1
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Chen X, Hu J, Zhong H, Wu Q, Fang Z, Cai Y, Huang P, Abubakar YS, Zhou J, Naqvi NI, Wang Z, Zheng W. Vacuolar recruitment of retromer by a SNARE complex enables infection-related trafficking in rice blast. THE NEW PHYTOLOGIST 2024; 244:997-1012. [PMID: 39180241 DOI: 10.1111/nph.20069] [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] [Received: 04/02/2024] [Accepted: 08/02/2024] [Indexed: 08/26/2024]
Abstract
The retromer complex is a conserved sorting machinery that maintains cellular protein homeostasis by transporting vesicles containing cargo proteins to defined destinations. It is known to sort proteins at the vacuole membranes for retrograde trafficking, preventing their degradation in the vacuole. However, the detailed mechanism of retromer recruitment to the vacuole membrane has not yet been elucidated. Here, we show that the vacuolar SNARE complex MoPep12-MoVti1-MoVam7-MoYkt6 regulates retromer-mediated vesicle trafficking by recruiting the retromer to the vacuole membrane, which promotes host invasion in Magnaporthe oryzae. Such recruitment is also essential for the retrieval of the autophagy regulator MoAtg8 and enables appressorium-mediated host penetration. Furthermore, the vacuolar SNARE subunits are involved in suppressing the host defense response by regulating the deployment of retromer-MoSnc1-mediated effector secretion. Altogether, our results provide insights into the mechanism of vacuolar SNAREs-dependent retromer recruitment which is necessary for pathogenicity-related membrane trafficking events in the rice blast fungus.
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Affiliation(s)
- Xin Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Key Laboratory of Bio-pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
| | - Jiexiong Hu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Key Laboratory of Bio-pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
| | - Haoming Zhong
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Key Laboratory of Bio-pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
| | - Qiuqiu Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Key Laboratory of Bio-pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
| | - Zhenyu Fang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Key Laboratory of Bio-pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
| | - Yan Cai
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Key Laboratory of Bio-pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
| | - Panpan Huang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Key Laboratory of Bio-pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
| | - Yakubu Saddeeq Abubakar
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Key Laboratory of Bio-pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Department of Biochemistry, Faculty of Life Science, Ahmadu Bello University, Zaria, 810281, Nigeria
| | - Jie Zhou
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
| | - Naweed I Naqvi
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117604, Singapore
| | - Zonghua Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Wenhui Zheng
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
- Key Laboratory of Bio-pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350000, China
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2
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Cook GD, Stasulli NM. Employing synthetic biology to expand antibiotic discovery. SLAS Technol 2024; 29:100120. [PMID: 38340893 DOI: 10.1016/j.slast.2024.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Antimicrobial-resistant (AMR) bacterial pathogens are a continually growing threat as our methods for combating these infections continue to be overcome by the evolution of resistance mechanisms. Recent therapeutic methods have not staved off the concern of AMR infections, so continued research focuses on new ways of identifying small molecules to treat AMR pathogens. While chemical modification of existing antibiotics is possible, there has been rapid development of resistance by pathogens that were initially susceptible to these compounds. Synthetic biology is becoming a key strategy in trying to predict and induce novel, natural antibiotics. Advances in cloning and mutagenesis techniques applied through a synthetic biology lens can help characterize the native regulation of antibiotic biosynthetic gene clusters (BGCs) to identify potential modifications leading to more potent antibiotic activity. Additionally, many cryptic antibiotic BGCs are derived from non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) biosynthetic pathways; complex, clustered genetic sequences that give rise to amino acid-derived natural products. Synthetic biology can be applied to modify and metabolically engineer these enzyme-based systems to promote rapid and sustainable production of natural products and their variants. This review will focus on recent advances related to synthetic biology as applied to genetic pathway characterization and identification of antibiotics from naturally occurring BGCs. Specifically, we will summarize recent efforts to characterize BGCs via general genomic mutagenesis, endogenous gene expression, and heterologous gene expression.
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Affiliation(s)
- Greta D Cook
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA
| | - Nikolas M Stasulli
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA.
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3
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Heucken N, Tang K, Hüsemann L, Heßler N, Müntjes K, Feldbrügge M, Göhre V, Zurbriggen MD. Engineering and Implementation of Synthetic Molecular Tools in the Basidiomycete Fungus Ustilago maydis. J Fungi (Basel) 2023; 9:jof9040480. [PMID: 37108934 PMCID: PMC10140897 DOI: 10.3390/jof9040480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The basidiomycete Ustilago maydis is a well-characterized model organism for studying pathogen-host interactions and of great interest for a broad spectrum of biotechnological applications. To facilitate research and enable applications, in this study, three luminescence-based and one enzymatic quantitative reporter were implemented and characterized. Several dual-reporter constructs were generated for ratiometric normalization that can be used as a fast-screening platform for reporter gene expression, applicable to in vitro and in vivo detection. Furthermore, synthetic bidirectional promoters that enable bicisitronic expression for gene expression studies and engineering strategies were constructed and implemented. These noninvasive, quantitative reporters and expression tools will significantly widen the application range of biotechnology in U. maydis and enable the in planta detection of fungal infection.
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Affiliation(s)
- Nicole Heucken
- Institute of Synthetic Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Kun Tang
- Institute of Synthetic Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Lisa Hüsemann
- Institute of Synthetic Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Natascha Heßler
- Institute of Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Kira Müntjes
- Institute of Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute of Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Vera Göhre
- Institute of Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
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4
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Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1029114. [PMID: 37746190 PMCID: PMC10512375 DOI: 10.3389/ffunb.2022.1029114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/28/2022] [Indexed: 09/26/2023]
Abstract
Ustilago maydis is a biotrophic phytopathogenic fungus that causes corn smut disease. As a well-established model system, U. maydis is genetically fully accessible with large omics datasets available and subject to various biological questions ranging from DNA-repair, RNA-transport, and protein secretion to disease biology. For many genetic approaches, tight control of transgene regulation is important. Here we established an optimised version of the Tetracycline-ON (TetON) system for U. maydis. We demonstrate the Tetracycline concentration-dependent expression of fluorescent protein transgenes and the system's suitability for the induced expression of the toxic protein BCL2 Associated X-1 (Bax1). The Golden Gate compatible vector system contains a native minimal promoter from the mating factor a-1 encoding gene, mfa with ten copies of the tet-regulated operator (tetO) and a codon optimised Tet-repressor (tetR*) which is translationally fused to the native transcriptional corepressor Mql1 (UMAG_05501). The metabolism-independent transcriptional regulator system is functional both, in liquid culture as well as on solid media in the presence of the inducer and can become a useful tool for toxin-antitoxin studies, identification of antifungal proteins, and to study functions of toxic gene products in Ustilago maydis.
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Affiliation(s)
- Kishor D. Ingole
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Nithya Nagarajan
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Simon Uhse
- Austrian Academy of Sciences (OEAW), Vienna Biocentre (VBC), Gregor Mendel Institute (GMI), Vienna, Austria
| | - Caterina Giannini
- Austrian Academy of Sciences (OEAW), Vienna Biocentre (VBC), Gregor Mendel Institute (GMI), Vienna, Austria
| | - Armin Djamei
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
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5
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Mózsik L, Iacovelli R, Bovenberg RAL, Driessen AJM. Transcriptional Activation of Biosynthetic Gene Clusters in Filamentous Fungi. Front Bioeng Biotechnol 2022; 10:901037. [PMID: 35910033 PMCID: PMC9335490 DOI: 10.3389/fbioe.2022.901037] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Filamentous fungi are highly productive cell factories, many of which are industrial producers of enzymes, organic acids, and secondary metabolites. The increasing number of sequenced fungal genomes revealed a vast and unexplored biosynthetic potential in the form of transcriptionally silent secondary metabolite biosynthetic gene clusters (BGCs). Various strategies have been carried out to explore and mine this untapped source of bioactive molecules, and with the advent of synthetic biology, novel applications, and tools have been developed for filamentous fungi. Here we summarize approaches aiming for the expression of endogenous or exogenous natural product BGCs, including synthetic transcription factors, assembly of artificial transcription units, gene cluster refactoring, fungal shuttle vectors, and platform strains.
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Affiliation(s)
- László Mózsik
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, Delft, Netherlands
- Department of Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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6
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Beattie SR, Jezewski AJ, Ristow LC, Wellington M, Krysan DJ. FKS1 Is Required for Cryptococcus neoformans Fitness In Vivo: Application of Copper-Regulated Gene Expression to Mouse Models of Cryptococcosis. mSphere 2022; 7:e0016322. [PMID: 35506343 PMCID: PMC9241531 DOI: 10.1128/msphere.00163-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/15/2022] [Indexed: 11/20/2022] Open
Abstract
There is an urgent need for new antifungals to treat cryptococcal meningoencephalitis, a leading cause of mortality in people living with HIV/AIDS. An important aspect of antifungal drug development is the validation of targets to determine whether they are required for the survival of the organism in animal models of disease. In Cryptococcus neoformans, a copper-regulated promoter (pCTR4-2) has been used previously to modulate gene expression in vivo. The premise for these experiments is that copper concentrations differ depending on the host niche. Here, we directly test this premise and confirm that the expression of CTR4, the promoter used to regulate gene expression, is much lower in the mouse lung compared to the brain. To further explore this approach, we applied it to the gene encoding 1,3-β-glucan synthase, FKS1. In vitro, reduced expression of FKS1 has little effect on growth but does activate the cell wall integrity stress response and increase susceptibility to caspofungin, a direct inhibitor of Fks1. These data suggest that compensatory pathways that reduce C. neoformans resistance do so through posttranscriptional effects. In vivo, however, a less pronounced reduction in FKS1 expression leads to a much more significant reduction in lung fungal burden (~1 log10 CFU), indicating that the compensatory responses to a reduction in FKS1 expression are not as effective in vivo as they are in vitro. In summary, use of copper-regulated expression of putative drug targets in vitro and in vivo can provide insights into the biological consequences of reduced activity of the target during infection. IMPORTANCE Conditional expression systems are widely used to genetically validate antifungal drug targets in mouse models of infection. Copper-regulated expression using the promoter of the CTR4 gene has been sporadically used for this purpose in C. neoformans. Here, we show that CTR4 expression is low in the lung and high in the brain, establishing the basic premise behind this approach. We applied the approach to the study of FKS1, the gene encoding the target of the echinocandin class of 1,3-β-glucan synthase inhibitors. Our in vitro and in vivo studies indicate that C. neoformans tolerates extremely low levels of FKS1 expression. This observation provides a potential explanation for the poor activity of 1,3-β-glucan synthase inhibitors toward C. neoformans.
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Affiliation(s)
- Sarah R. Beattie
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Andrew J. Jezewski
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Laura C. Ristow
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Melanie Wellington
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Damian J. Krysan
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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7
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de la Torre A, Jurca M, Hoffmann K, Schmitz L, Heimel K, Kämper J, Pérez-Martín J. Robust Cre recombinase activity in the biotrophic smut fungus Ustilago maydis enables efficient conditional null mutants in planta. Genetics 2022; 220:iyab152. [PMID: 34849846 PMCID: PMC8733456 DOI: 10.1093/genetics/iyab152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/10/2021] [Indexed: 11/12/2022] Open
Abstract
Site-specific recombinases have been used in higher eukaryotes, especially in animals, for a broad range of applications, including chromosomal translocations, large deletions, site-specific integration, and tissue-specific as well as conditional knock-outs. The application of site-specific recombination has also been demonstrated in simple eukaryotes like fungi and protozoa. However, its use in fungal research, especially in phytopathogenic fungi, has often been limited to "recycle" the marker genes used in transformation experiments. We show that Cre recombinase can be used for conditional gene deletions in the phytopathogenic fungus Ustilago maydis. Conditional gene knock-outs can be generated via the transcriptional control of the recombinase by U. maydis promoters specifically activated during the biotrophic phase of fungal growth, enabling gene deletions at defined developmental stages inside the plant tissue. Also, we show that a tamoxifen-activated Cre-recombinase allows the tight control necessary for the induced deletion of essential genes by the addition of tamoxifen. These tools will be helpful to address the function of genes under both axenic and in planta conditions for the U. maydis-maize pathosystem and should pave the way for similar approaches in other plant pathosystems.
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Affiliation(s)
| | - Matteo Jurca
- Department of Genetics, Karlsruhe Institute of Technology, Institute for Applied Biosciences, 76131 Karlsruhe, Germany
| | - Kai Hoffmann
- Department of Genetics, Karlsruhe Institute of Technology, Institute for Applied Biosciences, 76131 Karlsruhe, Germany
| | - Lara Schmitz
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen 37073, Germany
| | - Kai Heimel
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen 37073, Germany
| | - Jörg Kämper
- Department of Genetics, Karlsruhe Institute of Technology, Institute for Applied Biosciences, 76131 Karlsruhe, Germany
| | - José Pérez-Martín
- Instituto de Biología Funcional y Genómica (CSIC), Salamanca 37007, Spain
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8
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Mózsik L, Pohl C, Meyer V, Bovenberg RAL, Nygård Y, Driessen AJM. Modular Synthetic Biology Toolkit for Filamentous Fungi. ACS Synth Biol 2021; 10:2850-2861. [PMID: 34726388 PMCID: PMC8609570 DOI: 10.1021/acssynbio.1c00260] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Filamentous fungi
are highly productive cell factories, often used
in industry for the production of enzymes and small bioactive compounds.
Recent years have seen an increasing number of synthetic-biology-based
applications in fungi, emphasizing the need for a synthetic biology
toolkit for these organisms. Here we present a collection of 96 genetic
parts, characterized in Penicillium or Aspergillus species, that are
compatible and interchangeable with the Modular Cloning system. The
toolkit contains natural and synthetic promoters (constitutive and
inducible), terminators, fluorescent reporters, and selection markers.
Furthermore, there are regulatory and DNA-binding domains of transcriptional
regulators and components for implementing different CRISPR-based
technologies. Genetic parts can be assembled into complex multipartite
assemblies and delivered through genomic integration or expressed
from an AMA1-sequence-based, fungal-replicating shuttle vector. With
this toolkit, synthetic transcription units with established promoters,
fusion proteins, or synthetic transcriptional regulation devices can
be more rapidly assembled in a standardized and modular manner for
novel fungal cell factories.
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Affiliation(s)
- László Mózsik
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Carsten Pohl
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, 2613 AX Delft, The Netherlands
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Yvonne Nygård
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Arnold J. M. Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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Hussnaetter KP, Philipp M, Müntjes K, Feldbrügge M, Schipper K. Controlling Unconventional Secretion for Production of Heterologous Proteins in Ustilago maydis through Transcriptional Regulation and Chemical Inhibition of the Kinase Don3. J Fungi (Basel) 2021; 7:jof7030179. [PMID: 33802393 PMCID: PMC7999842 DOI: 10.3390/jof7030179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/27/2022] Open
Abstract
Heterologous protein production is a highly demanded biotechnological process. Secretion of the product to the culture broth is advantageous because it drastically reduces downstream processing costs. We exploit unconventional secretion for heterologous protein expression in the fungal model microorganism Ustilago maydis. Proteins of interest are fused to carrier chitinase Cts1 for export via the fragmentation zone of dividing yeast cells in a lock-type mechanism. The kinase Don3 is essential for functional assembly of the fragmentation zone and hence, for release of Cts1-fusion proteins. Here, we are first to develop regulatory systems for unconventional protein secretion using Don3 as a gatekeeper to control when export occurs. This enables uncoupling the accumulation of biomass and protein synthesis of a product of choice from its export. Regulation was successfully established at two different levels using transcriptional and post-translational induction strategies. As a proof-of-principle, we applied autoinduction based on transcriptional don3 regulation for the production and secretion of functional anti-Gfp nanobodies. The presented developments comprise tailored solutions for differentially prized products and thus constitute another important step towards a competitive protein production platform.
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10
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Lee J, Hilgers F, Loeschke A, Jaeger KE, Feldbrügge M. Ustilago maydis Serves as a Novel Production Host for the Synthesis of Plant and Fungal Sesquiterpenoids. Front Microbiol 2020; 11:1655. [PMID: 32849341 PMCID: PMC7396576 DOI: 10.3389/fmicb.2020.01655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022] Open
Abstract
Sesquiterpenoids are important secondary metabolites with various pharma- and nutraceutical properties. In particular, higher basidiomycetes possess a versatile biosynthetic repertoire for these bioactive compounds. To date, only a few microbial production systems for fungal sesquiterpenoids have been established. Here, we introduce Ustilago maydis as a novel production host. This model fungus is a close relative of higher basidiomycetes. It offers the advantage of metabolic compatibility and potential tolerance for substances toxic to other microorganisms. We successfully implemented a heterologous pathway to produce the carotenoid lycopene that served as a straightforward read-out for precursor pathway engineering. Overexpressing genes encoding enzymes of the mevalonate pathway resulted in increased lycopene levels. Verifying the subcellular localization of the relevant enzymes revealed that initial metabolic reactions might take place in peroxisomes: despite the absence of a canonical peroxisomal targeting sequence, acetyl-CoA C-acetyltransferase Aat1 localized to peroxisomes. By expressing the plant (+)-valencene synthase CnVS and the basidiomycete sesquiterpenoid synthase Cop6, we succeeded in producing (+)-valencene and α-cuprenene, respectively. Importantly, the fungal compound yielded about tenfold higher titers in comparison to the plant substance. This proof of principle demonstrates that U. maydis can serve as promising novel chassis for the production of terpenoids.
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Affiliation(s)
- Jungho Lee
- Bioeconomy Science Centre, Cluster of Excellence on Plant Sciences, Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fabienne Hilgers
- Institute for Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, and Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anita Loeschke
- Institute for Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, and Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute for Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, and Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Michael Feldbrügge
- Bioeconomy Science Centre, Cluster of Excellence on Plant Sciences, Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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11
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Müntjes K, Philipp M, Hüsemann L, Heucken N, Weidtkamp-Peters S, Schipper K, Zurbriggen MD, Feldbrügge M. Establishing Polycistronic Expression in the Model Microorganism Ustilago maydis. Front Microbiol 2020; 11:1384. [PMID: 32670239 PMCID: PMC7326815 DOI: 10.3389/fmicb.2020.01384] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic microorganisms use monocistronic mRNAs to encode proteins. For synthetic biological approaches like metabolic engineering, precise co-expression of several proteins in space and time is advantageous. A straightforward approach is the application of viral 2A peptides to design synthetic polycistronic mRNAs in eukaryotes. During translation of these peptides the ribosome stalls, the peptide chain is released and the ribosome resumes translation. Thus, two independent polypeptide chains can be encoded from a single mRNA when a 2A peptide sequence is placed inbetween the two open reading frames. Here, we establish such a system in the well-studied model microorganism Ustilago maydis. Using two fluorescence reporter proteins, we compared the activity of five viral 2A peptides. Their activity was evaluated in vivo using fluorescence microscopy and validated using fluorescence resonance energy transfer (FRET). Activity ranged from 20 to 100% and the best performing 2A peptide was P2A from porcine teschovirus-1. As proof of principle, we followed regulated gene expression efficiently over time and synthesised a tri-cistronic mRNA encoding biosynthetic enzymes to produce mannosylerythritol lipids (MELs). In essence, we evaluated 2A peptides in vivo and demonstrated the applicability of 2A peptide technology for U. maydis in basic and applied science.
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Affiliation(s)
- Kira Müntjes
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Magnus Philipp
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lisa Hüsemann
- Institute of Synthetic Biology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicole Heucken
- Institute of Synthetic Biology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Kerstin Schipper
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute of Synthetic Biology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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12
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Becker J, Hosseinpour Tehrani H, Gauert M, Mampel J, Blank LM, Wierckx N. An Ustilago maydis chassis for itaconic acid production without by-products. Microb Biotechnol 2019; 13:350-362. [PMID: 31880860 PMCID: PMC7017832 DOI: 10.1111/1751-7915.13525] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 11/28/2022] Open
Abstract
Ustilago maydis is a promising yeast for the production of a range of valuable metabolites, including itaconate, malate, glycolipids and triacylglycerols. However, wild-type strains generally produce a potpourri of all of these metabolites, which hinders efficient production of single target chemicals. In this study, the diverse by-product spectrum of U. maydis was reduced through strain engineering using CRISPR/Cas9 and FLP/FRT, greatly increasing the metabolic flux into the targeted itaconate biosynthesis pathway. With this strategy, a marker-free chassis strain could be engineered, which produces itaconate from glucose with significantly enhanced titre, rate and yield. The lack of by-product formation not only benefited itaconate production, it also increases the efficiency of downstream processing improving cell handling and product purity.
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Affiliation(s)
- Johanna Becker
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Hamed Hosseinpour Tehrani
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Marc Gauert
- BRAIN AG (Biotechnology, Research and Information Network), Darmstädter Str. 34-36, Zwingenberg, 64673, Germany
| | - Jörg Mampel
- BRAIN AG (Biotechnology, Research and Information Network), Darmstädter Str. 34-36, Zwingenberg, 64673, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
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13
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Steinhauer D, Salat M, Frey R, Mosbach A, Luksch T, Balmer D, Hansen R, Widdison S, Logan G, Dietrich RA, Kema GHJ, Bieri S, Sierotzki H, Torriani SFF, Scalliet G. A dispensable paralog of succinate dehydrogenase subunit C mediates standing resistance towards a subclass of SDHI fungicides in Zymoseptoria tritici. PLoS Pathog 2019; 15:e1007780. [PMID: 31860693 PMCID: PMC6941823 DOI: 10.1371/journal.ppat.1007780] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 01/03/2020] [Accepted: 11/20/2019] [Indexed: 11/24/2022] Open
Abstract
Succinate dehydrogenase inhibitor (SDHI) fungicides are widely used for the control of a broad range of fungal diseases. This has been the most rapidly expanding fungicide group in terms of new molecules discovered and introduced for agricultural use over the past fifteen years. A particular pattern of differential sensitivity (resistance) to the stretched heterocycle amide SDHIs (SHA-SDHIs), a subclass of chemically-related SDHIs, was observed in naïve Zymoseptoria tritici populations not previously exposed to these chemicals. Subclass-specific resistance was confirmed at the enzyme level but did not correlate with the genotypes of the succinate dehydrogenase (SDH) encoding genes. Mapping and characterization of the molecular mechanisms responsible for standing SHA-SDHI resistance in natural field isolates identified a gene paralog of SDHC, termed ZtSDHC3, which encodes for an alternative C subunit of succinate dehydrogenase, named alt-SDHC. Using reverse genetics, we showed that alt-SDHC associates with the three other SDH subunits, leading to a fully functional enzyme and that a unique Qp-site residue within the alt-SDHC protein confers SHA-SDHI resistance. Enzymatic assays, computational modelling and docking simulations for the two SQR enzymes (altC-SQR, WT_SQR) enabled us to describe enzyme-inhibitor interactions at an atomistic level and to propose rational explanations for differential potency and resistance across SHA-SDHIs. European Z. tritici populations displayed a presence (20–30%) / absence polymorphism of ZtSDHC3, as well as differences in ZtSDHC3 expression levels and splicing efficiency. These polymorphisms have a strong impact on SHA-SDHI resistance phenotypes. Characterization of the ZtSDHC3 promoter in European Z. tritici populations suggests that transposon insertions are associated with the strongest resistance phenotypes. These results establish that a dispensable paralogous gene determines SHA-SDHIs fungicide resistance in natural populations of Z. tritici. This study paves the way to an increased awareness of the role of fungicidal target paralogs in resistance to fungicides and demonstrates the paramount importance of population genomics in fungicide discovery. Zymoseptoria tritici is the causal agent of Septoria tritici leaf blotch (STB) of wheat, the most devastating disease for cereal production in Europe. Multiple succinate dehydrogenase inhibitor (SDHI) fungicides have been developed and introduced for the control of STB. We report the discovery and detailed characterization of a paralog of the C subunit of the SDH enzyme conferring standing resistance towards the SHA-SDHIs, a particular chemical subclass of the SDHIs. The SDHC paralog is characterized by its presence/absence, expression and alternative splicing polymorphisms, which in turn influence resistance levels. The identified mechanisms exemplify the importance of population genomics for the discovery and rational design of the most adapted solutions.
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Affiliation(s)
| | - Marie Salat
- Syngenta Crop Protection AG, Stein, Switzerland
| | - Regula Frey
- Syngenta Crop Protection AG, Stein, Switzerland
| | | | | | - Dirk Balmer
- Syngenta Crop Protection AG, Stein, Switzerland
| | - Rasmus Hansen
- Syngenta Jealott’s Hill Int. Research Centre, Bracknell Berkshire, United Kingdom
| | - Stephanie Widdison
- Syngenta Jealott’s Hill Int. Research Centre, Bracknell Berkshire, United Kingdom
| | - Grace Logan
- Syngenta Jealott’s Hill Int. Research Centre, Bracknell Berkshire, United Kingdom
| | - Robert A. Dietrich
- Syngenta Biotechnology Inc., Research Triangle Park, North Carolina, United States of America
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14
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Mózsik L, Büttel Z, Bovenberg RAL, Driessen AJM, Nygård Y. Synthetic control devices for gene regulation in Penicillium chrysogenum. Microb Cell Fact 2019; 18:203. [PMID: 31739777 PMCID: PMC6859608 DOI: 10.1186/s12934-019-1253-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/10/2019] [Indexed: 12/01/2022] Open
Abstract
Background Orthogonal, synthetic control devices were developed for Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. In the synthetic transcription factor, the QF DNA-binding domain of the transcription factor of the quinic acid gene cluster of Neurospora crassa is fused to the VP16 activation domain. This synthetic transcription factor controls the expression of genes under a synthetic promoter containing quinic acid upstream activating sequence (QUAS) elements, where it binds. A gene cluster may demand an expression tuned individually for each gene, which is a great advantage provided by this system. Results The control devices were characterized with respect to three of their main components: expression of the synthetic transcription factors, upstream activating sequences, and the affinity of the DNA binding domain of the transcription factor to the upstream activating domain. This resulted in synthetic expression devices, with an expression ranging from hardly detectable to a level similar to that of highest expressed native genes. The versatility of the control device was demonstrated by fluorescent reporters and its application was confirmed by synthetically controlling the production of penicillin. Conclusions The characterization of the control devices in microbioreactors, proved to give excellent indications for how the devices function in production strains and conditions. We anticipate that these well-characterized and robustly performing control devices can be widely applied for the production of secondary metabolites and other compounds in filamentous fungi.![]()
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Affiliation(s)
- László Mózsik
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Zsófia Büttel
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Roel A L Bovenberg
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Yvonne Nygård
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. .,DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands. .,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
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15
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Schuster M, Kahmann R. CRISPR-Cas9 genome editing approaches in filamentous fungi and oomycetes. Fungal Genet Biol 2019; 130:43-53. [PMID: 31048007 DOI: 10.1016/j.fgb.2019.04.016] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/27/2019] [Accepted: 04/28/2019] [Indexed: 12/26/2022]
Abstract
Due to their biotechnological relevance as well as their importance as disease agents, filamentous fungi and oomycetes have been prime candidates for genetic selection and in vitro manipulation for decades. With the advent of new genome editing technologies such manipulations have reached a new level of speed and sophistication. The CRISPR-Cas9 genome editing technology in particular has revolutionized the ways how desired mutations can be introduced. To date, the CRISPR-Cas9 genome editing system has been established in more than 40 different species of filamentous fungi and oomycetes. In this review we describe the various approaches taken to assure expression of the components necessary for editing and describe the varying strategies used to achieve gene disruptions, gene replacements and precise editing. We discuss potential problems faced when establishing the system, propose ways to circumvent them and suggest future approaches not yet realized in filamentous fungi or oomycetes.
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Affiliation(s)
- Mariana Schuster
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, 35043 Marburg, Germany.
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, 35043 Marburg, Germany.
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16
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Pinter N, Hach CA, Hampel M, Rekhter D, Zienkiewicz K, Feussner I, Poehlein A, Daniel R, Finkernagel F, Heimel K. Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis. PLoS Pathog 2019; 15:e1007734. [PMID: 30998787 PMCID: PMC6490947 DOI: 10.1371/journal.ppat.1007734] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/30/2019] [Accepted: 03/27/2019] [Indexed: 11/18/2022] Open
Abstract
The corn smut fungus Ustilago maydis requires the unfolded protein response (UPR) to maintain homeostasis of the endoplasmic reticulum (ER) during the biotrophic interaction with its host plant Zea mays (maize). Crosstalk between the UPR and pathways controlling pathogenic development is mediated by protein-protein interactions between the UPR regulator Cib1 and the developmental regulator Clp1. Cib1/Clp1 complex formation results in mutual modification of the connected regulatory networks thereby aligning fungal proliferation in planta, efficient effector secretion with increased ER stress tolerance and long-term UPR activation in planta. Here we address UPR-dependent gene expression and its modulation by Clp1 using combinatorial RNAseq/ChIPseq analyses. We show that increased ER stress resistance is connected to Clp1-dependent alterations of Cib1 phosphorylation, protein stability and UPR gene expression. Importantly, we identify by deletion screening of UPR core genes the signal peptide peptidase Spp1 as a novel key factor that is required for establishing a compatible biotrophic interaction between U. maydis and its host plant maize. Spp1 is dispensable for ER stress resistance and vegetative growth but requires catalytic activity to interfere with the plant defense, revealing a novel virulence specific function for signal peptide peptidases in a biotrophic fungal/plant interaction. Biotrophic pathogens establish compatible interactions with their host to cause disease. A critical step in this process is the suppression of plant defense responses by secreted effector proteins. In the maize infecting fungus Ustilago maydis expression of effector encoding genes is coordinately upregulated at defined stages of pathogenic development in so-called effector waves. Efficient secretion of the multitude of effectors relies on the unfolded protein response (UPR) to maintain homeostasis of the endoplasmic reticulum. Activation of the UPR is connected to the control of fungal proliferation through direct protein-protein interactions between the UPR regulator Cib1 and the developmental regulator Clp1. Here, we show that this interaction leads to functional modification of Cib1 and modulation of UPR gene expression to adapt the UPR for long-term activity in the plant. Within a core set of UPR regulated genes we identify the signal peptide peptidase Spp1 as a key factor for fungal virulence. We show that Spp1 requires its conserved catalytic activity to suppress the plant defense and cause disease. The virulence specific function of Spp1 does not involve pathways previously known to be associated with Spp1-like proteins or plant defense suppression, suggesting a novel role for Spp1 substrates in biotrophic interactions.
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Affiliation(s)
- Niko Pinter
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Christina Andrea Hach
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Martin Hampel
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Dmitrij Rekhter
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Krzysztof Zienkiewicz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Florian Finkernagel
- Center for Tumor Biology and Immunology (ZTI), Institute of Molecular Biology and Tumor Research (IMT), Marburg, Germany
| | - Kai Heimel
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
- * E-mail:
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17
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The interplay between transport and metabolism in fungal itaconic acid production. Fungal Genet Biol 2019; 125:45-52. [DOI: 10.1016/j.fgb.2019.01.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/03/2019] [Accepted: 01/17/2019] [Indexed: 11/27/2022]
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18
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Core components of endosomal mRNA transport are evolutionarily conserved in fungi. Fungal Genet Biol 2019; 126:12-16. [PMID: 30738139 DOI: 10.1016/j.fgb.2019.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 12/21/2022]
Abstract
Active movement of mRNAs by sophisticated transport machineries determines precise spatiotemporal expression of encoded proteins. A prominent example discovered in fungi is microtubule-dependent transport via endosomes. This mode of transport was thought to be only operational in the basidiomycete Ustilago maydis. Here, we report that distinct core components are evolutionarily conserved in fungal species of distantly related phyla like Mucoromycota. Interestingly, orthologues of the key RNA-binding protein Rrm4 from the higher basidiomycete Coprinopsis cinerea and the mucoromycete Rhizophagus irregularis shuttle on endosomes in hyphae of U. maydis. Thus, endosomal mRNA transport appears to be more wide-spread than initially anticipated.
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19
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Haag C, Klein T, Feldbrügge M. ESCRT Mutant Analysis and Imaging of ESCRT Components in the Model Fungus Ustilago maydis. Methods Mol Biol 2019; 1998:251-271. [PMID: 31250308 DOI: 10.1007/978-1-4939-9492-2_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ESCRT machinery (endosomal sorting complex required for transport) is an evolutionarily highly conserved multiprotein complex involved in numerous cellular processes like endocytosis, membrane repair, or endosomal long-distance transport. In fungal hyphae, endocytosis and long-distance mRNA transport are tightly linked, as endocytotic vesicles are also the key carrier vehicles for mRNAs. Studying the regulatory component Did2 (CHMP1) in the plant pathogen Ustilago maydis revealed that loss of Did2 resulted in disturbed endosomal maturation, thereby causing defects in microtubule-dependent transport of early endosomes. Here, we describe methods and protocols that allow studying the role of ESCRT components during endosomal transport. We present experimental strategies to analyze U. maydis ESCRT mutant phenotypes and test complementation with heterologous components, such as ESCRT regulators from Drosophila melanogaster.
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Affiliation(s)
- Carl Haag
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Microbiology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Thomas Klein
- Institute of Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Feldbrügge
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Microbiology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany.
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20
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Müller MJ, Stachurski S, Stoffels P, Schipper K, Feldbrügge M, Büchs J. Online evaluation of the metabolic activity of Ustilago maydis on (poly)galacturonic acid. J Biol Eng 2018; 12:34. [PMID: 30574186 PMCID: PMC6299674 DOI: 10.1186/s13036-018-0128-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/03/2018] [Indexed: 11/10/2022] Open
Abstract
Background Pectin is a rather complex and highly branched polysaccharide strengthening the plant cell wall. Thus, many different pectinases are required for an efficient microbial conversion of biomass waste streams with a high pectin content like citrus peel, apple pomace or sugar beet pulp. The screening and optimization of strains growing on pectic substrates requires both, quantification of the residual substrate and an accurate determination of the enzymatic activity. Galacturonic acid, the main sugar unit of pectin, is an uncommon substrate for microbial fermentations. Thus, growth and enzyme production of the applied strain has to be characterized in detail to understand the microbial system. An essential step to reach this goal is the development of online monitoring tools. Results In this study, a method for the online determination of residual substrate was developed for the growth of the plant pathogenic fungus Ustilago maydis on pectic substrates such as galacturonic acid. To this end, an U. maydis strain was used that expressed a heterologous exo-polygalacturonase for growth on polygalacturonic acid. The growth behavior on galacturonic acid was analyzed by online measurement of the respiration activity. A method for the online prediction of the residual galacturonic acid concentration during the cultivation, based on the overall oxygen consumption, was developed and verified by offline sampling. This sensitive method was extended towards polygalacturonic acid, which is challenging to quantify via offline measurements. Finally, the enzymatic activity in the culture supernatant was calculated and the enzyme stability during the course of the cultivation was confirmed. Conclusion The introduced method can reliably predict the residual (poly)galacturonic acid concentration based on the overall oxygen consumption. Based on this method, the enzymatic activity of the culture broth of an U. maydis strain expressing a heterologous exo-polygalacturonase could be calculated. It was demonstrated that the method is especially advantageous for determination of low enzymatic activities. In future, it will be applied to U. maydis strains in which the number of produced hydrolytic enzymes is increased for more efficient degradation. Electronic supplementary material The online version of this article (10.1186/s13036-018-0128-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Markus Jan Müller
- 1AVT - Biochemical Engineering, RWTH Aachen University, Jochen Büchs, Forckenbeckstr. 51, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), 52426 Jülich, Germany
| | - Sarah Stachurski
- 1AVT - Biochemical Engineering, RWTH Aachen University, Jochen Büchs, Forckenbeckstr. 51, 52074 Aachen, Germany
| | - Peter Stoffels
- 2Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,Bioeconomy Science Center (BioSC), 52426 Jülich, Germany
| | - Kerstin Schipper
- 2Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,Bioeconomy Science Center (BioSC), 52426 Jülich, Germany
| | - Michael Feldbrügge
- 2Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,Bioeconomy Science Center (BioSC), 52426 Jülich, Germany
| | - Jochen Büchs
- 1AVT - Biochemical Engineering, RWTH Aachen University, Jochen Büchs, Forckenbeckstr. 51, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), 52426 Jülich, Germany
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21
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Zhou L, Obhof T, Schneider K, Feldbrügge M, Nienhaus GU, Kämper J. Cytoplasmic Transport Machinery of the SPF27 Homologue Num1 in Ustilago maydis. Sci Rep 2018; 8:3611. [PMID: 29483520 PMCID: PMC5832149 DOI: 10.1038/s41598-018-21628-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/07/2018] [Indexed: 01/15/2023] Open
Abstract
In the phytopathogenic basidiomycete Ustilago maydis, the Num1 protein has a pivotal function in hyphal morphogenesis. Num1 functions as a core component of the spliceosome-associated Prp19/CDC5 complex (NTC). The interaction of Num1 with the kinesin motor Kin1 suggests a connection between a component of the splicing machinery and cytoplasmic trafficking processes. Previously it was shown that Num1 localizes predominantly in the nucleus; however, due to the diffraction-limited spatial resolution of conventional optical microscopy, it was not possible to attribute the localization to specific structures within the cytoplasm. We have now employed super-resolution localization microscopy to visualize Num1 in the cytoplasm by fusing it to a tandem dimeric Eos fluorescent protein (tdEosFP). The Num1 protein is localized within the cytoplasm with an enhanced density in the vicinity of microtubules. Num1 movement is found predominantly close to the nucleus. Movement is dependent on its interaction partner Kin1, but independent of Kin3. Our results provide strong evidence that, in addition to its involvement in splicing in the nucleus, Num1 has an additional functional role in the cytosol connected to the Kin1 motor protein.
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Affiliation(s)
- Lu Zhou
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Theresa Obhof
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Karina Schneider
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Michael Feldbrügge
- Institute of Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, Düsseldorf, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
| | - Jörg Kämper
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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22
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Zambanini T, Hartmann SK, Schmitz LM, Büttner L, Hosseinpour Tehrani H, Geiser E, Beudels M, Venc D, Wandrey G, Büchs J, Schwarzländer M, Blank LM, Wierckx N. Promoters from the itaconate cluster of Ustilago maydis are induced by nitrogen depletion. Fungal Biol Biotechnol 2017; 4:11. [PMID: 29209508 PMCID: PMC5706154 DOI: 10.1186/s40694-017-0040-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/18/2017] [Indexed: 12/31/2022] Open
Abstract
Background Ustilago maydis is known for its natural potential to produce a broad range of valuable chemicals, such as itaconate, from both industrial carbon waste streams and renewable biomass. Production of itaconate, and many other secondary metabolites, is induced by nitrogen limitation in U. maydis. The clustered genes responsible for itaconate production have recently been identified, enabling the development of new expression tools that are compatible with biotechnological processes. Results Here we report on the investigation of two of the native promoters, Ptad1 and Pmtt1, from the itaconate cluster of U. maydis MB215. For both promoters the specific activation upon nitrogen limitation, which is known to be the trigger for itaconate production in Ustilago, could be demonstrated by gfp expression. The promoters cover a broad range of expression levels, especially when combined with the possibility to create single- and multicopy construct integration events. In addition, these reporter constructs enable a functional characterization of gene induction patterns associated with itaconate production. Conclusions The promoters are well suited to induce gene expression in response to nitrogen limitation, coupled to the itaconate production phase, which contributes towards the further improvement of organic acid production with Ustilago.
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Affiliation(s)
- Thiemo Zambanini
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Sandra K Hartmann
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany.,BioSC, c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Lisa M Schmitz
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Linda Büttner
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
| | - Hamed Hosseinpour Tehrani
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Elena Geiser
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Melanie Beudels
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Dominik Venc
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Georg Wandrey
- AVT-Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Jochen Büchs
- AVT-Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Markus Schwarzländer
- BioSC, c/o Forschungszentrum Jülich, 52425 Jülich, Germany.,Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany.,Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
| | - Nick Wierckx
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074 Germany
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Applying Unconventional Secretion in Ustilago maydis for the Export of Functional Nanobodies. Int J Mol Sci 2017; 18:ijms18050937. [PMID: 28468279 PMCID: PMC5454850 DOI: 10.3390/ijms18050937] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/21/2017] [Accepted: 04/24/2017] [Indexed: 12/25/2022] Open
Abstract
Exploiting secretory pathways for production of heterologous proteins is highly advantageous with respect to efficient downstream processing. In eukaryotic systems the vast majority of heterologous proteins for biotechnological application is exported via the canonical endoplasmic reticulum–Golgi pathway. In the endomembrane system target proteins are often glycosylated and may thus be modified with foreign glycan patterns. This can be destructive for their activity or cause immune reactions against therapeutic proteins. Hence, using unconventional secretion for protein expression is an attractive alternative. In the fungal model Ustilago maydis, chitinase Cts1 is secreted via an unconventional pathway connected to cell separation which can be used to co-export heterologous proteins. Here, we apply this mechanism for the production of nanobodies. First, we achieved expression and unconventional secretion of a functional nanobody directed against green fluorescent protein (Gfp). Second, we found that Cts1 binds to chitin and that this feature can be applied to generate a Gfp-trap. Thus, we demonstrated the dual use of Cts1 serving both as export vehicle and as purification tag. Finally, we established and optimized the production of a nanobody against botulinum toxin A and hence describe the first pharmaceutically relevant target exported by Cts1-mediated unconventional secretion.
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Activating Intrinsic Carbohydrate-Active Enzymes of the Smut Fungus Ustilago maydis for the Degradation of Plant Cell Wall Components. Appl Environ Microbiol 2016; 82:5174-85. [PMID: 27316952 DOI: 10.1128/aem.00713-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The microbial conversion of plant biomass to valuable products in a consolidated bioprocess could greatly increase the ecologic and economic impact of a biorefinery. Current strategies for hydrolyzing plant material mostly rely on the external application of carbohydrate-active enzymes (CAZymes). Alternatively, production organisms can be engineered to secrete CAZymes to reduce the reliance on externally added enzymes. Plant-pathogenic fungi have a vast repertoire of hydrolytic enzymes to sustain their lifestyle, but expression of the corresponding genes is usually highly regulated and restricted to the pathogenic phase. Here, we present a new strategy in using the biotrophic smut fungus Ustilago maydis for the degradation of plant cell wall components by activating its intrinsic enzyme potential during axenic growth. This fungal model organism is fully equipped with hydrolytic enzymes, and moreover, it naturally produces value-added substances, such as organic acids and biosurfactants. To achieve the deregulated expression of hydrolytic enzymes during the industrially relevant yeast-like growth in axenic culture, the native promoters of the respective genes were replaced by constitutively active synthetic promoters. This led to an enhanced conversion of xylan, cellobiose, and carboxymethyl cellulose to fermentable sugars. Moreover, a combination of strains with activated endoglucanase and β-glucanase increased the release of glucose from carboxymethyl cellulose and regenerated amorphous cellulose, suggesting that mixed cultivations could be a means for degrading more complex substrates in the future. In summary, this proof of principle demonstrates the potential applicability of activating the expression of native CAZymes from phytopathogens in a biocatalytic process. IMPORTANCE This study describes basic experiments that aim at the degradation of plant cell wall components by the smut fungus Ustilago maydis As a plant pathogen, this fungus contains a set of lignocellulose-degrading enzymes that may be suited for biomass degradation. However, its hydrolytic enzymes are specifically expressed only during plant infection. Here, we provide the proof of principle that these intrinsic enzymes can be synthetically activated during the industrially relevant yeast-like growth. The fungus is known to naturally synthesize valuable compounds, such as itaconate or glycolipids. Therefore, it could be suited for use in a consolidated bioprocess in which more complex and natural substrates are simultaneously converted to fermentable sugars and to value-added compounds in the future.
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Wanka F, Cairns T, Boecker S, Berens C, Happel A, Zheng X, Sun J, Krappmann S, Meyer V. Tet-on, or Tet-off, that is the question: Advanced conditional gene expression in Aspergillus. Fungal Genet Biol 2016; 89:72-83. [DOI: 10.1016/j.fgb.2015.11.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/28/2015] [Accepted: 11/03/2015] [Indexed: 12/20/2022]
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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: 144] [Impact Index Per Article: 16.0] [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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Schuler D, Wahl R, Wippel K, Vranes M, Münsterkötter M, Sauer N, Kämper J. Hxt1, a monosaccharide transporter and sensor required for virulence of the maize pathogen Ustilago maydis. THE NEW PHYTOLOGIST 2015; 206:1086-1100. [PMID: 25678342 DOI: 10.1111/nph.13314] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/23/2014] [Indexed: 05/23/2023]
Abstract
The smut Ustilago maydis, a ubiquitous pest of corn, is highly adapted to its host to parasitize on its organic carbon sources. We have identified a hexose transporter, Hxt1, as important for fungal development during both the saprophytic and the pathogenic stage of the fungus. Hxt1 was characterized as a high-affinity transporter for glucose, fructose, and mannose; ∆hxt1 strains show significantly reduced growth on these substrates, setting Hxt1 as the main hexose transporter during saprophytic growth. After plant infection, ∆hxt1 strains show decreased symptom development. However, expression of a Hxt1 protein with a mutation leading to constitutively active signaling in the yeast glucose sensors Snf3p and Rgt2p results in completely apathogenic strains. Fungal development is stalled immediately after plant penetration, implying a dual function of Hxt1 as transporter and sensor. As glucose sensors are only known for yeasts, 'transceptor' as Hxt1 may constitute a general mechanism for sensing of glucose in fungi. In U. maydis, Hxt1 links a nutrient-dependent environmental signal to the developmental program during pathogenic development.
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Affiliation(s)
- David Schuler
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Hertzstrasse 16, Karlsruhe, 76187, Germany
| | - Ramon Wahl
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Hertzstrasse 16, Karlsruhe, 76187, Germany
| | - Kathrin Wippel
- Molecular Plant Physiology, Friedrich Alexander University Erlangen-Nuremberg, Staudtstrasse 5, Erlangen, 91058, Germany
| | - Miroslav Vranes
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Hertzstrasse 16, Karlsruhe, 76187, Germany
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Norbert Sauer
- Molecular Plant Physiology, Friedrich Alexander University Erlangen-Nuremberg, Staudtstrasse 5, Erlangen, 91058, Germany
| | - Jörg Kämper
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Hertzstrasse 16, Karlsruhe, 76187, Germany
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Sarkari P, Reindl M, Stock J, Müller O, Kahmann R, Feldbrügge M, Schipper K. Improved expression of single-chain antibodies in Ustilago maydis. J Biotechnol 2014; 191:165-75. [DOI: 10.1016/j.jbiotec.2014.06.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/17/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
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Terfrüchte M, Joehnk B, Fajardo-Somera R, Braus GH, Riquelme M, Schipper K, Feldbrügge M. Establishing a versatile Golden Gate cloning system for genetic engineering in fungi. Fungal Genet Biol 2014; 62:1-10. [DOI: 10.1016/j.fgb.2013.10.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/24/2013] [Accepted: 10/27/2013] [Indexed: 11/25/2022]
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Chacko N, Lin X. Non-coding RNAs in the development and pathogenesis of eukaryotic microbes. Appl Microbiol Biotechnol 2013; 97:7989-97. [PMID: 23948725 DOI: 10.1007/s00253-013-5160-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/26/2013] [Accepted: 07/29/2013] [Indexed: 12/15/2022]
Abstract
RNA has long been regarded as the important intermediary in the central dogma of gene expression. Recently, the importance of RNAs in the regulation of gene expression became evident with the identification and characterization of non-protein coding transcripts named non-coding RNAs (ncRNAs). The ncRNAs, small and long, are ubiquitously present in all three domains of life and are being recognized for their important roles in genome defense and development. Some of the ncRNAs have been associated with diseases, and therefore, they offer diagnostic and therapeutic potential. In this mini-review, we have highlighted some recent research on the ncRNAs identified in eukaryotic microbes, with special emphasis on fungi that are pathogenic to humans or plants when possible. It is our contention that further elucidation and understanding of ncRNAs will advance our understanding of the development and pathogenesis of eukaryotic microbes and offer alternatives in the diagnosis and treatment of the diseases caused by these pathogens.
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Affiliation(s)
- Nadia Chacko
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843-3258, USA
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31
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Feldbrügge M, Kellner R, Schipper K. The biotechnological use and potential of plant pathogenic smut fungi. Appl Microbiol Biotechnol 2013; 97:3253-65. [DOI: 10.1007/s00253-013-4777-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/12/2013] [Accepted: 02/13/2013] [Indexed: 01/03/2023]
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Stock J, Sarkari P, Kreibich S, Brefort T, Feldbrügge M, Schipper K. Applying unconventional secretion of the endochitinase Cts1 to export heterologous proteins in Ustilago maydis. J Biotechnol 2012; 161:80-91. [DOI: 10.1016/j.jbiotec.2012.03.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 02/17/2012] [Accepted: 03/08/2012] [Indexed: 01/30/2023]
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König J, Baumann S, Koepke J, Pohlmann T, Zarnack K, Feldbrügge M. The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs. EMBO J 2009; 28:1855-66. [PMID: 19494833 DOI: 10.1038/emboj.2009.145] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 05/08/2009] [Indexed: 11/09/2022] Open
Abstract
Cytoskeletal transport promotes polar growth in filamentous fungi. In Ustilago maydis, the RNA-binding protein Rrm4 shuttles along microtubules and is crucial for polarity in infectious filaments. Mutations in the RNA-binding domain cause loss of function. However, it was unclear which RNAs are bound and transported. Here, we applied in vivo RNA binding studies and live imaging to determine the molecular function of Rrm4. This new combination revealed that Rrm4 mediates microtubule-dependent transport of distinct mRNAs encoding, for example, the ubiquitin fusion protein Ubi1 and the small G protein Rho3. These transcripts accumulate in ribonucleoprotein particles (mRNPs) that move bidirectionally along microtubules and co-localise with Rrm4. Importantly, the 3' untranslated region of ubi1 containing a CA-rich binding site functions as zipcode during mRNA transport. Furthermore, motile mRNPs are not formed when the RNA-binding domain of Rrm4 is deleted, although the protein is still shuttling. Thus, Rrm4 constitutes an integral component of the transport machinery. We propose that microtubule-dependent mRNP trafficking is crucial for hyphal growth introducing U. maydis as attractive model for studying mRNA transport in higher eukaryotes.
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Affiliation(s)
- Julian König
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Role of Blm and collaborating factors in recombination and survival following replication stress in Ustilago maydis. DNA Repair (Amst) 2009; 8:752-9. [PMID: 19349216 DOI: 10.1016/j.dnarep.2009.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 01/16/2009] [Accepted: 02/06/2009] [Indexed: 11/20/2022]
Abstract
Inactivation of the structural gene for the RecQ family member, BLM in human, Sgs1 in budding yeast, or Rqh1 in fission yeast leads to inappropriate recombination, chromosome abnormalities, and disturbed replication fork progression. Studies with yeasts have demonstrated that auxiliary gene functions can contribute in overlapping ways with Sgs1 or Rqh1 to circumvent or overcome lesions in DNA caused by certain genotoxic agents. In the combined absence of these functions, recombination-mediated processes lead to severe loss of fitness. Here we performed a genetic study to determine the role of the Ustilago maydis Blm homolog in DNA repair and in alleviating replication stress. We characterized the single mutant as well as double mutants additionally deleted of genes encoding Srs2, Fbh1, Mus81, or Exo1. Unlike yeasts, neither the blm srs2, blm exo1, nor blm mus81 double mutant exhibited extreme loss of fitness. Inactivation of Brh2, the BRCA2 homolog, suppressed toxicity to hydroxyurea caused by loss of Blm function. However, differential suppression by Brh2 derivatives lacking the canonical DNA-binding region suggests that the particular domain structure comprising this DNA-binding region may be instrumental in promoting the observed hydroxyurea toxicity.
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Steinberg G, Perez-Martin J. Ustilago maydis, a new fungal model system for cell biology. Trends Cell Biol 2008; 18:61-7. [PMID: 18243705 DOI: 10.1016/j.tcb.2007.11.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2007] [Revised: 09/30/2007] [Accepted: 11/14/2007] [Indexed: 11/26/2022]
Abstract
The use of fungal model systems, such as Saccharomyces cerevisisae and Schizosaccharomyces pombe, has contributed enormously to our understanding of essential cellular processes in animals. Here, we introduce the corn smut fungus Ustilago maydis as a new model organism for studying cell biological processes. Genome-wide analysis demonstrates that U. maydis is more closely related to humans than to budding yeast, and numerous proteins are shared only by U. maydis and Homo sapiens. Growing evidence suggests that basic principles of long-distance transport, mitosis and motor-based microtubule organization are conserved between U. maydis and humans. The fungus U. maydis, therefore, offers a unique system for the study of certain mammalian processes.
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Affiliation(s)
- Gero Steinberg
- Max Planck-Institut für Terrestrische Mikrobiologie, Karl-von-Frisch-Str., D-35037 Marburg, Germany; School of Bioscience, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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Judelson HS, Narayan R, Fong AMVA, Tani S, Kim KS. Performance of a tetracycline-responsive transactivator system for regulating transgenes in the oomycete Phytophthora infestans. Curr Genet 2007; 51:297-307. [PMID: 17377792 DOI: 10.1007/s00294-007-0125-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 02/23/2007] [Accepted: 02/24/2007] [Indexed: 11/27/2022]
Abstract
The oomycete genus Phytophthora includes many important plant pathogens for which extensive genome data exist, but lacking is an inducible expression system to study contributions of their genes to growth and pathogenicity. Here the adaptation of the reverse tetracycline transactivator (rtTA) system to P. infestans is described. Vectors were developed containing rtTA expressed from an oomycete promoter, and beta-glucuronidase (GUS) controlled by TetR binding sites fused to a minimal oomycete promoter. Transformants were obtained in which GUS was expressed in a dose-dependent manner by the rtTA inducer doxycycline, indicating that the gene switch functions in P. infestans. However, toxicity of rtTA hindered the isolation of transformants if expressed on the same plasmid as the nptII selection marker. Better results were obtained by cotransforming those genes on separate plasmids, with 92% of transformants acquiring both DNAs although only 4% expressed rtTA at detectable levels. Low levels of reporter activity were measured in such transformants, suggesting that rtTA activated transcription weakly. Also, significant variation in the sensitivity of isolates to doxycycline and tetracycline was observed. These results are useful both in terms of developing tools for functional genomics and understanding the fate of DNA during Phytophthora transformation.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology, University of California, Riverside, CA 92521, USA.
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Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Müller O, Perlin MH, Wösten HAB, de Vries R, Ruiz-Herrera J, Reynaga-Peña CG, Snetselaar K, McCann M, Pérez-Martín J, Feldbrügge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, González-Prieto JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Münch K, Rössel N, Scherer M, Vranes M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng S, Ho ECH, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Häuser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schlüter T, Margolis J, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Güldener U, Münsterkötter M, Haase D, Oesterheld M, Mewes HW, Mauceli EW, DeCaprio D, Wade CM, Butler J, Young S, Jaffe DB, Calvo S, Nusbaum C, Galagan J, Birren BW. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 2006; 444:97-101. [PMID: 17080091 DOI: 10.1038/nature05248] [Citation(s) in RCA: 826] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Accepted: 09/15/2006] [Indexed: 01/30/2023]
Abstract
Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence strategies to kill its host. U. maydis belongs to the group of biotrophic parasites (the smuts) that depend on living tissue for proliferation and development. Here we report the genome sequence for a member of this economically important group of biotrophic fungi. The 20.5-million-base U. maydis genome assembly contains 6,902 predicted protein-encoding genes and lacks pathogenicity signatures found in the genomes of aggressive pathogenic fungi, for example a battery of cell-wall-degrading enzymes. However, we detected unexpected genomic features responsible for the pathogenicity of this organism. Specifically, we found 12 clusters of genes encoding small secreted proteins with unknown function. A significant fraction of these genes exists in small gene families. Expression analysis showed that most of the genes contained in these clusters are regulated together and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from a complete lack of symptoms to hypervirulence. Despite years of research into the mechanism of pathogenicity in U. maydis, no 'true' virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi. Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens.
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Affiliation(s)
- Jörg Kämper
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse, D-35043 Marburg, Germany.
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