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Scott CJR, McGregor NGS, Leadbeater DR, Oates NC, Hoßbach J, Abood A, Setchfield A, Dowle A, Overkleeft HS, Davies GJ, Bruce NC. Parascedosporium putredinis NO1 tailors its secretome for different lignocellulosic substrates. Microbiol Spectr 2024; 12:e0394323. [PMID: 38757984 PMCID: PMC11218486 DOI: 10.1128/spectrum.03943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Parascedosporium putredinis NO1 is a plant biomass-degrading ascomycete with a propensity to target the most recalcitrant components of lignocellulose. Here we applied proteomics and activity-based protein profiling (ABPP) to investigate the ability of P. putredinis NO1 to tailor its secretome for growth on different lignocellulosic substrates. Proteomic analysis of soluble and insoluble culture fractions following the growth of P. putredinis NO1 on six lignocellulosic substrates highlights the adaptability of the response of the P. putredinis NO1 secretome to different substrates. Differences in protein abundance profiles were maintained and observed across substrates after bioinformatic filtering of the data to remove intracellular protein contamination to identify the components of the secretome more accurately. These differences across substrates extended to carbohydrate-active enzymes (CAZymes) at both class and family levels. Investigation of abundant activities in the secretomes for each substrate revealed similar variation but also a high abundance of "unknown" proteins in all conditions investigated. Fluorescence-based and chemical proteomic ABPP of secreted cellulases, xylanases, and β-glucosidases applied to secretomes from multiple growth substrates for the first time confirmed highly adaptive time- and substrate-dependent glycoside hydrolase production by this fungus. P. putredinis NO1 is a promising new candidate for the identification of enzymes suited to the degradation of recalcitrant lignocellulosic feedstocks. The investigation of proteomes from the biomass bound and culture supernatant fractions provides a more complete picture of a fungal lignocellulose-degrading response. An in-depth understanding of this varied response will enhance efforts toward the development of tailored enzyme systems for use in biorefining.IMPORTANCEThe ability of the lignocellulose-degrading fungus Parascedosporium putredinis NO1 to tailor its secreted enzymes to different sources of plant biomass was revealed here. Through a combination of proteomic, bioinformatic, and fluorescent labeling techniques, remarkable variation was demonstrated in the secreted enzyme response for this ascomycete when grown on multiple lignocellulosic substrates. The maintenance of this variation over time when exploring hydrolytic polysaccharide-active enzymes through fluorescent labeling, suggests that this variation results from an actively tailored secretome response based on substrate. Understanding the tailored secretomes of wood-degrading fungi, especially from underexplored and poorly represented families, will be important for the development of effective substrate-tailored treatments for the conversion and valorization of lignocellulose.
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Affiliation(s)
- Conor J R Scott
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Janina Hoßbach
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Amira Abood
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Alexander Setchfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
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Beier S, Stiegler M, Hitzenhammer E, Monika S. Screening for genes involved in cellulase regulation by expression under the control of a novel constitutive promoter in Trichoderma reesei. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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3
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Promoter regulation and genetic engineering strategies for enhanced cellulase expression in Trichoderma reesei. Microbiol Res 2022; 259:127011. [DOI: 10.1016/j.micres.2022.127011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/18/2023]
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Industrially Important Genes from Trichoderma. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Polozsányi Z, Kaliňák M, Babjak M, Šimkovič M, Varečka Ľ. How to enter the state of dormancy? A suggestion by Trichoderma atroviride conidia. Fungal Biol 2021; 125:934-949. [PMID: 34649680 DOI: 10.1016/j.funbio.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 06/12/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
It is generally accepted that conidia, propagules of filamentous fungi, exist in the state of dormancy. This state is defined mostly phenomenologically, e.g., by germination requirements. Its molecular characteristics are scarce and are concentrated on the water or osmolyte content, and/or respiration. However, a question of whether conidia are metabolic or ametabolic forms of life cannot be answered on the basis of available experimental data. In other words, are mature conidia open thermodynamic systems as are mycelia, or do they become closed upon the transition to the dormant state? In this article, we present observations which may help to define the transition of freshly formed conidia to the putative dormant forms using measurements of selected enzyme activities, 1H- and 13C-NMR and LC-MS-metabolomes, and 14C-bicarbonate or 45Ca2+ inward transport. We have found that Trichoderma atroviride and Aspergillus niger conidia arrest the 45Ca2+ uptake during the development stopping thereby the cyclic (i.e., bidirectional) Ca2+ flow existing in vegetative mycelia and conidia of T. atroviride across the cytoplasmic membrane. Furthermore, we have found that the activity of α-ketoglutarate dehydrogenase was rendered completely inactive after 3 weeks from the conidia formation unlike of other central carbon metabolism enzymes. This may explain the loss of conidial respiration. Finally, we found that conidia take up the H14CO3- and convert it into few stable compounds within 80 d of maturation, with minor quantitative differences in the extent of this process. The uptake of H13CO3- confirmed these observation and demonstrated the incorporation of H13CO3- even in the absence of exogenous substrates. These results suggest that T. atroviride conidia remain metabolically active during first ten weeks of maturation. Under these circumstances, their metabolism displays features similar to those of chemoautotrophic microorganisms. However, the Ca2+ homeostasis changed from the open to the closed thermodynamic state during the early period of conidial maturation. These results may be helpful for studying the conidial ageing and/or maturation, and for defining the conidial dormant state in biochemical terms.
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Affiliation(s)
- Zoltán Polozsányi
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Michal Kaliňák
- Central Laboratories, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Matej Babjak
- Department of Organic Chemistry, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Martin Šimkovič
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia.
| | - Ľudovít Varečka
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia
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Pirayre A, Duval L, Blugeon C, Firmo C, Perrin S, Jourdier E, Margeot A, Bidard F. Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30. BMC Genomics 2020; 21:885. [PMID: 33302864 PMCID: PMC7731781 DOI: 10.1186/s12864-020-07281-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually performed by enzymes produced and secreted by the fungus Trichoderma reesei. Studies identifying transcription factors involved in the regulation of cellulase production have been conducted but no overview of the whole regulation network is available. A transcriptomic approach with mixtures of glucose and lactose, used as a substrate for cellulase induction, was used to help us decipher missing parts in the network of T. reesei Rut-C30. RESULTS Experimental results on the Rut-C30 hyperproducing strain confirmed the impact of sugar mixtures on the enzymatic cocktail composition. The transcriptomic study shows a temporal regulation of the main transcription factors and a lactose concentration impact on the transcriptional profile. A gene regulatory network built using BRANE Cut software reveals three sub-networks related to i) a positive correlation between lactose concentration and cellulase production, ii) a particular dependence of the lactose onto the β-glucosidase regulation and iii) a negative regulation of the development process and growth. CONCLUSIONS This work is the first investigating a transcriptomic study regarding the effects of pure and mixed carbon sources in a fed-batch mode. Our study expose a co-orchestration of xyr1, clr2 and ace3 for cellulase and hemicellulase induction and production, a fine regulation of the β-glucosidase and a decrease of growth in favor of cellulase production. These conclusions provide us with potential targets for further genetic engineering leading to better cellulase-producing strains in industry-like conditions.
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Affiliation(s)
- Aurélie Pirayre
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France.
| | - Laurent Duval
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
- Laboratoire d'Informatique Gaspard-Monge (LIGM), ESIEE Paris, Université-Gustave Eiffel, Marne-la-Vallée, F-77454, France
| | - Corinne Blugeon
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Cyril Firmo
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Sandrine Perrin
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Etienne Jourdier
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
| | - Frédérique Bidard
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
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Dubey M, Jensen DF, Karlsson M. Functional characterization of the AGL1 aegerolysin in the mycoparasitic fungus Trichoderma atroviride reveals a role in conidiation and antagonism. Mol Genet Genomics 2020; 296:131-140. [PMID: 33052533 PMCID: PMC7840653 DOI: 10.1007/s00438-020-01732-3] [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: 05/07/2020] [Accepted: 09/29/2020] [Indexed: 11/28/2022]
Abstract
Aegerolysins are small secreted pore-forming proteins that are found in both prokaryotes and eukaryotes. The role of aegerolysins in sporulation, fruit body formation, and in lysis of cellular membrane is suggested in fungi. The aim of the present study was to characterize the biological function of the aegerolysin gene agl1 in the mycoparasitic fungus Trichoderma atroviride, used for biological control of plant diseases. Gene expression analysis showed higher expression of agl1 during conidiation and during growth in medium supplemented with cell wall material from the plant pathogenic fungus Rhizoctonia solani as the sole carbon source. Expression of agl1 was supressed under iron-limiting condition, while agl1 transcript was not detected during T. atroviride interactions with the prey fungi Botrytis cinerea or R. solani. Phenotypic analysis of agl1 deletion strains (Δagl1) showed reduced conidiation compared to T. atroviride wild type, thus suggesting the involvement of AGL1 in conidiation. Furthermore, the Δagl1 strains display reduced antagonism towards B. cinerea and R. solani based on a secretion assay, although no difference was detected during direct interactions. These data demonstrate the role of AGL1 in conidiation and antagonism in the mycoparasitic fungus T. atroviride.
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Affiliation(s)
- Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007, Uppsala, Sweden.
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007, Uppsala, Sweden
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Carreras-Villaseñor N, Rico-Ruiz JG, Chávez Montes RA, Yong-Villalobos L, López-Hernández JF, Martínez-Hernández P, Herrera-Estrella L, Herrera-Estrella A, López-Arredondo D. Assessment of the ptxD gene as a growth and selective marker in Trichoderma atroviride using Pccg6, a novel constitutive promoter. Microb Cell Fact 2020; 19:69. [PMID: 32188455 PMCID: PMC7081547 DOI: 10.1186/s12934-020-01326-z] [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: 12/10/2019] [Accepted: 03/08/2020] [Indexed: 01/08/2023] Open
Abstract
Background Trichoderma species are among the most effective cell factories to produce recombinant proteins, whose productivity relies on the molecular toolkit and promoters available for the expression of the target protein. Although inducible promoter systems have been developed for producing recombinant proteins in Trichoderma, constitutive promoters are often a desirable alternative. Constitutive promoters are simple to use, do not require external stimuli or chemical inducers to be activated, and lead to purer enzyme preparations. Moreover, most of the promoters for homologous and heterologous expression reported in Trichoderma have been commonly evaluated by directly assessing production of industrial enzymes, requiring optimization of laborious protocols. Results Here we report the identification of Pccg6, a novel Trichoderma atroviride constitutive promoter, that has similar transcriptional strength as that of the commonly used pki1 promoter. Pccg6 displayed conserved arrangements of transcription factor binding sites between promoter sequences of Trichoderma ccg6 orthologues genes, potentially involved in their regulatory properties. The predicted ccg6-encoded protein potentially belongs to the SPE1/SPI1 protein family and shares high identity with CCG6 orthologue sequences from other fungal species including Trichoderma reesei, Trichoderma virens, Trichoderma asperellum, and to a lesser extent to that of Neurospora crassa. We also report the use of the Pccg6 promoter to drive the expression of PTXD, a phosphite oxidoreductase of bacterial origin, which allowed T. atroviride to utilize phosphite as a sole source of phosphorus. We propose ptxD as a growth reporter gene that allows real-time comparison of the functionality of different promoters by monitoring growth of Trichoderma transgenic lines and enzymatic activity of PTXD. Finally, we show that constitutive expression of ptxD provided T. atroviride a competitive advantage to outgrow bacterial contaminants when supplied with phosphite as a sole source of phosphorus. Conclusions A new constitutive promoter, ccg6, for expression of homologous and heterologous proteins has been identified and tested in T. atroviride to express PTXD, which resulted in an effective and visible phenotype to evaluate transcriptional activity of sequence promoters. Use of PTXD as a growth marker holds great potential for assessing activity of other promoters and for biotechnological applications as a contamination control system.
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Affiliation(s)
- Nohemí Carreras-Villaseñor
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato s/n, 36821, Irapuato, Guanajuato, Mexico.,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, 91070, Mexico
| | - José Guillermo Rico-Ruiz
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato s/n, 36821, Irapuato, Guanajuato, Mexico.,Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico
| | - Ricardo A Chávez Montes
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - Lenin Yong-Villalobos
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - José Fabricio López-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico.,Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Pedro Martínez-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico.,Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico
| | - Damar López-Arredondo
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato s/n, 36821, Irapuato, Guanajuato, Mexico. .,Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA.
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10
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Protein phosphatases regulate growth, development, cellulases and secondary metabolism in Trichoderma reesei. Sci Rep 2019; 9:10995. [PMID: 31358805 PMCID: PMC6662751 DOI: 10.1038/s41598-019-47421-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/03/2019] [Indexed: 12/15/2022] Open
Abstract
Trichoderma reesei represents one of the most prolific producers of plant cell wall degrading enzymes. Recent research showed broad regulation by phosphorylation in T. reesei, including important transcription factors involved in cellulase regulation. To evaluate factors crucial for changes in these phosphorylation events, we studied non-essential protein phosphatases (PPs) of T. reesei. Viable deletion strains were tested for growth on different carbon sources, osmotic and oxidative stress response, asexual and sexual development, cellulase and protease production as well as secondary metabolism. Six PPs were found to be positive or negative regulators for cellulase production. A correlation of the effects of PPs on protease activities and cellulase activities was not detected. Hierarchical clustering of regulation patterns and phenotypes of deletion indicated functional specialization within PP classes and common as well as variable effects. Our results confirmed the central role of catalytic and regulatory subunits of PP2A which regulates several aspects of cell growth and metabolism. Moreover we show that the additional homologue of PPH5 in Trichoderma spp., PPH5-2 assumes distinct functions in metabolism, development and stress response, different from PPH5. The influence of PPs on both cellulase gene expression and secondary metabolite production support an interrelationship in the underlying regulation mechanisms.
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Hitzenhammer E, Büschl C, Sulyok M, Schuhmacher R, Kluger B, Wischnitzki E, Schmoll M. YPR2 is a regulator of light modulated carbon and secondary metabolism in Trichoderma reesei. BMC Genomics 2019; 20:211. [PMID: 30866811 PMCID: PMC6417087 DOI: 10.1186/s12864-019-5574-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/28/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Filamentous fungi have evolved to succeed in nature by efficient growth and degradation of substrates, but also due to the production of secondary metabolites including mycotoxins. For Trichoderma reesei, as a biotechnological workhorse for homologous and heterologous protein production, secondary metabolite secretion is of particular importance for industrial application. Recent studies revealed an interconnected regulation of enzyme gene expression and carbon metabolism with secondary metabolism. RESULTS Here, we investigated gene regulation by YPR2, one out of two transcription factors located within the SOR cluster of T. reesei, which is involved in biosynthesis of sorbicillinoids. Transcriptome analysis showed that YPR2 exerts its major function in constant darkness upon growth on cellulose. Targets (direct and indirect) of YPR2 overlap with induction specific genes as well as with targets of the carbon catabolite repressor CRE1 and a considerable proportion is regulated by photoreceptors as well. Functional category analysis revealed both effects on carbon metabolism and secondary metabolism. Further, we found indications for an involvement of YPR2 in regulation of siderophores. In agreement with transcriptome data, mass spectrometric analyses revealed a broad alteration in metabolite patterns in ∆ypr2. Additionally, YPR2 positively influenced alamethicin levels along with transcript levels of the alamethicin synthase tex1 and is essential for production of orsellinic acid in darkness. CONCLUSIONS YPR2 is an important regulator balancing secondary metabolism with carbon metabolism in darkness and depending on the carbon source. The function of YPR2 reaches beyond the SOR cluster in which ypr2 is located and happens downstream of carbon catabolite repression mediated by CRE1.
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Affiliation(s)
- Eva Hitzenhammer
- AIT - Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Christoph Büschl
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Michael Sulyok
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Bernhard Kluger
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Elisabeth Wischnitzki
- AIT - Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Monika Schmoll
- AIT - Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
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Fitz E, Wanka F, Seiboth B. The Promoter Toolbox for Recombinant Gene Expression in Trichoderma reesei. Front Bioeng Biotechnol 2018; 6:135. [PMID: 30364340 PMCID: PMC6193071 DOI: 10.3389/fbioe.2018.00135] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/12/2018] [Indexed: 01/05/2023] Open
Abstract
The ascomycete Trichoderma reesei is one of the main fungal producers of cellulases and xylanases based on its high production capacity. Its enzymes are applied in food, feed, and textile industry or in lignocellulose hydrolysis in biofuel and biorefinery industry. Over the last years, the demand to expand the molecular toolbox for T. reesei to facilitate genetic engineering and improve the production of heterologous proteins grew. An important instrument to modify the expression of key genes are promoters to initiate and control their transcription. To date, the most commonly used promoter for T. reesei is the strong inducible promoter of the main cellobiohydrolase cel7a. Beside this one, there is a number of alternative inducible promoters derived from other cellulase- and xylanase encoding genes and a few constitutive promoters. With the advances in genomics and transcriptomics the identification of new constitutive and tunable promoters with different expression strength was simplified. In this review, we will discuss new developments in the field of promoters and compare their advantages and disadvantages. Synthetic expression systems constitute a new option to control gene expression and build up complex gene circuits. Therefore, we will address common structural features of promoters and describe options for promoter engineering and synthetic design of promoters. The availability of well-characterized gene expression control tools is essential for the analysis of gene function, detection of bottlenecks in gene networks and yield increase for biotechnology applications.
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Affiliation(s)
- Elisabeth Fitz
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB) GmbH, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Franziska Wanka
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB) GmbH, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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13
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Fatema U, Broberg A, Jensen DF, Karlsson M, Dubey M. Functional analysis of polyketide synthase genes in the biocontrol fungus Clonostachys rosea. Sci Rep 2018; 8:15009. [PMID: 30301915 PMCID: PMC6177402 DOI: 10.1038/s41598-018-33391-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/27/2018] [Indexed: 01/07/2023] Open
Abstract
Clonostachys rosea is a mycoparasitic fungus used for biological control of plant diseases. Its genome contains 31 genes putatively encoding for polyketide synthases (PKSs), 75% of which are arranged in biosynthetic gene clusters. Gene expression analysis during C. rosea interactions with the fungal plant pathogens Botrytis cinerea and Fusarium graminearum showed common and species-specific induction of PKS genes. Our data showed a culture media dependent correlation between PKS gene expression and degree of antagonism in C. rosea. The pks22 and pks29 genes were highly induced during fungal-fungal interactions but not during pigmentation, and gene deletion studies revealed that PKS29 was required for full antagonism against B. cinerea, and for biocontrol of fusarium foot rot on barley. Metabolite analysis revealed that Δpks29 strains has a 50% reduced production (P = 0.001) of an unknown polyketide with molecular formula C15H28O3, while Δpks22 strains lost the ability to produce four previously unknown polyketides named Clonorosein A-D. Clonorosein A and B were purified, their structures determined, and showed strong antifungal activity against B. cinerea and F. graminearum. These results show that PKS22 is required for production of antifungal polyketide Clonorosein A-D, and demonstrate the role of PKS29 in antagonism and biocontrol of fungal plant diseases.
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Affiliation(s)
- Umma Fatema
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden.,Department of Plant and Soil Sciences, 412 Plant Science Building 1405 Veterans Drive, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Anders Broberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden.
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Bazafkan H, Dattenböck C, Stappler E, Beier S, Schmoll M. Interrelationships of VEL1 and ENV1 in light response and development in Trichoderma reesei. PLoS One 2017; 12:e0175946. [PMID: 28423024 PMCID: PMC5397039 DOI: 10.1371/journal.pone.0175946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/03/2017] [Indexed: 12/25/2022] Open
Abstract
Sexual development is regulated by a complex regulatory mechanism in fungi. For Trichoderma reesei, the light response pathway was shown to impact sexual development, particularly through the photoreceptor ENVOY. Moreover, T. reesei communicates chemically with a potential mating partner in its vicinity, a response which is mediated by the velvet family protein VEL1 and its impact on secondary metabolism. We therefore studied the regulatory interactions of ENV1 and VEL1 with a focus on sexual development. Although individual mutants in both genes are female sterile under standard crossing conditions (light—dark cycles), an altered light regime enabled sexual development, which we found to be due to conditional female sterility of Δenv1, but not Δvel1. Phenotypes of growth and asexual sporulation as well as regulation of the peptide pheromone precursors of double mutants suggested that ENV1 and VEL1 balance positive and negative regulators of these functions. Additionally, VEL1 contributed to the strong deregulation of the pheromone system observed in env1 mutants. Female sterility of Δvel1 was rescued by deletion of env1 in darkness in MAT1-1, indicating a block of sexual development by ENV1 in darkness that is balanced by VEL1 in the wild-type. We conclude that ENV1 and VEL1 exert complementing functions in development of T. reesei. Our results further showed that the different developmental phenotypes of vel1/veA mutants in T. reesei and Aspergillus nidulans are not due to the presence or function of ENV1 in the VELVET regulatory pathway in T. reesei.
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Affiliation(s)
- Hoda Bazafkan
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
| | - Christoph Dattenböck
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
| | - Eva Stappler
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
| | - Sabrina Beier
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
| | - Monika Schmoll
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
- * E-mail:
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15
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Ramoni J, Marchetti-Deschmann M, Seidl-Seiboth V, Seiboth B. Trichoderma reesei xylanase 5 is defective in the reference strain QM6a but functional alleles are present in other wild-type strains. Appl Microbiol Biotechnol 2017; 101:4139-4149. [PMID: 28229208 PMCID: PMC5403845 DOI: 10.1007/s00253-017-8161-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/23/2017] [Accepted: 01/27/2017] [Indexed: 11/07/2022]
Abstract
Trichoderma reesei is a paradigm for the regulation and industrial production of plant cell wall-degrading enzymes. Among these, five xylanases, including the glycoside hydrolase (GH) family 11 XYN1 and XYN2, the GH10 XYN3, and the GH30 XYN4 and XYN6, were described. By genome mining and transcriptome analysis, a further putative xylanase, encoded by xyn5, was identified. Analysis of xyn5 from the genome-sequenced reference strain T. reesei QM6a shows that it encodes a non-functional, truncated form of XYN5. However, non-truncated orthologues are present in other genome sequenced Trichoderma spp., and sequencing of xyn5 in other T. reesei wild-type isolates shows that they harbor a putative functional xyn5 allele. In silico analysis and 3D modeling revealed that the encoded XYN5 has significant structural similarities to xylanases of the GH11 family, including a GH-typical substrate binding groove and a carboxylate pair in the active site. The xyn5 of wild-type strain TUCIM1282 was recombinantly expressed in a T. reesei strain with a (hemi)cellulase-free background and the corresponding protein purified to apparent homogeneity. The pH and temperature optima and the kinetic parameters of the purified XYN5 were pH 4, 50 °C, and Vmax = 2646 nkat/mg with a Km of 9.68 mg/ml. This functional xyn5 allele was used to replace the mutated version which led to an overall increase of the xylanolytic activity. These findings are of particular importance as GH11 xylanases are of high biotechnological relevance, and T. reesei is one of the main industrial producers of such lignocellulose-degrading enzymes.
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Affiliation(s)
- Jonas Ramoni
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria
| | | | - Verena Seidl-Seiboth
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria
| | - Bernhard Seiboth
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria.
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16
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Ivanova C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, Bidard F. Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:209. [PMID: 28912831 PMCID: PMC5588705 DOI: 10.1186/s13068-017-0897-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/29/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identification of mutations underlying this cellulase-negative phenotype. RESULTS Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identified a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identified 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confirming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no effect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions. CONCLUSION We were able to establish a link between a chromosomal translocation in QM9978 and the cellulase-negative phenotype of the strain. We identified the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specific trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.
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Affiliation(s)
- Christa Ivanova
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
- Present Address: Genetics of Biofilms Unit, Department of Microbiology, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jonas Ramoni
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Thiziri Aouam
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Alexa Frischmann
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Stéphane Le Crom
- Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, 75005 Paris, France
| | - Sophie Lemoine
- École normale supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l’École normale supérieure (IBENS), Plateforme Génomique, 75005 Paris, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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17
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Li Y, Zheng X, Zhang X, Bao L, Zhu Y, Qu Y, Zhao J, Qin Y. The Different Roles of Penicillium oxalicum LaeA in the Production of Extracellular Cellulase and β-xylosidase. Front Microbiol 2016; 7:2091. [PMID: 28066400 PMCID: PMC5177634 DOI: 10.3389/fmicb.2016.02091] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/09/2016] [Indexed: 12/16/2022] Open
Abstract
Cellulolytic enzyme hydrolysis of lignocellulose biomass to release fermentable sugars is one of the key steps in biofuel refining. Gene expression of fungal cellulolytic enzymes is tightly controlled at the transcriptional level. Key transcription factors such as activator ClrB/CLR2 and XlnR/XYR1, as well as repressor CreA/CRE1 play crucial roles in this process. The putative protein methyltransferase LaeA/LAE1 has also been reported to regulate the gene expression of the cellulolytic enzyme. The formation and gene expression of the cellulolytic enzyme was compared among Penicillium oxalicum wild type (WT) and seven mutants, including ΔlaeA (deletion of laeA), OEclrB (clrB overexpression), OEclrBΔlaeA (clrB overexpression with deletion of laeA), OExlnR (xlnR overexpression), OExlnRΔlaeA (xlnR overexpression with deletion of laeA), ΔcreA (deletion of creA), and ΔcreAΔlaeA (double deletion of creA and laeA). Results revealed that LaeA extensively affected the expression of glycoside hydrolase genes. The expression of genes that encoded the top 10 glycoside hydrolases assayed in secretome was remarkably downregulated especially in later phases of prolonged batch cultures by the deletion of laeA. Cellulase synthesis of four mutants ΔlaeA, OEclrBΔlaeA, OExlnRΔlaeA, and ΔcreAΔlaeA was repressed remarkably compared with their parent strains WT, OEclrB, OExlnR, and ΔcreA, respectively. The overexpression of clrB or xlnR could not rescue the impairment of cellulolytic enzyme gene expression and cellulase synthesis when LaeA was absent, suggesting that LaeA was necessary for the expression of cellulolytic enzyme gene activated by ClrB or XlnR. In contrast to LaeA positive roles in regulating prominent cellulase and hemicellulase, the extracellular β-xylosidase formation was negatively regulated by LaeA. The extracellular β-xylosidase activities improved over 5-fold in the OExlnRΔlaeA mutant compared with that of WT, and the expression of prominent β-xylosidase gene xyl3A was activated remarkably. The cumulative effect of LaeA and transcription factor XlnR has potential applications in the production of more β-xylosidase.
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Affiliation(s)
- Yanan Li
- State Key Lab of Microbial Technology and National Glycoengineering Research Center, Shandong UniversityJinan, China; Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong UniversityJinan, China
| | - Xiaoju Zheng
- State Key Lab of Microbial Technology and National Glycoengineering Research Center, Shandong University Jinan, China
| | - Xiujun Zhang
- State Key Lab of Microbial Technology and National Glycoengineering Research Center, Shandong University Jinan, China
| | - Longfei Bao
- State Key Lab of Microbial Technology and National Glycoengineering Research Center, Shandong University Jinan, China
| | - Yingying Zhu
- State Key Lab of Microbial Technology and National Glycoengineering Research Center, Shandong University Jinan, China
| | - Yinbo Qu
- State Key Lab of Microbial Technology and National Glycoengineering Research Center, Shandong University Jinan, China
| | - Jian Zhao
- State Key Lab of Microbial Technology and National Glycoengineering Research Center, Shandong University Jinan, China
| | - Yuqi Qin
- State Key Lab of Microbial Technology and National Glycoengineering Research Center, Shandong UniversityJinan, China; Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong UniversityJinan, China
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18
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Druzhinina IS, Kubicek EM, Kubicek CP. Several steps of lateral gene transfer followed by events of 'birth-and-death' evolution shaped a fungal sorbicillinoid biosynthetic gene cluster. BMC Evol Biol 2016; 16:269. [PMID: 28010735 PMCID: PMC5182515 DOI: 10.1186/s12862-016-0834-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/21/2016] [Indexed: 11/19/2022] Open
Abstract
Background Sorbicillinoids are a family of complex cyclic polyketides produced by only a small number of distantly related ascomycete fungi such as Trichoderma (Sordariomycetes) and Penicillium (Eurotiomycetes). In T. reesei, they are synthesized by a gene cluster consisting of eight genes including two polyketide synthases (PKS). To reconstruct the evolutionary origin of this gene cluster, we examined the occurrence of these eight genes in ascomycetes. Results A cluster comprising at least six of them was only found in Hypocreales (Acremonium chrysogenum, Ustilaginoidea virens, Trichoderma species from section Longibrachiatum) and in Penicillium rubens (Eurotiales). In addition, Colletotrichum graminicola contained the two pks (sor1 and sor2), but not the other sor genes. A. chrysogenum was the evolutionary eldest species in which sor1, sor2, sor3, sor4 and sor6 were present. Sor5 was gained by lateral gene transfer (LGT) from P. rubens. In the younger Hypocreales (U. virens, Trichoderma spp.), the cluster evolved by vertical transfer, but sor2 was lost and regained by LGT from C. graminicola. SorB (=sor2) and sorD (=sor4) were symplesiomorphic in P. rubens, whereas sorA, sorC and sorF were obtained by LGT from A. chrysogenum, and sorE by LGT from Pestalotiopsis fici (Xylariales). The sorbicillinoid gene cluster in Trichoderma section Longibrachiatum is under strong purifying selection. The T. reesei sor genes are expressed during fast vegetative growth, during antagonism of other fungi and regulated by the secondary metabolism regulator LAE1. Conclusions Our findings pinpoint the evolution of the fungal sorbicillinoid biosynthesis gene cluster. The core cluster arose in early Hypocreales, and was complemented by LGT. During further speciation in the Hypocreales, it became subject to birth and death evolution in selected lineages. In P. rubrens (Eurotiales), two cluster genes were symplesiomorphic, and the whole cluster formed by LGT from at least two different fungal donors. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0834-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irina S Druzhinina
- Microbiology Group, Research Area Biochemical Technology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Eva M Kubicek
- Microbiology Group, Research Area Biochemical Technology, Institute of Chemical Engineering, TU Wien, Vienna, Austria.,, Present address: Steinschötelgasse 7, 1100, Wien, Austria
| | - Christian P Kubicek
- Microbiology Group, Research Area Biochemical Technology, Institute of Chemical Engineering, TU Wien, Vienna, Austria. .,, Present address: Steinschötelgasse 7, 1100, Wien, Austria.
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19
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M. S, Singh S, Tiwari R, Goel R, Nain L. Do cultural conditions induce differential protein expression: Profiling of extracellular proteome of Aspergillus terreus CM20. Microbiol Res 2016; 192:73-83. [DOI: 10.1016/j.micres.2016.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 06/07/2016] [Accepted: 06/17/2016] [Indexed: 11/29/2022]
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20
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Daly P, van Munster JM, Kokolski M, Sang F, Blythe MJ, Malla S, Velasco de Castro Oliveira J, Goldman GH, Archer DB. Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression. Fungal Genet Biol 2016; 102:4-21. [PMID: 27150814 PMCID: PMC5476202 DOI: 10.1016/j.fgb.2016.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/20/2016] [Accepted: 04/29/2016] [Indexed: 12/15/2022]
Abstract
First genome-wide transcriptional response in fungal mixed species straw cultures. In mixed cultures, rRNA abundance was used to predict RNA-seq read abundance. Subset of P. chrysogenum CAZy with mixed cultures increased abundance pattern. Lack of overall higher CAZy transcripts/activities due to inter-species antagonism. Induction of secondary metabolite producing gene clusters in mixed cultures.
Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw. Based on quantification of species-specific rRNA, a set of conditions was identified where mixed cultures could be sampled so as to obtain sufficient RNA-seq reads for analysis from each species. The number of differentially-expressed genes varied from a couple of thousand to fewer than one hundred. The proportion of carbohydrate active enzyme (CAZy) encoding transcripts was lower in the majority of the mixed cultures compared to the respective straw monocultures. A small subset of P. chrysogenum CAZy genes showed five to ten-fold significantly increased transcript abundance in a two-species mixed culture with T. reesei. However, a substantial number of T. reesei CAZy transcripts showed reduced abundance in mixed cultures. The highly induced genes in mixed cultures indicated that fungal antagonism was a major part of the mixed cultures. In line with this, secondary metabolite producing gene clusters showed increased transcript abundance in mixed cultures and also mixed cultures with T. reesei led to a decrease in the mycelial biomass of A. niger. Significantly higher monomeric sugar release from straw was only measured using a minority of the mixed culture filtrates and there was no overall improvement. This study demonstrates fungal interaction with changes in transcripts, enzyme activities and biomass in the mixed cultures and whilst there were minor beneficial effects for CAZy transcripts and activities, the competitive interaction between T. reesei and the other fungi was the most prominent feature of this study.
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Affiliation(s)
- Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Jolanda M van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Fei Sang
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Martin J Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Sunir Malla
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro 10000, Campinas, São Paulo 13083-100, Brazil.
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, São Paulo 14040-903, Brazil.
| | - David B Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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21
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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A novel proteomics sample preparation method for secretome analysis of Hypocrea jecorina growing on insoluble substrates. J Proteomics 2016; 131:104-112. [DOI: 10.1016/j.jprot.2015.10.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/21/2015] [Accepted: 10/12/2015] [Indexed: 11/23/2022]
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Druzhinina IS, Kubicek CP. Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:69-147. [PMID: 27261782 DOI: 10.1016/bs.aambs.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.
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Affiliation(s)
- I S Druzhinina
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - C P Kubicek
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
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Druzhinina IS, Kopchinskiy AG, Kubicek EM, Kubicek CP. A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:75. [PMID: 27030800 PMCID: PMC4812632 DOI: 10.1186/s13068-016-0488-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/15/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Investigations on a few eukaryotic model organisms showed that many genes are non-randomly distributed on chromosomes. In addition, chromosome ends frequently possess genes that are important for the fitness of the organisms. Trichoderma reesei is an industrial producer of enzymes for food, feed and biorefinery production. Its seven chromosomes have recently been assembled, thus making an investigation of its chromosome architecture possible. RESULTS We manually annotated and mapped 9194 ORFs on their respective chromosomes and investigated the clustering of the major gene categories and of genes encoding carbohydrate-active enzymes (CAZymes), and the relationship between clustering and expression. Genes responsible for RNA processing and modification, amino acid metabolism, transcription, translation and ribosomal structure and biogenesis indeed showed loose clustering, but this had no impact on their expression. A third of the genes encoding CAZymes also occurred in loose clusters that also contained a high number of genes encoding small secreted cysteine-rich proteins. Five CAZyme clusters were located less than 50 kb apart from the chromosome ends. These genes exhibited the lowest basal (but not induced) expression level, which correlated with an enrichment of H3K9 methylation in the terminal 50 kb areas indicating gene silencing. No differences were found in the expression of CAZyme genes present in other parts of the chromosomes. The putative subtelomeric areas were also enriched in genes encoding secreted proteases, amino acid permeases, enzyme clusters for polyketide synthases (PKS)-non-ribosomal peptide synthase (NRPS) fusion proteins (PKS-NRPS) and proteins involved in iron scavenging. They were strongly upregulated during conidiation and interaction with other fungi. CONCLUSIONS Our findings suggest that gene clustering on the T. reesei chromosomes occurs but generally has no impact on their expression. CAZyme genes, located in subtelomers, however, exhibited a much lower basal expression level. The gene inventory of the subtelomers suggests a major role of competition for nitrogen and iron supported by antibiosis for the fitness of T. reesei. The availability of fully annotated chromosomes will facilitate the use of genetic crossings in identifying still unknown genes responsible for specific traits of T. reesei.
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Affiliation(s)
- Irina S. Druzhinina
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
| | - Alexey G. Kopchinskiy
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
| | - Eva M. Kubicek
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
- />Steinschötelgasse 7, 1100 Vienna, Austria
| | - Christian P. Kubicek
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
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25
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Zhang J, Debets AJM, Verweij PE, Melchers WJG, Zwaan BJ, Schoustra SE. Asexual sporulation facilitates adaptation: The emergence of azole resistance in Aspergillus fumigatus. Evolution 2015; 69:2573-86. [PMID: 26315993 DOI: 10.1111/evo.12763] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 07/11/2015] [Accepted: 08/03/2015] [Indexed: 12/26/2022]
Abstract
Understanding the occurrence and spread of azole resistance in Aspergillus fumigatus is crucial for public health. It has been hypothesized that asexual sporulation, which is abundant in nature, is essential for phenotypic expression of azole resistance mutations in A. fumigatus facilitating subsequent spread through natural selection. Furthermore, the disease aspergilloma is associated with asexual sporulation within the lungs of patients and the emergence of azole resistance. This study assessed the evolutionary advantage of asexual sporulation by growing the fungus under pressure of one of five different azole fungicides over seven weeks and by comparing the rate of adaptation between scenarios of culturing with and without asexual sporulation. Results unequivocally show that asexual sporulation facilitates adaptation. This can be explained by the combination of more effective selection because of the transition from a multicellular to a unicellular stage, and by increased mutation supply due to the production of spores, which involves numerous mitotic divisions. Insights from this study are essential to unravel the resistance mechanisms of sporulating pathogens to chemical compounds and disease agents in general, and for designing strategies that prevent or overcome the emerging threat of azole resistance in particular.
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Affiliation(s)
- Jianhua Zhang
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Alfons J M Debets
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Centre, 6500 HB, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, 6500 HB, Nijmegen, The Netherlands
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Sijmen E Schoustra
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
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26
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Šimkovič M, Olejníková P, Mat'at'a M, Žemla P, Vilimová V, Farkašová L, Varečka L. Nutrient transport into germinating Trichoderma atroviride conidia and development of its driving force. MICROBIOLOGY-SGM 2015; 161:1240-50. [PMID: 25777081 DOI: 10.1099/mic.0.000079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The exit from dormancy and the start of growth should be preceded or at least accompanied by the uptake of nutrients. In this work we studied changes in the transport of several nutrients into Trichoderma atroviride conidia. Germination started with a short period of isodiametric growth (conidial swelling), followed by polarized growth (germ tube formation) after about 8 h at 26 °C. The onset of isodiametric growth required the presence of external both phosphate and nitrate. At the same time, an increased uptake of precursors of macromolecules and phospholipids ((14)C- or (3)H-labelled valine, uracil, N-acetylglucosamine and choline) occurred. A low uptake of these precursors was observed also in non-germinating conidia. Concomitantly, this uptake developed an increased sensitivity to the uncoupler 3,3',4',5-tetrachlorosalicylanilide. Expression and activity of H(+)-ATPase started after completing isodiametric growth, suggesting that the proton-motive force (PMF) generated by H(+)-ATPase may be an accelerator of nutrient uptake and metabolism. (14)C-valine uptake was also measured into a mutant with disrupted pma1 gene. This mutant did not form conidia. The mutant also exhibited uncoupler sensitivity of (14)C-valine uptake. These observations showed that a PMF must have been generated by a mechanism(s) other than the H(+)-ATPase activity in the WT before H(+)-ATPase expression and in mycelia with disrupted H(+)-ATPase.
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Affiliation(s)
- Martin Šimkovič
- Department of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237-Bratislava, Slovakia
| | - Petra Olejníková
- Department of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237-Bratislava, Slovakia
| | - Matej Mat'at'a
- Department of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237-Bratislava, Slovakia
| | - Peter Žemla
- Department of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237-Bratislava, Slovakia
| | - Viera Vilimová
- Department of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237-Bratislava, Slovakia
| | - Lenka Farkašová
- Department of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237-Bratislava, Slovakia
| | - L'udovít Varečka
- Department of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237-Bratislava, Slovakia
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27
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Ghassemi S, Lichius A, Bidard F, Lemoine S, Rossignol MN, Herold S, Seidl-Seiboth V, Seiboth B, Espeso EA, Margeot A, Kubicek CP. The ß-importin KAP8 (Pse1/Kap121) is required for nuclear import of the cellulase transcriptional regulator XYR1, asexual sporulation and stress resistance in Trichoderma reesei. Mol Microbiol 2015; 96:405-18. [PMID: 25626518 PMCID: PMC4390390 DOI: 10.1111/mmi.12944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 11/26/2022]
Abstract
The ascomycete Trichoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes, and serves as a prime model for their genetic regulation. Most of its (hemi-)cellulolytic enzymes are obligatorily dependent on the transcriptional activator XYR1. Here, we investigated the nucleo-cytoplasmic shuttling mechanism that transports XYR1 across the nuclear pore complex. We identified 14 karyopherins in T. reesei, of which eight were predicted to be involved in nuclear import, and produced single gene-deletion mutants of all. We found KAP8, an ortholog of Aspergillus nidulans KapI, and Saccharomyces cerevisiae Kap121/Pse1, to be essential for nuclear recruitment of GFP-XYR1 and cellulase gene expression. Transformation with the native gene rescued this effect. Transcriptomic analyses of Δkap8 revealed that under cellulase-inducing conditions 42 CAZymes, including all cellulases and hemicellulases known to be under XYR1 control, were significantly down-regulated. Δkap8 strains were capable of forming fertile fruiting bodies but exhibited strongly reduced conidiation both in light and darkness, and showed enhanced sensitivity towards abiotic stress, including high osmotic pressure, low pH and high temperature. Together, these data underscore the significance of nuclear import of XYR1 in cellulase and hemicellulase gene regulation in T. reesei, and identify KAP8 as the major karyopherin required for this process.
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Affiliation(s)
- Sara Ghassemi
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Alexander Lichius
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Fréderique Bidard
- IFP Energies nouvelles1-4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Sophie Lemoine
- Ecole Normale Supérieure, Institut de Biologie de l'ENSIBENS, Plateforme Génomique, Paris, F-75005, France
| | - Marie-Noëlle Rossignol
- Ecole Normale Supérieure, Institut de Biologie de l'ENSIBENS, Plateforme Génomique, Paris, F-75005, France
| | - Silvia Herold
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
- ACIB GmbH, c/o Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
| | - Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Antoine Margeot
- IFP Energies nouvelles1-4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Christian P Kubicek
- Research Division Biotechnology and Microbiology, Institute of Chemical EngineeringTU Wien, Vienna, 1060, Austria
- *For correspondence. E-mail ; Tel. (+ 1) 43 1 58801 166085; Fax (+ 1) 43 1 58801 17299
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Karlsson M, Durling MB, Choi J, Kosawang C, Lackner G, Tzelepis GD, Nygren K, Dubey MK, Kamou N, Levasseur A, Zapparata A, Wang J, Amby DB, Jensen B, Sarrocco S, Panteris E, Lagopodi AL, Pöggeler S, Vannacci G, Collinge DB, Hoffmeister D, Henrissat B, Lee YH, Jensen DF. Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea. Genome Biol Evol 2015; 7:465-80. [PMID: 25575496 PMCID: PMC4350171 DOI: 10.1093/gbe/evu292] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2014] [Indexed: 11/14/2022] Open
Abstract
Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. Here, we report on the genome sequencing of C. rosea and a comparative genome analysis, in order to resolve the phylogenetic placement of C. rosea and to study the evolution of mycoparasitism as a fungal lifestyle. The genome of C. rosea is estimated to 58.3 Mb, and contains 14,268 predicted genes. A phylogenomic analysis shows that C. rosea clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/saprotrophic Trichoderma species in an ancestral position. A comparative analysis of gene family evolution reveals several distinct differences between the included mycoparasites. Clonostachys rosea contains significantly more ATP-binding cassette (ABC) transporters, polyketide synthases, cytochrome P450 monooxygenases, pectin lyases, glucose-methanol-choline oxidoreductases, and lytic polysaccharide monooxygenases compared with other fungi in the Hypocreales. Interestingly, the increase of ABC transporter gene number in C. rosea is associated with phylogenetic subgroups B (multidrug resistance proteins) and G (pleiotropic drug resistance transporters), whereas an increase in subgroup C (multidrug resistance-associated proteins) is evident in Trichoderma virens. In contrast with mycoparasitic Trichoderma species, C. rosea contains very few chitinases. Expression of six group B and group G ABC transporter genes was induced in C. rosea during exposure to the Fusarium mycotoxin zearalenone, the fungicide Boscalid or metabolites from the biocontrol bacterium Pseudomonas chlororaphis. The data suggest that tolerance toward secondary metabolites is a prominent feature in the biology of C. rosea.
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Affiliation(s)
- Magnus Karlsson
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Chatchai Kosawang
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
| | - Gerald Lackner
- Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany
| | - Georgios D Tzelepis
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kristiina Nygren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mukesh K Dubey
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nathalie Kamou
- Plant Pathology Laboratory, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anthony Levasseur
- INRA and Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, Marseille, France
| | - Antonio Zapparata
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Jinhui Wang
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Daniel Buchvaldt Amby
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
| | - Birgit Jensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Emmanuel Panteris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasia L Lagopodi
- Plant Pathology Laboratory, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stefanie Pöggeler
- Department of Genetics of Eukaryotic Microorganisms, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Giovanni Vannacci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - David B Collinge
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, Marseille, France, and Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Dan Funck Jensen
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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29
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Meyer V, Fiedler M, Nitsche B, King R. The Cell Factory Aspergillus Enters the Big Data Era: Opportunities and Challenges for Optimising Product Formation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 149:91-132. [PMID: 25616499 DOI: 10.1007/10_2014_297] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living with limits. Getting more from less. Producing commodities and high-value products from renewable resources including waste. What is the driving force and quintessence of bioeconomy outlines the lifestyle and product portfolio of Aspergillus, a saprophytic genus, to which some of the top-performing microbial cell factories belong: Aspergillus niger, Aspergillus oryzae and Aspergillus terreus. What makes them so interesting for exploitation in biotechnology and how can they help us to address key challenges of the twenty-first century? How can these strains become trimmed for better growth on second-generation feedstocks and how can we enlarge their product portfolio by genetic and metabolic engineering to get more from less? On the other hand, what makes it so challenging to deduce biological meaning from the wealth of Aspergillus -omics data? And which hurdles hinder us to model and engineer industrial strains for higher productivity and better rheological performance under industrial cultivation conditions? In this review, we will address these issues by highlighting most recent findings from the Aspergillus research with a focus on fungal growth, physiology, morphology and product formation. Indeed, the last years brought us many surprising insights into model and industrial strains. They clearly told us that similar is not the same: there are different ways to make a hypha, there are more protein secretion routes than anticipated and there are different molecular and physical mechanisms which control polar growth and the development of hyphal networks. We will discuss new conceptual frameworks derived from these insights and the future scientific advances necessary to create value from Aspergillus Big Data.
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Affiliation(s)
- Vera Meyer
- Department Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355, Berlin, Germany,
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30
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Karimi Aghcheh R, Németh Z, Atanasova L, Fekete E, Paholcsek M, Sándor E, Aquino B, Druzhinina IS, Karaffa L, Kubicek CP. The VELVET A orthologue VEL1 of Trichoderma reesei regulates fungal development and is essential for cellulase gene expression. PLoS One 2014; 9:e112799. [PMID: 25386652 PMCID: PMC4227869 DOI: 10.1371/journal.pone.0112799] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/15/2014] [Indexed: 11/25/2022] Open
Abstract
Trichoderma reesei is the industrial producer of cellulases and hemicellulases for biorefinery processes. Their expression is obligatorily dependent on the function of the protein methyltransferase LAE1. The Aspergillus nidulans orthologue of LAE1 - LaeA - is part of the VELVET protein complex consisting of LaeA, VeA and VelB that regulates secondary metabolism and sexual as well as asexual reproduction. Here we have therefore investigated the function of VEL1, the T. reesei orthologue of A. nidulans VeA. Deletion of the T. reesei vel1 locus causes a complete and light-independent loss of conidiation, and impairs formation of perithecia. Deletion of vel1 also alters hyphal morphology towards hyperbranching and formation of thicker filaments, and with consequently reduced growth rates. Growth on lactose as a sole carbon source, however, is even more strongly reduced and growth on cellulose as a sole carbon source eliminated. Consistent with these findings, deletion of vel1 completely impaired the expression of cellulases, xylanases and the cellulase regulator XYR1 on lactose as a cellulase inducing carbon source, but also in resting mycelia with sophorose as inducer. Our data show that in T. reesei VEL1 controls sexual and asexual development, and this effect is independent of light. VEL1 is also essential for cellulase gene expression, which is consistent with the assumption that their regulation by LAE1 occurs by the VELVET complex.
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Affiliation(s)
- Razieh Karimi Aghcheh
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Microbiology Group, Vienna University of Technology, 1060 Vienna, Austria
| | - Zoltán Németh
- Department of Biochemical Engineering, Faculty of Sciences and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Lea Atanasova
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Microbiology Group, Vienna University of Technology, 1060 Vienna, Austria
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Sciences and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Melinda Paholcsek
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Erzsébet Sándor
- Faculty of Agricultural and Food Science and Environmental Management, Institute of Food Science, H-4032 Debrecen, Hungary
| | - Benigno Aquino
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Microbiology Group, Vienna University of Technology, 1060 Vienna, Austria
| | - Irina S. Druzhinina
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Microbiology Group, Vienna University of Technology, 1060 Vienna, Austria
- Austrian Center of Industrial Biotechnology, c/o Institute of Chemical Engineering, Vienna University of Technology, 1060 Vienna, Austria
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Sciences and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Christian P. Kubicek
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Microbiology Group, Vienna University of Technology, 1060 Vienna, Austria
- Austrian Center of Industrial Biotechnology, 8010 Graz, Austria
- * E-mail:
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31
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Lichius A, Seidl-Seiboth V, Seiboth B, Kubicek CP. Nucleo-cytoplasmic shuttling dynamics of the transcriptional regulators XYR1 and CRE1 under conditions of cellulase and xylanase gene expression in Trichoderma reesei. Mol Microbiol 2014; 94:1162-1178. [PMID: 25302561 PMCID: PMC4282317 DOI: 10.1111/mmi.12824] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2014] [Indexed: 01/26/2023]
Abstract
Trichoderma reesei is a model for investigating the regulation of (hemi-)cellulase gene expression. Cellulases are formed adaptively, and the transcriptional activator XYR1 and the carbon catabolite repressor CRE1 are main regulators of their expression. We quantified the nucleo-cytoplasmic shuttling dynamics of GFP-fusion proteins of both transcription factors under cellulase and xylanase inducing conditions, and correlated their nuclear presence/absence with transcriptional changes. We also compared their subcellular localization in conidial germlings and mature hyphae. We show that cellulase gene expression requires de novo biosynthesis of XYR1 and its simultaneous nuclear import, whereas carbon catabolite repression is regulated through preformed CRE1 imported from the cytoplasmic pool. Termination of induction immediately stopped cellulase gene transcription and was accompanied by rapid nuclear degradation of XYR1. In contrast, nuclear CRE1 rapidly decreased upon glucose depletion, and became recycled into the cytoplasm. In mature hyphae, nuclei containing activated XYR1 were concentrated in the colony center, indicating that this is the main region of XYR1 synthesis and cellulase transcription. CRE1 was found to be evenly distributed throughout the entire mycelium. Taken together, our data revealed novel aspects of the dynamic shuttling and spatial bias of the major regulator of (hemi-)cellulase gene expression, XYR1, in T. reesei.
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Affiliation(s)
- Alexander Lichius
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of TechnologyVienna, Austria
| | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of TechnologyVienna, Austria
| | - Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of TechnologyVienna, Austria
| | - Christian P Kubicek
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of TechnologyVienna, Austria
- Austrian Center of Industrial BiotechnologyGraz, Austria
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Fekete E, Karaffa L, Karimi Aghcheh R, Németh Z, Fekete E, Orosz A, Paholcsek M, Stágel A, Kubicek CP. The transcriptome of lae1 mutants of Trichoderma reesei cultivated at constant growth rates reveals new targets of LAE1 function. BMC Genomics 2014; 15:447. [PMID: 24909838 PMCID: PMC4061448 DOI: 10.1186/1471-2164-15-447] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/04/2014] [Indexed: 01/02/2023] Open
Abstract
Background The putative methyltransferase LaeA is a global regulator that affects the expression of multiple secondary metabolite gene clusters in several fungi. In Trichoderma reesei, its ortholog LAE1 appears to predominantly regulate genes involved in increasing competitive fitness in its environment, including expression of cellulases and polysaccharide hydrolases. A drawback in all studies related to LaeA/LAE1 function so far, however, is that the respective loss-of-function and overexpressing mutants display different growth rates. Thus some of the properties attributed to LaeA/LAE1 could be simply due to changes of the growth rate. Results We cultivated T. reesei, a Δlae1 mutant and a lae1-overexpressing strain in chemostats on glucose at two different growth rates (0.075 and 0.020 h-1) which resemble growth rates at repressing and derepressing conditions, respectively. Under these conditions, the effect of modulating LAE1 expression was mainly visible in the Δlae1 mutant, whereas the overexpressing strain showed little differences to the parent strain. The effect on the expression of some gene categories identified earlier (polyketide synthases, heterokaryon incompatibility proteins, PTH11-receptors) was confirmed, but in addition GCN5-N-acetyltransferases, amino acid permeases and flavin monooxygenases were identified as so far unknown major targets of LAE1 action. LAE1 was also shown to interfere with the regulation of expression of several genes by the growth rate. About a tenth of the genes differentially expressed in the Δlae1 mutant under either growth condition were found to be clustered in the genome, but no specific gene group was associated with this phenomenon. Conclusions Our data show that – using T. reesei LAE1 as a model - the investigation of transcriptome in regulatory mutants at constant growth rates leads to new insights into the physiological roles of the respective regulator. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-447) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.
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[Mechanisms and regulation of enzymatic hydrolysis of cellulose in filamentous fungi: classical cases and new models]. Rev Iberoam Micol 2014; 32:1-12. [PMID: 24607657 DOI: 10.1016/j.riam.2013.10.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 09/25/2013] [Accepted: 10/23/2013] [Indexed: 11/21/2022] Open
Abstract
Cellulose is the most abundant renewable carbon source on earth. However, this polymer structure comprises a physical and chemical barrier for carbon access, which has limited its exploitation. In nature, only a few percentage of microorganisms may degrade this polymer by cellulase expression. Filamentous fungi are one of the most active and efficient groups among these microorganisms. This review describes similarities and differences between cellulase activity mechanisms and regulatory mechanisms controlling gene expression for 3 of the most studied cellulolytic filamentous fungi models: Trichoderma reesei, Aspergillus niger and Aspergillus nidulans, and the recently described model Neurospora crassa. Unlike gene expression mechanisms, it was found that enzymatic activity mechanisms are similar for all the studied models. Understanding the distinctive elements of each system is essential for the development of strategies for the improvement of cellulase production, either by providing the optimum environment (fermentation conditions) or increasing gene expression in these microorganisms by genetic engineering.
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Chen X, Luo Y, Yu H, Sun Y, Wu H, Song S, Hu S, Dong Z. Transcriptional profiling of biomass degradation-related genes during Trichoderma reesei growth on different carbon sources. J Biotechnol 2014; 173:59-64. [DOI: 10.1016/j.jbiotec.2014.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 12/23/2013] [Accepted: 01/01/2014] [Indexed: 10/25/2022]
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Häkkinen M, Valkonen MJ, Westerholm-Parvinen A, Aro N, Arvas M, Vitikainen M, Penttilä M, Saloheimo M, Pakula TM. Screening of candidate regulators for cellulase and hemicellulase production in Trichoderma reesei and identification of a factor essential for cellulase production. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:14. [PMID: 24472375 PMCID: PMC3922861 DOI: 10.1186/1754-6834-7-14] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 01/14/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND The soft rot ascomycetal fungus Trichoderma reesei is utilized for industrial production of secreted enzymes, especially lignocellulose degrading enzymes. T. reesei uses several different enzymes for the degradation of plant cell wall-derived material, including 9 characterized cellulases, 15 characterized hemicellulases and at least 42 genes predicted to encode cellulolytic or hemicellulolytic activities. Production of cellulases and hemicellulases is modulated by environmental and physiological conditions. Several regulators affecting the expression of cellulase and hemicellulase genes have been identified but more factors still unknown are believed to be present in the genome of T. reesei. RESULTS We have used transcriptional profiling data from T. reesei cultures in which cellulase/hemicellulase production was induced by the addition of different lignocellulose-derived materials to identify putative novel regulators for cellulase and hemicellulase genes. Based on this induction data, supplemented with other published genome-wide data on different protein production conditions, 28 candidate regulatory genes were selected for further studies and they were overexpressed in T. reesei. Overexpression of seven genes led to at least 1.5-fold increased production of cellulase and/or xylanase activity in the modified strains as compared to the parental strain. Deletion of gene 77513, here designated as ace3, was found to be detrimental for cellulase production and for the expression of several cellulase genes studied. This deletion also significantly reduced xylanase activity and expression of xylan-degrading enzyme genes. Furthermore, our data revealed the presence of co-regulated chromosomal regions containing carbohydrate-active enzyme genes and candidate regulatory genes. CONCLUSIONS Transcriptional profiling results from glycoside hydrolase induction experiments combined with a previous study of specific protein production conditions was shown to be an effective method for finding novel candidate regulatory genes affecting the production of cellulases and hemicellulases. Recombinant strains with improved cellulase and/or xylanase production properties were constructed, and a gene essential for cellulase gene expression was found. In addition, more evidence was gained on the chromatin level regional regulation of carbohydrate-active enzyme gene expression.
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Affiliation(s)
- Mari Häkkinen
- VTT Technical Research Centre of Finland, PO Box 1000 Tietotie 2, Espoo FI-02044, VTT, Finland
| | - Mari J Valkonen
- VTT Technical Research Centre of Finland, PO Box 1000 Tietotie 2, Espoo FI-02044, VTT, Finland
| | - Ann Westerholm-Parvinen
- VTT Technical Research Centre of Finland, PO Box 1000 Tietotie 2, Espoo FI-02044, VTT, Finland
| | - Nina Aro
- VTT Technical Research Centre of Finland, PO Box 1000 Tietotie 2, Espoo FI-02044, VTT, Finland
| | - Mikko Arvas
- VTT Technical Research Centre of Finland, PO Box 1000 Tietotie 2, Espoo FI-02044, VTT, Finland
| | - Marika Vitikainen
- VTT Technical Research Centre of Finland, PO Box 1000 Tietotie 2, Espoo FI-02044, VTT, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, PO Box 1000 Tietotie 2, Espoo FI-02044, VTT, Finland
| | - Markku Saloheimo
- VTT Technical Research Centre of Finland, PO Box 1000 Tietotie 2, Espoo FI-02044, VTT, Finland
| | - Tiina M Pakula
- VTT Technical Research Centre of Finland, PO Box 1000 Tietotie 2, Espoo FI-02044, VTT, Finland
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Gorsche R, Jovanovic B, Gudynaite-Savitch L, Mach RL, Mach-Aigner AR. A highly sensitive in vivo footprinting technique for condition-dependent identification of cis elements. Nucleic Acids Res 2013; 42:e1. [PMID: 24097437 PMCID: PMC3874196 DOI: 10.1093/nar/gkt883] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Knowing which regions of a gene are targeted by transcription factors during induction or repression is essential for understanding the mechanisms responsible for regulation. Therefore, we re-designed the traditional in vivo footprinting method to obtain a highly sensitive technique, which allows identification of the cis elements involved in condition-dependent gene regulation. Data obtained through DMS methylation, HCl DNA cleavage and optimized ligation-mediated PCR using fluorescent labelling followed by capillary gel electrophoresis are analysed by ivFAST. In this work we have developed this command line-based program, which is designed to ensure automated and fast data processing and visualization. The new method facilitates a quantitative, high-throughput approach because it enables the comparison of any number of in vivo footprinting results from different conditions (e.g. inducing, repressing, de-repressing) to one another by employing an internal standard. For validation of the method the well-studied upstream regulatory region of the Trichoderma reesei xyn1 (endoxylanase 1) gene was used. Applying the new method we could identify the motives involved in condition-dependent regulation of the cbh2 (cellobiohydrolase 2) and xyn2 (endoxylanase 2) genes.
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Affiliation(s)
- Rita Gorsche
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Str. 1 a, A-1060 Vienna, Austria and Department of Biology, University of Ottawa, Gendron Hall, 30 Marie Curie, Ottawa, ON, K1N6N5, Canada
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Tisch D, Schmoll M. Targets of light signalling in Trichoderma reesei. BMC Genomics 2013; 14:657. [PMID: 24070552 PMCID: PMC3831817 DOI: 10.1186/1471-2164-14-657] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/24/2013] [Indexed: 11/21/2022] Open
Abstract
Background The tropical ascomycete Trichoderma reesei (Hypocrea jecorina) represents one of the most efficient plant cell wall degraders. Regulation of the enzymes required for this process is affected by nutritional signals as well as other environmental signals including light. Results Our transcriptome analysis of strains lacking the photoreceptors BLR1 and BLR2 as well as ENV1 revealed a considerable increase in the number of genes showing significantly different transcript levels in light and darkness compared to wild-type. We show that members of all glycoside hydrolase families can be subject to light dependent regulation, hence confirming nutrient utilization including plant cell wall degradation as a major output pathway of light signalling. In contrast to N. crassa, photoreceptor mediated regulation of carbon metabolism in T. reesei occurs primarily by BLR1 and BLR2 via their positive effect on induction of env1 transcription, rather than by a presumed negative effect of ENV1 on the function of the BLR complex. Nevertheless, genes consistently regulated by photoreceptors in N. crassa and T. reesei are significantly enriched in carbon metabolic functions. Hence, different regulatory mechanisms are operative in these two fungi, while the light dependent regulation of plant cell wall degradation appears to be conserved. Analysis of growth on different carbon sources revealed that the oxidoreductive D-galactose and pentose catabolism is influenced by light and ENV1. Transcriptional regulation of the target enzymes in these pathways is enhanced by light and influenced by ENV1, BLR1 and/or BLR2. Additionally we detected an ENV1-regulated genomic cluster of 9 genes including the D-mannitol dehydrogenase gene lxr1, with two genes of this cluster showing consistent regulation in N. crassa. Conclusions We show that one major output pathway of light signalling in Trichoderma reesei is regulation of glycoside hydrolase genes and the degradation of hemicellulose building blocks. Targets of ENV1 and BLR1/BLR2 are for the most part distinct and indicate individual functions for ENV1 and the BLR complex besides their postulated regulatory interrelationship.
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Affiliation(s)
- Doris Tisch
- Department Health and Environment - Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz Strasse 24, Tulln 3430, Austria.
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38
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The polyketide synthase gene pks4 of Trichoderma reesei provides pigmentation and stress resistance. EUKARYOTIC CELL 2013; 12:1499-508. [PMID: 24036343 DOI: 10.1128/ec.00103-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Species of the fungal genus Trichoderma (Hypocreales, Ascomycota) are well-known for their production of various secondary metabolites. Nonribosomal peptides and polyketides represent a major portion of these products. In a recent phylogenomic investigation of Trichoderma polyketide synthase (PKS)-encoding genes, the pks4 from T. reesei was shown to be an orthologue of pigment-forming PKSs involved in synthesis of aurofusarin and bikaverin in Fusarium spp. In this study, we show that deletion of this gene in T. reesei results in loss of green conidial pigmentation and in pigmentation alteration of teleomorph structures. It also has an impact on conidial cell wall stability and the antagonistic abilities of T. reesei against other fungi, including formation of inhibitory metabolites. In addition, deletion of pks4 significantly influences the expression of other PKS-encoding genes of T. reesei. To our knowledge, this is the first indication that a low-molecular-weight pigment-forming PKS is involved in defense, mechanical stability, and stress resistance in fungi.
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Bischof R, Fourtis L, Limbeck A, Gamauf C, Seiboth B, Kubicek CP. Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:127. [PMID: 24016404 PMCID: PMC3847502 DOI: 10.1186/1754-6834-6-127] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/04/2013] [Indexed: 05/05/2023]
Abstract
BACKGROUND Renewable lignocellulosic biomass is an advantageous resource for the production of second generation biofuels and other biorefinery products. In Middle Europe, wheat straw is one of the most abundant low-cost sources of lignocellulosic biomass. For its efficient use, an efficient mix of cellulases and hemicellulases is required. In this paper, we investigated how cellulase production by T. reesei on wheat straw compares to that on lactose, the only soluble and also cheap inducing carbon source for enzyme production. RESULTS We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions. Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30% of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair, iron homeostatis and autophagy. Two thirds of the CAZome was expressed both on wheat straw as well as on lactose, but 60% of it at least >2-fold higher on the former. Major wheat straw specific genes comprised xylanases, chitinases and mannosidases. Interestingly, the latter two CAZyme families were significantly higher expressed in a strain in which xyr1 encoding the major regulator of cellulase and hemicellulase biosynthesis is non-functional. CONCLUSIONS Our data reveal several major differences in the transcriptome between wheat straw and lactose which may be related to the higher enzyme formation on the former and their further investigation could lead to the development of methods for increasing enzyme production on lactose.
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Affiliation(s)
- Robert Bischof
- Austrian Centre of Industrial Biotechnology (ACIB) GmBH c/o Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
| | - Lukas Fourtis
- Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
| | - Andreas Limbeck
- Institute of Chemical Technologies and Analytics, University of Technology of Vienna, Getreidemarkt 9, Vienna A-1060, Austria
| | - Christian Gamauf
- Biotech & Renewables Center, Clariant GmbH, München 81477, Germany
| | - Bernhard Seiboth
- Austrian Centre of Industrial Biotechnology (ACIB) GmBH c/o Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
- Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
| | - Christian P Kubicek
- Austrian Centre of Industrial Biotechnology (ACIB) GmBH c/o Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
- Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria
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Glass NL, Schmoll M, Cate JH, Coradetti S. Plant Cell Wall Deconstruction by Ascomycete Fungi. Annu Rev Microbiol 2013; 67:477-98. [DOI: 10.1146/annurev-micro-092611-150044] [Citation(s) in RCA: 244] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Monika Schmoll
- Austrian Institute of Technology GmbH (AIT), Health and Environment, Bioresources, 3430 Tulln, Austria
| | - Jamie H.D. Cate
- Molecular and Cellular Biology Department, and
- Chemistry Department, University of California, Berkeley, California 94720;
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Ivanova C, Bååth JA, Seiboth B, Kubicek CP. Systems analysis of lactose metabolism in Trichoderma reesei identifies a lactose permease that is essential for cellulase induction. PLoS One 2013; 8:e62631. [PMID: 23690947 PMCID: PMC3648571 DOI: 10.1371/journal.pone.0062631] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 03/22/2013] [Indexed: 11/18/2022] Open
Abstract
Trichoderma reesei colonizes predecayed wood in nature and metabolizes cellulose and hemicellulose from the plant biomass. The respective enzymes are industrially produced for application in the biofuel and biorefinery industry. However, these enzymes are also induced in the presence of lactose (1,4-0-ß-d-galactopyranosyl-d-glucose), a waste product from cheese manufacture or whey processing industries. In fact, lactose is the only soluble carbon source that induces these enzymes in T. reesei on an industrial level but the reason for this unique phenomenon is not understood. To answer this question, we used systems analysis of the T. reesei transcriptome during utilization of lactose. We found that the respective CAZome encoded all glycosyl hydrolases necessary for cellulose degradation and particularly for the attack of monocotyledon xyloglucan, from which ß-galactosides could be released that may act as the inducers of T. reesei’s cellulases and hemicellulases. In addition, lactose also induces a high number of putative transporters of the major facilitator superfamily. Deletion of fourteen of them identified one gene that is essential for lactose utilization and lactose uptake, and for cellulase induction by lactose (but not sophorose) in pregrown mycelia of T. reesei. These data shed new light on the mechanism by which T. reesei metabolizes lactose and offers strategies for its improvement. They also illuminate the key role of ß-D-galactosides in habitat specificity of this fungus.
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Affiliation(s)
- Christa Ivanova
- Institute of Chemical Engineering, University of Technology of Vienna, Vienna, Austria
| | - Jenny A. Bååth
- Institute of Chemical Engineering, University of Technology of Vienna, Vienna, Austria
- Lund University, Lund, Sweden
| | - Bernhard Seiboth
- Institute of Chemical Engineering, University of Technology of Vienna, Vienna, Austria
- Austrian Institute of Industrial Biotechnology (ACIB) GmBH c/o Institute of Chemical Engineering, University of Technology of Vienna, Vienna, Austria
| | - Christian P. Kubicek
- Institute of Chemical Engineering, University of Technology of Vienna, Vienna, Austria
- Austrian Institute of Industrial Biotechnology (ACIB) GmBH c/o Institute of Chemical Engineering, University of Technology of Vienna, Vienna, Austria
- * E-mail:
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Metz B, Mojzita D, Herold S, Kubicek CP, Richard P, Seiboth B. A novel L-xylulose reductase essential for L-arabinose catabolism in Trichoderma reesei. Biochemistry 2013; 52:2453-60. [PMID: 23506391 PMCID: PMC3623455 DOI: 10.1021/bi301583u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
l-Xylulose reductases belong
to the superfamily of short
chain dehydrogenases and reductases (SDRs) and catalyze the NAD(P)H-dependent
reduction of l-xylulose to xylitol in l-arabinose
and glucuronic acid catabolism. Here we report the identification
of a novel l-xylulose reductase LXR3 in the fungus Trichoderma reesei by a bioinformatic approach in combination
with a functional analysis. LXR3, a 31 kDa protein, catalyzes the
reduction of l-xylulose to xylitol via NADPH and is also
able to convert d-xylulose, d-ribulose, l-sorbose, and d-fructose to their corresponding polyols.
Transcription of lxr3 is specifically induced by l-arabinose and l-arabitol. Deletion of lxr3 affects growth on l-arabinose and l-arabitol and
reduces total NADPH-dependent LXR activity in cell free extracts.
A phylogenetic analysis of known l-xylulose reductases shows
that LXR3 is phylogenetically different from the Aspergillus
nigerl-xylulose reductase LxrA and, moreover, that
all identified true l-xylulose reductases belong to different
clades within the superfamily of SDRs. This indicates that the enzymes
responsible for the reduction of l-xylulose in l-arabinose and glucuronic acid catabolic pathways have evolved independently
and that even the fungal LXRs of the l-arabinose catabolic
pathway have evolved in different clades of the superfamily of SDRs.
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Affiliation(s)
- Benjamin Metz
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
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Atanasova L, Crom SL, Gruber S, Coulpier F, Seidl-Seiboth V, Kubicek CP, Druzhinina IS. Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism. BMC Genomics 2013; 14:121. [PMID: 23432824 PMCID: PMC3599271 DOI: 10.1186/1471-2164-14-121] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 02/19/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Trichoderma is a genus of mycotrophic filamentous fungi (teleomorph Hypocrea) which possess a bright variety of biotrophic and saprotrophic lifestyles. The ability to parasitize and/or kill other fungi (mycoparasitism) is used in plant protection against soil-borne fungal diseases (biological control, or biocontrol). To investigate mechanisms of mycoparasitism, we compared the transcriptional responses of cosmopolitan opportunistic species and powerful biocontrol agents Trichoderma atroviride and T. virens with tropical ecologically restricted species T. reesei during confrontations with a plant pathogenic fungus Rhizoctonia solani. RESULTS The three Trichoderma spp. exhibited a strikingly different transcriptomic response already before physical contact with alien hyphae. T. atroviride expressed an array of genes involved in production of secondary metabolites, GH16 ß-glucanases, various proteases and small secreted cysteine rich proteins. T. virens, on the other hand, expressed mainly the genes for biosynthesis of gliotoxin, respective precursors and also glutathione, which is necessary for gliotoxin biosynthesis. In contrast, T. reesei increased the expression of genes encoding cellulases and hemicellulases, and of the genes involved in solute transport. The majority of differentially regulated genes were orthologues present in all three species or both in T. atroviride and T. virens, indicating that the regulation of expression of these genes is different in the three Trichoderma spp. The genes expressed in all three fungi exhibited a nonrandom genomic distribution, indicating a possibility for their regulation via chromatin modification. CONCLUSION This genome-wide expression study demonstrates that the initial Trichoderma mycotrophy has differentiated into several alternative ecological strategies ranging from parasitism to predation and saprotrophy. It provides first insights into the mechanisms of interactions between Trichoderma and other fungi that may be exploited for further development of biofungicides.
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Affiliation(s)
- Lea Atanasova
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Stephane Le Crom
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, F-75005, Paris, France
- Inserm, U1024, F-75005, Paris, France
- CNRS, UMR 8197, F-75005, Paris, France
- UPMC Univ Paris 06, UMR7622, Laboratoire de Biologie du Développement, 9 quai St. Bernard, F-75005, Paris, France
- CNRS, UMR7622, Laboratoire de Biologie du Développement, 9 quai St. Bernard, F-75005, Paris, France
| | - Sabine Gruber
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Fanny Coulpier
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, F-75005, Paris, France
- Inserm, U1024, F-75005, Paris, France
- CNRS, UMR 8197, F-75005, Paris, France
| | - Verena Seidl-Seiboth
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Christian P Kubicek
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
- Austrian Center of Industrial Biotechnology (ACIB), GmBH c/o Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Irina S Druzhinina
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
- Austrian Center of Industrial Biotechnology (ACIB), GmBH c/o Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
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Mukherjee PK, Horwitz BA, Herrera-Estrella A, Schmoll M, Kenerley CM. Trichoderma research in the genome era. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:105-29. [PMID: 23915132 DOI: 10.1146/annurev-phyto-082712-102353] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Trichoderma species are widely used in agriculture and industry as biopesticides and sources of enzymes, respectively. These fungi reproduce asexually by production of conidia and chlamydospores and in wild habitats by ascospores. Trichoderma species are efficient mycoparasites and prolific producers of secondary metabolites, some of which have clinical importance. However, the ecological or biological significance of this metabolite diversity is sorely lagging behind the chemical significance. Many strains produce elicitors and induce resistance in plants through colonization of roots. Seven species have now been sequenced. Comparison of a primarily saprophytic species with two mycoparasitic species has provided striking contrasts and has established that mycoparasitism is an ancestral trait of this genus. Among the interesting outcomes of genome comparison is the discovery of a vast repertoire of secondary metabolism pathways and of numerous small cysteine-rich secreted proteins. Genomics has also facilitated investigation of sexual crossing in Trichoderma reesei, suggesting the possibility of strain improvement through hybridization.
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Affiliation(s)
- Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India.
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Häkkinen M, Arvas M, Oja M, Aro N, Penttilä M, Saloheimo M, Pakula TM. Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates. Microb Cell Fact 2012; 11:134. [PMID: 23035824 PMCID: PMC3526510 DOI: 10.1186/1475-2859-11-134] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trichoderma reesei is a soft rot Ascomycota fungus utilised for industrial production of secreted enzymes, especially lignocellulose degrading enzymes. About 30 carbohydrate active enzymes (CAZymes) of T. reesei have been biochemically characterised. Genome sequencing has revealed a large number of novel candidates for CAZymes, thus increasing the potential for identification of enzymes with novel activities and properties. Plenty of data exists on the carbon source dependent regulation of the characterised hydrolytic genes. However, information on the expression of the novel CAZyme genes, especially on complex biomass material, is very limited. RESULTS In this study, the CAZyme gene content of the T. reesei genome was updated and the annotations of the genes refined using both computational and manual approaches. Phylogenetic analysis was done to assist the annotation and to identify functionally diversified CAZymes. The analyses identified 201 glycoside hydrolase genes, 22 carbohydrate esterase genes and five polysaccharide lyase genes. Updated or novel functional predictions were assigned to 44 genes, and the phylogenetic analysis indicated further functional diversification within enzyme families or groups of enzymes. GH3 β-glucosidases, GH27 α-galactosidases and GH18 chitinases were especially functionally diverse. The expression of the lignocellulose degrading enzyme system of T. reesei was studied by cultivating the fungus in the presence of different inducing substrates and by subjecting the cultures to transcriptional profiling. The substrates included both defined and complex lignocellulose related materials, such as pretreated bagasse, wheat straw, spruce, xylan, Avicel cellulose and sophorose. The analysis revealed co-regulated groups of CAZyme genes, such as genes induced in all the conditions studied and also genes induced preferentially by a certain set of substrates. CONCLUSIONS In this study, the CAZyme content of the T. reesei genome was updated, the discrepancies between the different genome versions and published literature were removed and the annotation of many of the genes was refined. Expression analysis of the genes gave information on the enzyme activities potentially induced by the presence of the different substrates. Comparison of the expression profiles of the CAZyme genes under the different conditions identified co-regulated groups of genes, suggesting common regulatory mechanisms for the gene groups.
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Affiliation(s)
- Mari Häkkinen
- VTT Technical Research Centre of Finland, Tietotie 2, Espoo, FI-02044, VTT, Finland.
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Seiboth B, Karimi RA, Phatale PA, Linke R, Hartl L, Sauer DG, Smith KM, Baker SE, Freitag M, Kubicek CP. The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei. Mol Microbiol 2012; 84:1150-64. [PMID: 22554051 PMCID: PMC3370264 DOI: 10.1111/j.1365-2958.2012.08083.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Trichoderma reesei is an industrial producer of enzymes that degrade lignocellulosic polysaccharides to soluble monomers, which can be fermented to biofuels. Here we show that the expression of genes for lignocellulose degradation are controlled by the orthologous T. reesei protein methyltransferase LAE1. In a lae1 deletion mutant we observed a complete loss of expression of all seven cellulases, auxiliary factors for cellulose degradation, β-glucosidases and xylanases were no longer expressed. Conversely, enhanced expression of lae1 resulted in significantly increased cellulase gene transcription. Lae1-modulated cellulase gene expression was dependent on the function of the general cellulase regulator XYR1, but also xyr1 expression was LAE1-dependent. LAE1 was also essential for conidiation of T. reesei. Chromatin immunoprecipitation followed by high-throughput sequencing ('ChIP-seq') showed that lae1 expression was not obviously correlated with H3K4 di- or trimethylation (indicative of active transcription) or H3K9 trimethylation (typical for heterochromatin regions) in CAZyme coding regions, suggesting that LAE1 does not affect CAZyme gene expression by directly modulating H3K4 or H3K9 methylation. Our data demonstrate that the putative protein methyltransferase LAE1 is essential for cellulase gene expression in T. reesei through mechanisms that remain to be identified.
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Affiliation(s)
- Bernhard Seiboth
- Institute of Chemical Engineering, University of Technology of ViennaGumpendorferstrasse 1a, A-1060 Vienna, Austria
| | - Razieh Aghcheh Karimi
- Institute of Chemical Engineering, University of Technology of ViennaGumpendorferstrasse 1a, A-1060 Vienna, Austria
| | - Pallavi A Phatale
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State UniversityCorvallis, OR 97331, USA
| | - Rita Linke
- Institute of Chemical Engineering, University of Technology of ViennaGumpendorferstrasse 1a, A-1060 Vienna, Austria,Austrian Center of Industrial Biotechnology (ACIB), c/o Institute of Chemical Engineering, University of Technology of ViennaGumpendorferstrasse 1a, A-1060 Vienna, Austria
| | - Lukas Hartl
- Institute of Chemical Engineering, University of Technology of ViennaGumpendorferstrasse 1a, A-1060 Vienna, Austria
| | - Dominik G Sauer
- Institute of Chemical Engineering, University of Technology of ViennaGumpendorferstrasse 1a, A-1060 Vienna, Austria
| | - Kristina M Smith
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State UniversityCorvallis, OR 97331, USA
| | - Scott E Baker
- Fungal Biotechnology Team, Chemical and Biological Process Development Group, Pacific Northwest National Laboratory902 Battelle Blvd., Richland, WA 99352, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State UniversityCorvallis, OR 97331, USA
| | - Christian P Kubicek
- Institute of Chemical Engineering, University of Technology of ViennaGumpendorferstrasse 1a, A-1060 Vienna, Austria,*For correspondence. E-mail ; Tel. (+43) 1 58801 166500; Fax (+43) 15880 117299
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Fekete E, de Vries RP, Seiboth B, vanKuyk PA, Sándor E, Fekete E, Metz B, Kubicek CP, Karaffa L. D-Galactose uptake is nonfunctional in the conidiospores of Aspergillus niger. FEMS Microbiol Lett 2012; 329:198-203. [PMID: 22324294 DOI: 10.1111/j.1574-6968.2012.02524.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 02/02/2012] [Accepted: 02/03/2012] [Indexed: 11/28/2022] Open
Abstract
The majority of black Aspergilli (Aspergillus section Nigri), including Aspergillus niger, as well as many other Ascomycetes fail to germinate on d-galactose as a sole carbon source. Here, we provide evidence that the ability of A. niger to transport D-galactose is growth stage dependent, being absent in the conidiospores but present in the mycelia. Despite earlier claims, we could identify galactokinase activity in growing cells and all genes of the Leloir pathway (responsible for channelling D-galactose into the EMP pathway) are well induced on D-galactose (and also on lactose, D-xylose and L-arabinose) in the mycelial stage. Expression of all Leloir pathway genes was also detectable in conidiospores, although galE (encoding a galactokinase) and galD (encoding a galactose-1-phosphate uridylyl transferase) were expressed poorly. These results suggest that the D-galactose-negative phenotype of A. niger conidiospores may be due to the lack of inducer uptake.
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Affiliation(s)
- Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
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Seiboth B, Herold S, Kubicek CP. Metabolic engineering of inducer formation for cellulase and hemicellulase gene expression in Trichoderma reesei. Subcell Biochem 2012; 64:367-90. [PMID: 23080260 DOI: 10.1007/978-94-007-5055-5_18] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The filamentous fungus T. reeseiis today a paradigm for the commercial scale production of different plant cell wall degrading enzymes mainly cellulases and hemicellulases. Its enzymes have a long history of safe use in industry and well established applications are found within the pulp, paper, food, feed or textile processing industries. However, when these enzymes are to be used for the saccharification of cellulosic plant biomass to simple sugars which can be further converted to biofuels or other biorefinery products, and thus compete with chemicals produced from fossil sources, additional efforts are needed to reduce costs and maximize yield and efficiency of the produced enzyme mixtures. One approach to this end is the use of genetic engineering to manipulate the biochemical and regulatory pathways that operate during enzyme production and control enzyme yield. This review aims at a description of the state of art in this area.
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Affiliation(s)
- Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, 166-5, A-1060, Vienna, Austria
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Uzbas F, Sezerman U, Hartl L, Kubicek CP, Seiboth B. A homologous production system for Trichoderma reesei secreted proteins in a cellulase-free background. Appl Microbiol Biotechnol 2011; 93:1601-8. [PMID: 22080343 PMCID: PMC3275749 DOI: 10.1007/s00253-011-3674-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/06/2011] [Accepted: 10/26/2011] [Indexed: 12/20/2022]
Abstract
Recent demands for the production of biofuels from lignocellulose led to an increased interest in engineered cellulases from Trichoderma reesei or other fungal sources. While the methods to generate such mutant cellulases on DNA level are straightforward, there is often a bottleneck in their production since a correct posttranslational processing of these enzymes is needed to obtain highly active enzymes. Their production and subsequent enzymatic analysis in the homologous host T. reesei is, however, often disturbed by the concomitant production of other endogenous cellulases. As a useful alternative, we tested the production of cellulases in T. reesei in a genetic background where cellulase formation has been impaired by deletion of the major cellulase transcriptional activator gene xyr1. Three cellulase genes (cel7a, cel7b, and cel12a) were expressed under the promoter regions of the two highly expressed genes tef1 (encoding translation elongation factor 1-alpha) or cdna1 (encoding the hypothetical protein Trire2:110879). When cultivated on D: -glucose as carbon source, the Δxyr1 strain secreted all three cellulases into the medium. Related to the introduced gene copy number, the cdna1 promoter appeared to be superior to the tef1 promoter. No signs of proteolysis were detected, and the individual cellulases could be assayed over a background essentially free of other cellulases. Hence this system can be used as a vehicle for rapid and high-throughput testing of cellulase muteins in a homologous background.
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Affiliation(s)
- Fatma Uzbas
- Biological Sciences and Bioengineering, Sabanci University, Orhanli, Tuzla, Istanbul, Turkey
| | - Ugur Sezerman
- Biological Sciences and Bioengineering, Sabanci University, Orhanli, Tuzla, Istanbul, Turkey
| | - Lukas Hartl
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, 166-5, 1060 Vienna, Austria
| | - Christian P. Kubicek
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, 166-5, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, 166-5, 1060 Vienna, Austria
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