chromatin features, which would allow finding new functions of chromatin modifications during plant pathogenesis.
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Affiliation(s)
- Alberto Elías-Villalobos
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR5237-Centre National de la Recherche Scientifique-Université de Montpellier, Montpellier, France.
| | - Ramón R Barrales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain.
| | - José I Ibeas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain
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