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Castañeda-Casasola CC, Nieto-Jacobo MF, Soares A, Padilla-Padilla EA, Anducho-Reyes MA, Brown C, Soth S, Esquivel-Naranjo EU, Hampton J, Mendoza-Mendoza A. Unveiling a Microexon Switch: Novel Regulation of the Activities of Sugar Assimilation and Plant-Cell-Wall-Degrading Xylanases and Cellulases by Xlr2 in Trichoderma virens. Int J Mol Sci 2024; 25:5172. [PMID: 38791210 PMCID: PMC11121469 DOI: 10.3390/ijms25105172] [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: 03/20/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Functional microexons have not previously been described in filamentous fungi. Here, we describe a novel mechanism of transcriptional regulation in Trichoderma requiring the inclusion of a microexon from the Xlr2 gene. In low-glucose environments, a long mRNA including the microexon encodes a protein with a GAL4-like DNA-binding domain (Xlr2-α), whereas in high-glucose environments, a short mRNA that is produced encodes a protein lacking this DNA-binding domain (Xlr2-β). Interestingly, the protein isoforms differ in their impact on cellulase and xylanase activity. Deleting the Xlr2 gene reduced both xylanase and cellulase activity and growth on different carbon sources, such as carboxymethylcellulose, xylan, glucose, and arabinose. The overexpression of either Xlr2-α or Xlr2-β in T. virens showed that the short isoform (Xlr2-β) caused higher xylanase activity than the wild types or the long isoform (Xlr2-α). Conversely, cellulase activity did not increase when overexpressing Xlr2-β but was increased with the overexpression of Xlr2-α. This is the first report of a novel transcriptional regulation mechanism of plant-cell-wall-degrading enzyme activity in T. virens. This involves the differential expression of a microexon from a gene encoding a transcriptional regulator.
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Affiliation(s)
- Cynthia Coccet Castañeda-Casasola
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Centro Nacional de Referencia Fitosanitaria, Tecamac 55740, Mexico
| | | | - Amanda Soares
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Emir Alejandro Padilla-Padilla
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 04510, Mexico
| | - Miguel Angel Anducho-Reyes
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
| | - Chris Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
| | - Sereyboth Soth
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Edgardo Ulises Esquivel-Naranjo
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, Queretaro 76230, Mexico
| | - John Hampton
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Artemio Mendoza-Mendoza
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
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Zhang J, Li K, Sun Y, Yao C, Liu W, Liu H, Zhong Y. An efficient CRISPR/Cas9 genome editing system based on a multiple sgRNA processing platform in Trichoderma reesei for strain improvement and enzyme production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:22. [PMID: 38342915 DOI: 10.1186/s13068-024-02468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/29/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND The CRISPR/Cas9 technology is being employed as a convenient tool for genetic engineering of the industrially important filamentous fungus Trichoderma reesei. However, multiplex gene editing is still constrained by the sgRNA processing capability, hindering strain improvement of T. reesei for the production of lignocellulose-degrading enzymes and recombinant proteins. RESULTS Here, a CRISPR/Cas9 system based on a multiple sgRNA processing platform was established for genome editing in T. reesei. The platform contains the arrayed tRNA-sgRNA architecture directed by a 5S rRNA promoter to generate multiple sgRNAs from a single transcript by the endogenous tRNA processing system. With this system, two sgRNAs targeting cre1 (encoding the carbon catabolite repressor 1) were designed and the precise deletion of cre1 was obtained, demonstrating the efficiency of sgRNAs processing in the tRNA-sgRNA architecture. Moreover, overexpression of xyr1-A824V (encoding a key activator for cellulase/xylanase expression) at the ace1 (encoding a repressor for cellulase/xylanase expression) locus was achieved by designing two sgRNAs targeting ace1 in the system, resulting in the significantly enhanced production of cellulase (up to 1- and 18-fold on the Avicel and glucose, respectively) and xylanase (up to 11- and 41-fold on the Avicel and glucose, respectively). Furthermore, heterologous expression of the glucose oxidase gene from Aspergillus niger ATCC 9029 at the cbh1 locus with the simultaneous deletion of cbh1 and cbh2 (two cellobiohydrolase coding genes) by designing four sgRNAs targeting cbh1 and cbh2 in the system was acquired, and the glucose oxidase produced by T. reesei reached 43.77 U/mL. Besides, it was found the ER-associated protein degradation (ERAD) level was decreased in the glucose oxidase-producing strain, which was likely due to the reduction of secretion pressure by deletion of the major endogenous cellulase-encoding genes. CONCLUSIONS The tRNA-gRNA array-based CRISPR-Cas9 editing system was successfully developed in T. reesei. This system would accelerate engineering of T. reesei for high-level production of enzymes including lignocellulose-degrading enzymes and other recombinant enzymes. Furthermore, it would expand the CRISPR toolbox for fungal genome editing and synthetic biology.
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Affiliation(s)
- Jiaxin Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Kehang Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yu Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Cheng Yao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Hong Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
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Ran Y, Yang Q, Zeng J, Li F, Cao Y, Xu Q, Qiao D, Xu H, Cao Y. Potential xylose transporters regulated by CreA improved lipid yield and furfural tolerance in oleaginous yeast Saitozyma podzolica zwy-2-3. BIORESOURCE TECHNOLOGY 2023; 386:129413. [PMID: 37390935 DOI: 10.1016/j.biortech.2023.129413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Lignocellulose's hydrolysate, a significant renewable source, contains xylose and furfural, making it challenging for industrial production of oleaginous yeast. On xylose fermentation with furfural treatment, OE::DN7263 and OE::DN7661 increased lipid yield and furfural tolerance versus WT, while, which of OE::CreA were decreased owing to CreA regulating DN7263 and DN7661 negatively. OE::CreA generated reactive oxygen species (ROS) causing oxidative damage. OE::DN7263, OE::DN7661, and ΔCreA reduced furfural via NADH; while ΔCreA produced less ROS and OE::DN7263, and OE::DN7661 scavenged ROS quickly, minimizing oxidative damage. Overall, CreA knockout increased DN7263 and DN7661 expression to facilitate xylose assimilation, enhancing NADH generation and ROS clearance. Finally, with mixed sugar fermentation, ΔCreA and OE::DN7263's biomass and lipid yield rose without furfural addition, while that of ΔCreA remained higher than WT after furfural treatment. These findings revealed how oleaginous yeast zwy-2-3 resisted furfural stress and indicated ΔCreA and OE::DN7263 might develop into robust industrial chassis strains.
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Affiliation(s)
- Yulu Ran
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Qingzhuoma Yang
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Jie Zeng
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Fazhi Li
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Yu Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Qingrui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Dairong Qiao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China.
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China.
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Xu W, Fang Y, Ding M, Ren Y, Meng X, Chen G, Zhang W, Liu W. Elimination of the Sugar Transporter GAT1 Increased Xylanase I Production in Trichoderma reesei. Front Microbiol 2022; 13:810066. [PMID: 35154055 PMCID: PMC8825865 DOI: 10.3389/fmicb.2022.810066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
The filamentous fungus Trichoderma reesei secretes large quantities of cellulases and hemicellulases that have found wide applications in industry. Compared with extensive studies on the mechanism controlling cellulase gene expression, less is known about the regulatory mechanism behind xylanase gene expression. Herein, several putative sugar transporter encoding genes that showed significant upregulation on xylan were identified in T. reesei. Deletion of one such gene, gat1, resulted in increased xylanase production but hardly affected cellulase induction. Further analyses demonstrated that deletion of gat1 markedly increased XYNI production at the transcriptional level and only exerted a minor effect on XYNII synthesis. In contrast, overexpressing gat1 caused a continuous decrease in xyn1 expression. Deletion of gat1 also affected the expression of xyn1 and pectinase genes when T. reesei was cultivated with galacturonic acid as the sole carbon source. Transcriptome analyses of Δgat1 and its parental strain identified 255 differentially expressed genes that are enriched in categories of glycoside hydrolases, lipid metabolism, transporters, and transcriptional factors. The results thus implicate a repressive role of the sugar transporter GAT1 in xyn1 expression and reveal that distinct regulatory mechanisms may exist in controlling the expression of different xylanase genes in T. reesei.
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Affiliation(s)
- Wenqiang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Mingyang Ding
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yajing Ren
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Chroumpi T, Peng M, Aguilar‐Pontes MV, Müller A, Wang M, Yan J, Lipzen A, Ng V, Grigoriev IV, Mäkelä MR, de Vries RP. Revisiting a 'simple' fungal metabolic pathway reveals redundancy, complexity and diversity. Microb Biotechnol 2021; 14:2525-2537. [PMID: 33666344 PMCID: PMC8601170 DOI: 10.1111/1751-7915.13790] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 01/29/2023] Open
Abstract
Next to d-glucose, the pentoses l-arabinose and d-xylose are the main monosaccharide components of plant cell wall polysaccharides and are therefore of major importance in biotechnological applications that use plant biomass as a substrate. Pentose catabolism is one of the best-studied pathways of primary metabolism of Aspergillus niger, and an initial outline of this pathway with individual enzymes covering each step of the pathway has been previously established. However, although growth on l-arabinose and/or d-xylose of most pentose catabolic pathway (PCP) single deletion mutants of A. niger has been shown to be negatively affected, it was not abolished, suggesting the involvement of additional enzymes. Detailed analysis of the single deletion mutants of the known A. niger PCP genes led to the identification of additional genes involved in the pathway. These results reveal a high level of complexity and redundancy in this pathway, emphasizing the need for a comprehensive understanding of metabolic pathways before entering metabolic engineering of such pathways for the generation of more efficient fungal cell factories.
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Affiliation(s)
- Tania Chroumpi
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Mao Peng
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Maria Victoria Aguilar‐Pontes
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
- Present address:
Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B1R6Canada
| | - Astrid Müller
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Mei Wang
- US Department of Energy Joint Genome InstituteLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Juying Yan
- US Department of Energy Joint Genome InstituteLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Anna Lipzen
- US Department of Energy Joint Genome InstituteLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Vivian Ng
- US Department of Energy Joint Genome InstituteLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome InstituteLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCA94720USA
| | - Miia R. Mäkelä
- Department of MicrobiologyUniversity of HelsinkiP.O. Box 56Viikinkaari 9HelsinkiFinland
| | - Ronald P. de Vries
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
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Tomico-Cuenca I, Mach RL, Mach-Aigner AR, Derntl C. An overview on current molecular tools for heterologous gene expression in Trichoderma. Fungal Biol Biotechnol 2021; 8:11. [PMID: 34702369 PMCID: PMC8549263 DOI: 10.1186/s40694-021-00119-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/16/2021] [Indexed: 11/10/2022] Open
Abstract
Fungi of the genus Trichoderma are routinely used as biocontrol agents and for the production of industrial enzymes. Trichoderma spp. are interesting hosts for heterologous gene expression because their saprotrophic and mycoparasitic lifestyles enable them to thrive on a large number of nutrient sources and some members of this genus are generally recognized as safe (GRAS status). In this review, we summarize and discuss several aspects involved in heterologous gene expression in Trichoderma, including transformation methods, genome editing strategies, native and synthetic expression systems and implications of protein secretion. This review focuses on the industrial workhorse Trichoderma reesei because this fungus is the best-studied member of this genus for protein expression and secretion. However, the discussed strategies and tools can be expected to be transferable to other Trichoderma species.
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Affiliation(s)
- Irene Tomico-Cuenca
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060, Wien, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060, Wien, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060, Wien, Austria
| | - Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060, Wien, Austria.
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Havukainen S, Pujol-Giménez J, Valkonen M, Hediger MA, Landowski CP. Functional characterization of a highly specific L-arabinose transporter from Trichoderma reesei. Microb Cell Fact 2021; 20:177. [PMID: 34496831 PMCID: PMC8425032 DOI: 10.1186/s12934-021-01666-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Lignocellulose biomass has been investigated as a feedstock for second generation biofuels and other value-added products. Some of the processes for biofuel production utilize cellulases and hemicellulases to convert the lignocellulosic biomass into a range of soluble sugars before fermentation with microorganisms such as yeast Saccharomyces cerevisiae. One of these sugars is l-arabinose, which cannot be utilized naturally by yeast. The first step in l-arabinose catabolism is its transport into the cells, and yeast lacks a specific transporter, which could perform this task. Results We identified Trire2_104072 of Trichoderma reesei as a potential l-arabinose transporter based on its expression profile. This transporter was described already in 2007 as d-xylose transporter XLT1. Electrophysiology experiments with Xenopus laevis oocytes and heterologous expression in yeast revealed that Trire2_104072 is a high-affinity l-arabinose symporter with a Km value in the range of \documentclass[12pt]{minimal}
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\begin{document}$$\sim$$\end{document}∼ 0.1–0.2 mM. It can also transport d-xylose but with low affinity (Km\documentclass[12pt]{minimal}
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\begin{document}$$\sim$$\end{document}∼ 9 mM). In yeast, l-arabinose transport was inhibited slightly by d-xylose but not by d-glucose in an assay with fivefold excess of the inhibiting sugar. Comparison with known l-arabinose transporters revealed that the expression of Trire2_104072 enabled yeast to uptake l-arabinose at the highest rate in conditions with low extracellular l-arabinose concentration. Despite the high specificity of Trire2_104072 for l-arabinose, the growth of its T. reesei deletion mutant was only affected at low l-arabinose concentrations. Conclusions Due to its high affinity for l-arabinose and low inhibition by d-glucose or d-xylose, Trire2_104072 could serve as a good candidate for improving the existing pentose-utilizing yeast strains. The discovery of a highly specific l-arabinose transporter also adds to our knowledge of the primary metabolism of T. reesei. The phenotype of the deletion strain suggests the involvement of other transporters in l-arabinose transport in this species. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01666-4.
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Affiliation(s)
- Sami Havukainen
- VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Jonai Pujol-Giménez
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland.,Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland
| | - Mari Valkonen
- VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland.,Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland
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Havukainen S, Pujol-Giménez J, Valkonen M, Westerholm-Parvinen A, Hediger MA, Landowski CP. Electrophysiological characterization of a diverse group of sugar transporters from Trichoderma reesei. Sci Rep 2021; 11:14678. [PMID: 34282161 PMCID: PMC8290022 DOI: 10.1038/s41598-021-93552-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Trichoderma reesei is an ascomycete fungus known for its capability to secrete high amounts of extracellular cellulose- and hemicellulose-degrading enzymes. These enzymes are utilized in the production of second-generation biofuels and T. reesei is a well-established host for their production. Although this species has gained considerable interest in the scientific literature, the sugar transportome of T. reesei remains poorly characterized. Better understanding of the proteins involved in the transport of different sugars could be utilized for engineering better enzyme production strains. In this study we aimed to shed light on this matter by characterizing multiple T. reesei transporters capable of transporting various types of sugars. We used phylogenetics to select transporters for expression in Xenopus laevis oocytes to screen for transport activities. Of the 18 tested transporters, 8 were found to be functional in oocytes. 10 transporters in total were investigated in oocytes and in yeast, and for 3 of them no transport function had been described in literature. This comprehensive analysis provides a large body of new knowledge about T. reesei sugar transporters, and further establishes X. laevis oocytes as a valuable tool for studying fungal sugar transporters.
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Affiliation(s)
- Sami Havukainen
- Protein Production Team, VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Jonai Pujol-Giménez
- Membrane Transport Discovery Lab, Department of Biomedical Research, Inselspital, University of Bern, 3010, Bern, Switzerland
| | - Mari Valkonen
- Protein Production Team, VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Ann Westerholm-Parvinen
- Protein Production Team, VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Biomedical Research, Inselspital, University of Bern, 3010, Bern, Switzerland
| | - Christopher P Landowski
- Protein Production Team, VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland.
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Sukumaran RK, Christopher M, Kooloth-Valappil P, Sreeja-Raju A, Mathew RM, Sankar M, Puthiyamadam A, Adarsh VP, Aswathi A, Rebinro V, Abraham A, Pandey A. Addressing challenges in production of cellulases for biomass hydrolysis: Targeted interventions into the genetics of cellulase producing fungi. BIORESOURCE TECHNOLOGY 2021; 329:124746. [PMID: 33610429 DOI: 10.1016/j.biortech.2021.124746] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Lignocellulosic materials are the favoured feedstock for biorefineries due to their abundant availability and non-completion with food. Biobased technologies for refining these materials are limited mainly by the cost of biomass hydrolyzing enzymes, typically sourced from filamentous fungi. Therefore, considerable efforts have been directed at improving the quantity and quality of secreted lignocellulose degrading enzymes from fungi in order to attain overall economic viability. Process improvements and media engineering probably have reached their thresholds and further production enhancements require modifying the fungal metabolism to improve production and secretion of these enzymes. This review focusses on the types and mechanisms of action of known fungal biomass degrading enzymes, our current understanding of the genetic control exerted on their expression, and possible routes for intervention, especially on modulating catabolite repression, transcriptional regulators, signal transduction, secretion pathways etc., in order to improve enzyme productivity, activity and stability.
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Affiliation(s)
- Rajeev K Sukumaran
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Meera Christopher
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Prajeesh Kooloth-Valappil
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - AthiraRaj Sreeja-Raju
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Reshma M Mathew
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Meena Sankar
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Anoop Puthiyamadam
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Velayudhanpillai-Prasannakumari Adarsh
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Aswathi Aswathi
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Valan Rebinro
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Amith Abraham
- Department of Chemical Engineering, Hanyang University, Seoul, Republic of Korea
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
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10
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Novy V, Nielsen F, Cullen D, Sabat G, Houtman CJ, Hunt CG. The characteristics of insoluble softwood substrates affect fungal morphology, secretome composition, and hydrolytic efficiency of enzymes produced by Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:105. [PMID: 33902680 PMCID: PMC8074412 DOI: 10.1186/s13068-021-01955-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/11/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND On-site enzyme production using Trichoderma reesei can improve yields and lower the overall cost of lignocellulose saccharification by exploiting the fungal gene regulatory mechanism that enables it to continuously adapt enzyme secretion to the substrate used for cultivation. To harness this, the interrelation between substrate characteristics and fungal response must be understood. However, fungal morphology or gene expression studies often lack structural and chemical substrate characterization. Here, T. reesei QM6a was cultivated on three softwood substrates: northern bleached softwood Kraft pulp (NBSK) and lodgepole pine pretreated either by dilute-acid-catalyzed steam pretreatment (LP-STEX) or mild alkaline oxidation (LP-ALKOX). With different pretreatments of similar starting materials, we presented the fungus with systematically modified substrates. This allowed the elucidation of substrate-induced changes in the fungal response and the testing of the secreted enzymes' hydrolytic strength towards the same substrates. RESULTS Enzyme activity time courses correlated with hemicellulose content and cellulose accessibility. Specifically, increased amounts of side-chain-cleaving hemicellulolytic enzymes in the protein produced on the complex substrates (LP-STEX; LP-ALKOX) was observed by secretome analysis. Confocal laser scanning micrographs showed that fungal micromorphology responded to changes in cellulose accessibility and initial culture viscosity. The latter was caused by surface charge and fiber dimensions, and likely restricted mass transfer, resulting in morphologies of fungi in stress. Supplementing a basic cellulolytic enzyme mixture with concentrated T. reesei supernatant improved saccharification efficiencies of the three substrates, where cellulose, xylan, and mannan conversion was increased by up to 27, 45, and 2800%, respectively. The improvement was most pronounced for proteins produced on LP-STEX and LP-ALKOX on those same substrates, and in the best case, efficiencies reached those of a state-of-the-art commercial enzyme preparation. CONCLUSION Cultivation of T. reesei on LP-STEX and LP-ALKOX produced a protein mixture that increased the hydrolytic strength of a basic cellulase mixture to state-of-the-art performance on softwood substrates. This suggests that the fungal adaptation mechanism can be exploited to achieve enhanced performance in enzymatic hydrolysis without a priori knowledge of specific substrate requirements.
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Affiliation(s)
- Vera Novy
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA.
- Department of Biology and Bioengineering, Division of Industrial Biotechnology, Chalmers University of Technology, Kemivägen 10, 412 96, Göteborg, Sweden.
| | - Fredrik Nielsen
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Daniel Cullen
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Grzegorz Sabat
- University of Wisconsin Biotechnology Center, Madison, WI, 53706, USA
| | - Carl J Houtman
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Christopher G Hunt
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
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11
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Yan S, Xu Y, Yu XW. Rational engineering of xylanase hyper-producing system in Trichoderma reesei for efficient biomass degradation. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:90. [PMID: 33832521 PMCID: PMC8033665 DOI: 10.1186/s13068-021-01943-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/27/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Filamentous fungus Trichoderma reesei has been widely used as a workhorse for cellulase and xylanase productions. Xylanase has been reported as the crucial accessory enzyme in the degradation of lignocellulose for higher accessibility of cellulase. In addition, the efficient hydrolysis of xylan needs the co-work of multiple xylanolytic enzymes, which rise an increasing demand for the high yield of xylanase for efficient biomass degradation. RESULTS In this study, a xylanase hyper-producing system in T. reesei was established by tailoring two transcription factors, XYR1 and ACE1, and homologous overexpression of the major endo-xylanase XYNII. The expressed xylanase cocktail contained 5256 U/mL xylanase activity and 9.25 U/mL β-xylosidase (pNPXase) activity. Meanwhile, the transcription level of the xylanolytic genes in the strain with XYR1 overexpressed was upregulated, which was well correlated with the amount of XYR1-binding sites. In addition, the higher expression of associated xylanolytic enzymes would result in more efficient xylan hydrolysis. Besides, 2310-3085 U/mL of xylanase activities were achieved using soluble carbon source, which was more efficient and economical than the traditional strategy of xylan induction. Unexpectedly, deletion of ace1 in C30OExyr1 did not give any improvement, which might be the result of the disturbed function of the complex formed between ACE1 and XYR1. The enzymatic hydrolysis of alkali pretreated corn stover using the crude xylanase cocktails as accessory enzymes resulted in a 36.64% increase in saccharification efficiency with the ratio of xylanase activity vs FPase activity at 500, compared to that using cellulase alone. CONCLUSIONS An efficient and economical xylanase hyper-producing platform was developed in T. reesei RUT-C30. The novel platform with outstanding ability for crude xylanase cocktail production would greatly fit in biomass degradation and give a new perspective of further engineering in T. reesei for industrial purposes.
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Affiliation(s)
- Su Yan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Xiao-Wei Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China.
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12
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Novy V, Nielsen F, Seiboth B, Nidetzky B. The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:238. [PMID: 31624500 PMCID: PMC6781402 DOI: 10.1186/s13068-019-1571-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/20/2019] [Indexed: 05/21/2023]
Abstract
Biorefineries, designed for the production of lignocellulose-based chemicals and fuels, are receiving increasing attention from the public, governments, and industries. A major obstacle for biorefineries to advance to commercial scale is the high cost of the enzymes required to derive the fermentable sugars from the feedstock used. As summarized in this review, techno-economic studies suggest co-localization and integration of enzyme manufacturing with the cellulosic biorefinery as the most promising alternative to alleviate this problem. Thus, cultivation of Trichoderma reesei, the principal producer of lignocellulolytic enzymes, on the lignocellulosic biomass processed on-site can reduce the cost of enzyme manufacturing. Further, due to a complex gene regulation machinery, the fungus can adjust the gene expression of the lignocellulolytic enzymes towards the characteristics of the feedstock, increasing the hydrolytic efficiency of the produced enzyme cocktail. Despite extensive research over decades, the underlying regulatory mechanisms are not fully elucidated. One aspect that has received relatively little attention in literature is the influence the characteristics of a lignocellulosic substrate, i.e., its chemical and physical composition, has on the produced enzyme mixture. Considering that the fungus is dependent on efficient enzymatic degradation of the lignocellulose for continuous supply of carbon and energy, a relationship between feedstock characteristics and secretome composition can be expected. The aim of this review was to systematically collect, appraise, and aggregate data and integrate results from studies analyzing enzyme production by T. reesei on insoluble cellulosic model substrates and lignocellulosic biomass. The results show that there is a direct effect of the substrate's complexity (rated by structure, composition of the lignin-carbohydrate complex, and recalcitrance in enzymatic saccharification) on enzyme titers and the composition of specific activities in the secretome. It further shows that process-related factors, such as substrate loading and cultivation set-up, are direct targets for increasing enzyme yields. The literature on transcriptome and secretome composition further supports the proposed influence of substrate-related factors on the expression of lignocellulolytic enzymes. This review provides insights into the interrelation between the characteristics of the substrate and the enzyme production by T. reesei, which may help to advance integrated enzyme manufacturing of substrate-specific enzymes cocktails at scale.
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Affiliation(s)
- Vera Novy
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Fredrik Nielsen
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Bernhard Seiboth
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
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13
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Watanabe T, Nasukawa M, Yoshida Y, Kogo T, Ogihara J, Kasumi T. Generation of Trichoderma reesei Mutant with Enhanced Xylanase Activity by Using Disparity Mutagenesis. J Appl Glycosci (1999) 2019; 66:59-64. [PMID: 34354521 PMCID: PMC8056916 DOI: 10.5458/jag.jag.jag-2018_0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/08/2018] [Indexed: 11/27/2022] Open
Abstract
In the current study, we attempted to enhance the xylanase activity of Trichoderma reesei ATCC66589 by using disparity mutagenesis, wherein a plasmid harboring proofreading-impaired DNA polymerase δ was inserted. Following selection on xylan-rich media and successive plasmid curing, a mutant showing conidiospores strikingly different from those of the parent strain, with many small humped-surface spheres, was generated. Xylanase and β-xylosidase activities of the mutant XM1, cultivated in xylan medium, were 15.8- and 11.0-fold higher than those of the parent strain, respectively. Furthermore, xylanase activity was generated approximately 24 h in advance compared to that in the parent. In contrast, when cultivated in Avicel medium, its xylanase and β-xylosidase activities were 0.14- and 0.33-fold, respectively, compared to those in the parent. Among the xylan component sugars and related polyols, D-xylose and xylobiose exerted a distinct inductive effect on the xylanase activity in Avicel media, while xylitol and L-arabinose did not. Mutagenesis involved in xylose catabolism is suggestive of changes at the gene transcription level. Although the induction mechanism remains unclear in details, disparity mutagenesis may be useful for obtaining T. reesei mutants with high xylanase activity.
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Affiliation(s)
- Taisuke Watanabe
- 1 Applied Microbiology and Biotechnology Laboratory, College of Bioresource Sciences, Nihon University
| | - Masashi Nasukawa
- 1 Applied Microbiology and Biotechnology Laboratory, College of Bioresource Sciences, Nihon University.,2 Biotechnology Center, Chitose Laboratory Incorporated
| | - Yuki Yoshida
- 1 Applied Microbiology and Biotechnology Laboratory, College of Bioresource Sciences, Nihon University
| | - Takashi Kogo
- 1 Applied Microbiology and Biotechnology Laboratory, College of Bioresource Sciences, Nihon University
| | - Jun Ogihara
- 1 Applied Microbiology and Biotechnology Laboratory, College of Bioresource Sciences, Nihon University
| | - Takafumi Kasumi
- 1 Applied Microbiology and Biotechnology Laboratory, College of Bioresource Sciences, Nihon University
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14
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Han H, Ling Z, Khan A, Virk AK, Kulshrestha S, Li X. Improvements of thermophilic enzymes: From genetic modifications to applications. BIORESOURCE TECHNOLOGY 2019; 279:350-361. [PMID: 30755321 DOI: 10.1016/j.biortech.2019.01.087] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Thermozymes (from thermophiles or hyperthermophiles) offer obvious advantages due to their excellent thermostability, broad pH adaptation, and hydrolysis ability, resulting in diverse industrial applications including food, paper, and textile processing, biofuel production. However, natural thermozymes with low yield and poor adaptability severely hinder their large-scale applications. Extensive studies demonstrated that using genetic modifications such as directed evolution, semi-rational design, and rational design, expression regulations and chemical modifications effectively improved enzyme's yield, thermostability and catalytic efficiency. However, mechanism-based techniques for thermozymes improvements and applications need more attention. In this review, stabilizing mechanisms of thermozymes are summarized for thermozymes improvements, and these improved thermozymes eventually have large-scale industrial applications.
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Affiliation(s)
- Huawen Han
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Zhenmin Ling
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Amanpreet Kaur Virk
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India
| | - Saurabh Kulshrestha
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, People's Republic of China.
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15
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Benocci T, Aguilar-Pontes MV, Kun RS, Lubbers RJM, Lail K, Wang M, Lipzen A, Ng V, Grigoriev IV, Seiboth B, Daly P, de Vries RP. Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:81. [PMID: 31007715 PMCID: PMC6454604 DOI: 10.1186/s13068-019-1422-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/03/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Trichoderma reesei is one of the major producers of enzymes for the conversion of plant biomass to sustainable fuels and chemicals. Crude plant biomass can induce the production of CAZymes in T. reesei, but there is limited understanding of how the transcriptional response to crude plant biomass is regulated. In addition, it is unknown whether induction on untreated recalcitrant crude plant biomass (with a large diversity of inducers) can be sustained for longer. We investigated the transcriptomic response of T. reesei to the two industrial feedstocks, corn stover (CS) and soybean hulls (SBH), over time (4 h, 24 h and 48 h), and its regulatory basis using transcription factor deletion mutants (Δxyr1 and Δara1). We also investigated whether deletion of a xylulokinase gene (Δxki1) from the pentose catabolic pathway that converts potential inducers could lead to increased CAZyme gene expression. RESULTS By analyzing the transcriptomic responses using clustering as well as differential and cumulative expression of plant biomass degrading CAZymes, we found that corn stover induced a broader range and higher expression of CAZymes in T. reesei, while SBH induced more pectinolytic and mannanolytic transcripts. XYR1 was the major TF regulating CS utilization, likely due to the significant amount of d-xylose in this substrate. In contrast, ARA1 had a stronger effect on SBH utilization, which correlates with a higher abundance of l-arabinose in SBH that activates ARA1. Blocking pentose catabolism by deletion of xki1 led to higher expression of CAZyme encoding genes on both substrates at later time points. Surprisingly, this was also observed for Δara1 at later time points. Many of these genes were XYR1 regulated, suggesting that inducers for this regulator accumulated over time on both substrates. CONCLUSION Our data demonstrates the complexity of the regulatory system related to plant biomass degradation in T. reesei and the effect the feedstock composition has on this. Furthermore, this dataset provides leads to improve the efficiency of a T. reesei enzyme cocktail, such as by the choice of substrate or by deleting xki1 to obtain higher production of plant biomass degrading CAZymes.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roland Sándor Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ronnie J. M. Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94598 USA
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, 1060 Vienna, Austria
| | - Paul Daly
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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16
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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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17
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Alazi E, Ram AFJ. Modulating Transcriptional Regulation of Plant Biomass Degrading Enzyme Networks for Rational Design of Industrial Fungal Strains. Front Bioeng Biotechnol 2018; 6:133. [PMID: 30320082 PMCID: PMC6167437 DOI: 10.3389/fbioe.2018.00133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/05/2018] [Indexed: 01/08/2023] Open
Abstract
Filamentous fungi are the most important microorganisms for the industrial production of plant polysaccharide degrading enzymes due to their unique ability to secrete these proteins efficiently. These carbohydrate active enzymes (CAZymes) are utilized industrially for the hydrolysis of plant biomass for the subsequent production of biofuels and high-value biochemicals. The expression of the genes encoding plant biomass degrading enzymes is tightly controlled. Naturally, large amounts of CAZymes are produced and secreted only in the presence of the plant polysaccharide they specifically act on. The signal to produce is conveyed via so-called inducer molecules which are di- or mono-saccharides (or derivatives thereof) released from the specific plant polysaccharides. The presence of the inducer results in the activation of a substrate-specific transcription factor (TF), which is required not only for the controlled expression of the genes encoding the CAZymes, but often also for the regulation of the expression of the genes encoding sugar transporters and catabolic pathway enzymes needed to utilize the released monosaccharide. Over the years, several substrate-specific TFs involved in the degradation of cellulose, hemicellulose, pectin, starch and inulin have been identified in several fungal species and systems biology approaches have made it possible to uncover the enzyme networks controlled by these TFs. The requirement for specific inducers for TF activation and subsequently the expression of particular enzyme networks determines the choice of feedstock to produce enzyme cocktails for industrial use. It also results in batch-to-batch variation in the composition and amounts of enzymes due to variations in sugar composition and polysaccharide decorations of the feedstock which hampers the use of cheap feedstocks for constant quality of enzyme cocktails. It is therefore of industrial interest to produce specific enzyme cocktails constitutively and independently of inducers. In this review, we focus on the methods to modulate TF activities for inducer-independent production of CAZymes and highlight various approaches that are used to construct strains displaying constitutive expression of plant biomass degrading enzyme networks. These approaches and combinations thereof are also used to construct strains displaying increased expression of CAZymes under inducing conditions, and make it possible to design strains in which different enzyme mixtures are simultaneously produced independently of the carbon source.
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Affiliation(s)
| | - Arthur F. J. Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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18
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Dattenböck C, Tisch D, Schuster A, Monroy AA, Hinterdobler W, Schmoll M. Gene regulation associated with sexual development and female fertility in different isolates of Trichoderma reesei. Fungal Biol Biotechnol 2018; 5:9. [PMID: 29785273 PMCID: PMC5952832 DOI: 10.1186/s40694-018-0055-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 04/12/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Trichoderma reesei is one of the most frequently used filamentous fungi in industry for production of homologous and heterologous proteins. The ability to use sexual crossing in this fungus was discovered several years ago and opens up new perspectives for industrial strain improvement and investigation of gene regulation. RESULTS Here we investigated the female sterile strain QM6a in comparison to the fertile isolate CBS999.97 and backcrossed derivatives of QM6a, which have regained fertility (FF1 and FF2 strains) in both mating types under conditions of sexual development. We found considerable differences in gene regulation between strains with the CBS999.97 genetic background and the QM6a background. Regulation patterns of QM6a largely clustered with the backcrossed FF1 and FF2 strains. Differential regulation between QM6a and FF1/FF2 as well as clustering of QM6a patterns with those of CBS999.97 strains was also observed. Consistent mating type dependent regulation was limited to mating type genes and those involved in pheromone response, but included also nta1 encoding a putative N-terminal amidase previously not associated with development. Comparison of female sterile QM6a with female fertile strains showed differential expression in genes encoding several transcription factors, metabolic genes and genes involved in secondary metabolism. CONCLUSIONS Evaluation of the functions of genes specifically regulated under conditions of sexual development and of genes with highest levels of transcripts under these conditions indicated a relevance of secondary metabolism for sexual development in T. reesei. Among others, the biosynthetic genes of the recently characterized SOR cluster are in this gene group. However, these genes are not essential for sexual development, but rather have a function in protection and defence against competitors during reproduction.
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Affiliation(s)
- Christoph Dattenböck
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
| | - Doris Tisch
- Institute of Chemical Engineering, Research Area Molecular Biotechnology, TU Wien, 1060 Vienna, Austria
| | - Andre Schuster
- Institute of Chemical Engineering, Research Area Molecular Biotechnology, TU Wien, 1060 Vienna, Austria
| | - Alberto Alonso Monroy
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
| | - Wolfgang Hinterdobler
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
| | - Monika Schmoll
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
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19
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Gong W, Dai L, Zhang H, Zhang L, Wang L. A Highly Efficient Xylan-Utilization System in Aspergillus niger An76: A Functional-Proteomics Study. Front Microbiol 2018; 9:430. [PMID: 29623069 PMCID: PMC5874446 DOI: 10.3389/fmicb.2018.00430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/26/2018] [Indexed: 11/23/2022] Open
Abstract
Xylan constituted with β-1,4-D-xylose linked backbone and diverse substituted side-chains is the most abundant hemicellulose component of biomass, which can be completely and rapidly degraded into fermentable sugars by Aspergillus niger. This is of great value for obtaining renewable biofuels and biochemicals. To clarify the underlying mechanisms associated with highly efficient xylan degradation, assimilation, and metabolism by A. niger, we utilized functional proteomics to analyze the secreted proteins, sugar transporters, and intracellular proteins of A. niger An76 grown on xylan-based substrates. Results demonstrated that the complete xylanolytic enzyme system required for xylan degradation and composed of diverse isozymes was secreted in a sequential order. Xylan-backbone-degrading enzymes were preferentially induced by xylose or other soluble sugars, which efficiently produced large amounts of xylooligosaccharides (XOS) and xylose; however, XOS was more efficient than xylose in triggering the expression of the key transcription activator XlnR, resulting in higher xylanase activity and shortening xylanase-production time. Moreover, the substituted XOS was responsible for improving the abundance of side-chain-degrading enzymes, specific transporters, and key reductases and dehydrogenases in the pentose catabolic pathway. Our findings indicated that industries might be able to improve the species and concentrations of xylan-degrading enzymes and shorten fermentation time by adding abundant intermediate products of natural xylan (XOS) to cultures of filamentous fungi.
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Affiliation(s)
- Weili Gong
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Lin Dai
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Huaiqiang Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Lili Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Lushan Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.,State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
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20
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Hirasawa H, Shioya K, Furukawa T, Tani S, Sumitani JI, Kawaguchi T, Morikawa Y, Shida Y, Ogasawara W. Engineering of the Trichoderma reesei xylanase3 promoter for efficient enzyme expression. Appl Microbiol Biotechnol 2018; 102:2737-2752. [DOI: 10.1007/s00253-018-8763-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 12/21/2017] [Accepted: 01/09/2018] [Indexed: 12/15/2022]
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21
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Jiang F, Ma L, Cai R, Ma Q, Guo G, Du L, Xiao D. Efficient crude multi-enzyme produced by Trichoderma reesei using corncob for hydrolysis of lignocellulose. 3 Biotech 2017; 7:339. [PMID: 28955636 DOI: 10.1007/s13205-017-0982-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/15/2017] [Indexed: 01/02/2023] Open
Abstract
To improve the efficiency of enzymatic saccharification for lignocellulose, an efficient crude multi-enzyme was produced by Trichoderma reesei using corncob, a low cost inducer. Expression of cbh1, bgl1, egl1, xyn1 and positive regulator xyr1 induced by corncob increased significantly compared to that by cellulose. After 120 h induction by corncob, enzymatic activities on filter, CMC, β-glucose and xylan increased 86.5, 46.9, 120.9 and 291.2% compared to those induced by cellulose, and the concentration of secreted protein increased by 120.8%. FPase:β-glucosidase and FPase:xylanase values in crude multi-enzyme I (ECI, induced by corncob) were higher than that in crude multi-enzyme II (ECII, induced by cellulose). Under the same hydrolysis conditions, the volume dosage of ECI was only half of ECII, but ECI still showed a maximum of 12.5 and 33.4% higher than ECII in the total reducing sugar and glucose yield in lignocellulose hydrolysis. Corncob could be a candidate for low cost production of multi-enzyme for efficient lignocellulose degradation, and this work could guide the genetic modification of T. reesei to obtain efficient multi-enzyme for lignocellulose hydrolysis.
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Affiliation(s)
- Fengchao Jiang
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People's Republic of China
| | - Lijuan Ma
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People's Republic of China
| | - Rui Cai
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People's Republic of China
| | - Qing Ma
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People's Republic of China
| | - Gaojie Guo
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People's Republic of China
| | - Liping Du
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People's Republic of China
| | - Dongguang Xiao
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People's Republic of China
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22
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Zukovski L, Fontana RC, Pauletti G, Camassola M, Dillon AJP. Fodder radish cake (Raphanus sativus L.) as an alternative biomass for the production of cellulases and xylanases in solid-state cultivation. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2017. [DOI: 10.1590/0104-6632.20170343s20150818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Bedade D, Berezina O, Singhal R, Deska J, Shamekh S. Extracellular xylanase production from a new xylanase producer Tuber maculatum mycelium under submerged fermentation and its characterization. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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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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25
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Liu R, Chen L, Jiang Y, Zou G, Zhou Z. A novel transcription factor specifically regulates GH11 xylanase genes in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:194. [PMID: 28785310 PMCID: PMC5541735 DOI: 10.1186/s13068-017-0878-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/19/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei is widely utilized in industry for cellulase production, but its xylanase activity must be improved to enhance the accessibility of lignocellulose to cellulases. Several transcription factors play important roles in this progress; however, nearly all the reported transcription factors typically target both cellulase and hemi-cellulase genes. Specific xylanase transcription factor would be useful to regulate xylanase activity directly. RESULTS In this study, a novel zinc binuclear cluster transcription factor (jgi|Trire2|123881) was found to repress xylanase activity, but not cellulase activity, and was designated as SxlR (specialized xylanase regulator). Further investigations using real-time PCR and an electrophoretic mobility shift assay demonstrated that SxlR might bind the promoters of GH11 xylanase genes (xyn1, xyn2, and xyn5), but not those of GH10 (xyn3) and GH30 (xyn4) xylanase genes, and thus regulate their transcription and expression directly. We also identified the binding consensus sequence of SxlR as 5'- CATCSGSWCWMSA-3'. The deletion of SxlR in T. reesei RUT-C30 to generate the mutant ∆sxlr strain resulted in higher xylanase activity as well as higher hydrolytic efficiency on pretreated rice straw. CONCLUSIONS Our study characterizes a novel specific transcriptional repressor of GH11 xylanase genes, which adds to our understanding of the regulatory system for the synthesis and secretion of cellulase and hemi-cellulase in T. reesei. The deletion of SxlR may also help to improve the hydrolytic efficiency of T. reesei for lignocellulose degradation by increasing the xylanase-to-cellulase ratio.
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Affiliation(s)
- Rui Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Science, Fenglin Rd 300, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ling Chen
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Science, Fenglin Rd 300, Shanghai, 200032 China
| | - Yanping Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Science, Fenglin Rd 300, Shanghai, 200032 China
| | - Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Science, Fenglin Rd 300, Shanghai, 200032 China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Science, Fenglin Rd 300, Shanghai, 200032 China
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26
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Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de Vries RP. Regulators of plant biomass degradation in ascomycetous fungi. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:152. [PMID: 28616076 PMCID: PMC5468973 DOI: 10.1186/s13068-017-0841-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/05/2023]
Abstract
Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060 Vienna, Austria
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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27
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Zhang X, Zhu Y, Bao L, Gao L, Yao G, Li Y, Yang Z, Li Z, Zhong Y, Li F, Yin H, Qu Y, Qin Y. Putative methyltransferase LaeA and transcription factor CreA are necessary for proper asexual development and controlling secondary metabolic gene cluster expression. Fungal Genet Biol 2016; 94:32-46. [PMID: 27387217 DOI: 10.1016/j.fgb.2016.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 06/30/2016] [Accepted: 07/03/2016] [Indexed: 11/28/2022]
Abstract
The morphological development of fungi is a complex process and is often coupled with secondary metabolite production. In this study, we assessed the function of putative methyltransferase LaeA and transcription factor CreA in controlling asexual development and secondary metabolic gene cluster expression in Penicillium oxalicum. The deletion of laeA (ΔlaeA) impaired the conidiation in P. oxalicum, with a downregulated expression of brlA. Overexpression of P. oxalicum brlA in ΔlaeA could upregulate brlA and abaA remarkably, but could not rescue the conidiation defect; therefore, brlA and abaA expression were necessary but not sufficient for conidiation. Deletion of creA in ΔlaeA background (ΔlaeAΔcreA) blocked conidiation with a white fluffy phenotype. Nutrient-rich medium could not rescue developmental defects in ΔlaeAΔcreA mutant but could rescue defects in ΔlaeA. Expression of 10 genes, namely, albA/wA, abrB/yA, arpA, aygA, arpA-like, arpB, arpB-like, rodA, rodA-like, and rodB, for pigmentation and spore wall protein genes was silenced in ΔlaeAΔcreA, whereas only six of them were downregulated in ΔlaeA. Among the 28 secondary metabolism gene clusters in P. oxalicum, four secondary metabolism gene clusters were silenced in ΔlaeA and two were also silenced in ΔbrlA mutant. A total of 10 physically linked and coregulated genes were distributed over five chromosomes in ΔlaeA. Six of these genes were located in subtelomeric regions, thus demonstrating a positional bias for LaeA-regulated clusters toward subtelomeric regions. All of silenced clusters located in subtelomeric regions were derepressed in ΔlaeAΔcreA, hence showing that lack of CreA could remediate the repression of gene clusters in ΔlaeA background. Results show that both putative methyltransferase LaeA and transcription factor CreA are necessary for proper asexual development and controlling secondary metabolic gene cluster expression.
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Affiliation(s)
- Xiujun Zhang
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China; Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan 250100, China.
| | - Yingying Zhu
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Longfei Bao
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Liwei Gao
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Guangshan Yao
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Yanan Li
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China; Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan 250100, China.
| | - Zhifeng Yang
- School of Mathematics, Shandong University, Jinan 250100, China.
| | - Zhonghai Li
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Yaohua Zhong
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Fuli Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| | - Heng Yin
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yinbo Qu
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China.
| | - Yuqi Qin
- National Glycoengineering Research Center and State Key Lab of Microbial Technology, Shandong University, Jinan 250100, China; Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Jinan 250100, China.
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28
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Gong W, Zhang H, Tian L, Liu S, Wu X, Li F, Wang L. Determination of the modes of action and synergies of xylanases by analysis of xylooligosaccharide profiles over time using fluorescence-assisted carbohydrate electrophoresis. Electrophoresis 2016; 37:1640-50. [PMID: 27060349 DOI: 10.1002/elps.201600041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 01/06/2023]
Abstract
The structure of xylan, which has a 1,4-linked β-xylose backbone with various substituents, is much more heterogeneous and complex than that of cellulose. Because of this, complete degradation of xylan needs a large number of enzymes that includes GH10, GH11, and GH3 family xylanases together with auxiliary enzymes. Fluorescence-assisted carbohydrate electrophoresis (FACE) is able to accurately differentiate unsubstituted and substituted xylooligosaccharides (XOS) in the heterogeneous products generated by different xylanases and allows changes in concentrations of specific XOS to be analyzed quantitatively. Based on a quantitative analysis of XOS profiles over time using FACE, we have demonstrated that GH10 and GH11 family xylanases immediately degrade xylan into sizeable XOS, which are converted into smaller XOS in a much lower speed. The shortest substituted XOS produced by hydrolysis of the substituted xylan backbone by GH10 and GH11 family xylanases were MeGlcA(2) Xyl3 and MeGlcA(2) Xyl4 , respectively. The unsubstituted xylan backbone was degraded into xylose, xylobiose, and xylotriose by both GH10 and GH11 family xylanases; the product profiles are not family-specific but, instead, depend on different subsite binding affinities in the active sites of individual enzymes. Synergystic action between xylanases and β-xylosidase degraded MeGlcA(2) Xyl4 into xylose and MeGlcA(2) Xyl3 but further degradation of MeGlcA(2) Xyl3 required additional enzymes. Synergy between xylanases and β-xylosidase was also found to significantly accelerate the conversion of XOS into xylose.
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Affiliation(s)
- Weili Gong
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, P. R. China
| | - Huaiqiang Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, P. R. China
| | - Li Tian
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, P. R. China
| | - Shijia Liu
- Taishan College, Shandong University, Jinan, Shandong, P. R. China
| | - Xiuyun Wu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, P. R. China
| | - Fuli Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Lushan Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, P. R. China
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29
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Dos Santos Castro L, de Paula RG, Antoniêto ACC, Persinoti GF, Silva-Rocha R, Silva RN. Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis. Front Microbiol 2016; 7:175. [PMID: 26909077 PMCID: PMC4754417 DOI: 10.3389/fmicb.2016.00175] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
We defined the role of the transcriptional factor—XYR1—in the filamentous fungus Trichoderma reesei during cellulosic material degradation. In this regard, we performed a global transcriptome analysis using RNA-Seq of the Δxyr1 mutant strain of T. reesei compared with the parental strain QM9414 grown in the presence of cellulose, sophorose, and glucose as sole carbon sources. We found that 5885 genes were expressed differentially under the three tested carbon sources. Of these, 322 genes were upregulated in the presence of cellulose, while 367 and 188 were upregulated in sophorose and glucose, respectively. With respect to genes under the direct regulation of XYR1, 30 and 33 are exclusive to cellulose and sophorose, respectively. The most modulated genes in the Δxyr1 belong to Carbohydrate-Active Enzymes (CAZymes), transcription factors, and transporters families. Moreover, we highlight the downregulation of transporters belonging to the MFS and ABC transporter families. Of these, MFS members were mostly downregulated in the presence of cellulose. In sophorose and glucose, the expression of these transporters was mainly upregulated. Our results revealed that MFS and ABC transporters could be new players in cellulose degradation and their role was shown to be carbon source-dependent. Our findings contribute to a better understanding of the regulatory mechanisms of XYR1 to control cellulase gene expression in T. reesei in the presence of cellulosic material, thereby potentially enhancing its application in several biotechnology fields.
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Affiliation(s)
- Lilian Dos Santos Castro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Renato G de Paula
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Amanda C C Antoniêto
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Gabriela F Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais Campinas, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Laboratory, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Roberto N Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
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30
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Light-inducible genetic engineering and control of non-homologous end-joining in industrial eukaryotic microorganisms: LML 3.0 and OFN 1.0. Sci Rep 2016; 6:20761. [PMID: 26857594 PMCID: PMC4746737 DOI: 10.1038/srep20761] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/07/2016] [Indexed: 01/20/2023] Open
Abstract
Filamentous fungi play important roles in the production of plant cell-wall degrading enzymes. In recent years, homologous recombinant technologies have contributed significantly to improved enzymes production and system design of genetically manipulated strains. When introducing multiple gene deletions, we need a robust and convenient way to control selectable marker genes, especially when only a limited number of markers are available in filamentous fungi. Integration after transformation is predominantly nonhomologous in most fungi other than yeast. Fungal strains deficient in the non-homologous end-joining (NHEJ) pathway have limitations associated with gene function analyses despite they are excellent recipient strains for gene targets. We describe strategies and methods to address these challenges above and leverage the power of resilient NHEJ deficiency strains. We have established a foolproof light-inducible platform for one-step unmarked genetic modification in industrial eukaryotic microorganisms designated as 'LML 3.0', and an on-off control protocol of NHEJ pathway called 'OFN 1.0', using a synthetic light-switchable transactivation to control Cre recombinase-based excision and inversion. The methods provide a one-step strategy to sequentially modify genes without introducing selectable markers and NHEJ-deficiency. The strategies can be used to manipulate many biological processes in a wide range of eukaryotic cells.
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31
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A. L. Rocha V, N. Maeda R, Pereira N, F. Kern M, Elias L, Simister R, Steele-King C, Gómez LD, McQueen-Mason SJ. Characterization of the cellulolytic secretome ofTrichoderma harzianumduring growth on sugarcane bagasse and analysis of the activity boosting effects of swollenin. Biotechnol Prog 2016; 32:327-36. [DOI: 10.1002/btpr.2217] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/02/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Vanessa A. L. Rocha
- LADEBIO, Centre of Biofuels, Oil and its Derivatives, School of Chemistry; Department of Biochemical Engineering, Centre of Technology, Federal University of Rio De Janeiro; Rio De Janeiro 21941-909 Brazil
| | - Roberto N. Maeda
- LADEBIO, Centre of Biofuels, Oil and its Derivatives, School of Chemistry; Department of Biochemical Engineering, Centre of Technology, Federal University of Rio De Janeiro; Rio De Janeiro 21941-909 Brazil
| | - Nei Pereira
- LADEBIO, Centre of Biofuels, Oil and its Derivatives, School of Chemistry; Department of Biochemical Engineering, Centre of Technology, Federal University of Rio De Janeiro; Rio De Janeiro 21941-909 Brazil
| | - Marcelo F. Kern
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
| | - Luisa Elias
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
| | - Rachael Simister
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
| | - Clare Steele-King
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
| | - Leonardo D. Gómez
- MasonCNAP, Dept. of Biology; University of York; Wentworth Way, York YO10 5DD U.K
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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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Hansen GH, Lübeck M, Frisvad JC, Lübeck PS, Andersen B. Production of cellulolytic enzymes from ascomycetes: Comparison of solid state and submerged fermentation. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.05.017] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Comparative Secretome Analysis of Aspergillus niger, Trichoderma reesei, and Penicillium oxalicum During Solid-State Fermentation. Appl Biochem Biotechnol 2015; 177:1252-71. [DOI: 10.1007/s12010-015-1811-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
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Huang ZB, Chen XZ, Qin LN, Wu HQ, Su XY, Dong ZY. A novel major facilitator transporter TrSTR1 is essential for pentose utilization and involved in xylanase induction in Trichoderma reesei. Biochem Biophys Res Commun 2015; 460:663-9. [PMID: 25817789 DOI: 10.1016/j.bbrc.2015.03.087] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 01/15/2023]
Abstract
Trichoderma reesei (teleomorph Hypocrea jecorina) is an industrially important filamentous fungus for glycoside hydrolases production, with its xylanolytic enzymes widely applied in many areas. However, the molecular mechanisms underlying xylanase expression are still insufficiently understood. In particular, the effect of sugar transporter on the induction of xylanase expression is unclear. In this work, we identified a novel major facilitator transporter TrSTR1 that is capable of transporting xylose by using a xylose utilization system in Saccharomyces cerevisiae. In T. reesei, TrSTR1 is essential for the utilization of d-xylose, l-arabinose, and even their downstream metabolites D-xylitol and L-arabitol. TrSTR1 is also involved in the induction of xylanase expression since both the xylanase activity and extracellular protein concentration in the Tu6△str1 strain were decreased, which further confirmed by a qRT-PCR analysis of the transcript levels of the key transcriptional regulators. Our observations provide new insights into connections between pentose utilization and xylanase production in T. reesei.
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Affiliation(s)
- Zhen-Bang Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiu-Zhen Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Li-Na Qin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Hong-Qing Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiao-Yun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhi-Yang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Liaud N, Giniés C, Navarro D, Fabre N, Crapart S, Gimbert IH, Levasseur A, Raouche S, Sigoillot JC. RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger. Fungal Biol Biotechnol 2014; 1:1-14. [PMID: 26457194 PMCID: PMC4599204 DOI: 10.1186/s40694-014-0003-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/23/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers. RESULTS In this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study. CONCLUSIONS By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production.
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Affiliation(s)
- Nadège Liaud
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- ARD, Agro-Industry Research and Development, Pômacle, F-51100 France
| | - Christian Giniés
- INRA, UMR 1260, « Nutrition, Obésité et Risque Thrombotique », Marseille, F-13385 France
- INSERM, UMR 1062, « Nutrition, Obésité et Risque Thrombotique », Marseille, F-13385 France
- Université d’Aix-Marseille, UMR 1260, « Nutrition, Obésité et Risque Thrombotique », Faculté de Médecine, Marseille, F-13385 France
| | - David Navarro
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- INRA, International Center for Microbial Resources collection-Filamentous fungi CIRM-CF, Marseille, F-13288 France
| | - Nicolas Fabre
- ARD, Agro-Industry Research and Development, Pômacle, F-51100 France
| | - Sylvaine Crapart
- ARD, Agro-Industry Research and Development, Pômacle, F-51100 France
| | - Isabelle Herpoël- Gimbert
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
| | - Anthony Levasseur
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
| | - Sana Raouche
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Polytech’ Marseille (ex ESIL), UMR 1163 BCF - INRA / AMU, 163 Avenue de Luminy CP 925, Marseille, F-13288 France
| | - Jean-Claude Sigoillot
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
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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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Silva-Rocha R, Castro LDS, Antoniêto ACC, Guazzaroni ME, Persinoti GF, Silva RN. Deciphering the cis-regulatory elements for XYR1 and CRE1 regulators in Trichoderma reesei. PLoS One 2014; 9:e99366. [PMID: 24941042 PMCID: PMC4062390 DOI: 10.1371/journal.pone.0099366] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/13/2014] [Indexed: 12/22/2022] Open
Abstract
In this work, we report the in silico identification of the cis-regulatory elements for XYR1 and CRE1 proteins in the filamentous fungus Trichoderma reesei, two regulators that play a central role in the expression of cellulase genes. Using four datasets of condition-dependent genes from RNA-seq and RT-qPCR experiments, we performed unsupervised motif discovery and found two short motifs resembling the proposed binding consensus for XYR1 and CRE1. Using these motifs, we analysed the presence and arrangement of putative cis-regulatory elements recognized by both regulators and found that shortly spaced sites were more associated with XYR1- and CRE1-dependent promoters than single, high-score sites. Furthermore, the approach used here allowed the identification of the previously reported XYR1-binding sites from cel7a and xyn1 promoters, and we also mapped the potential target sequence for this regulator at the cel6a promoter that has been suggested but not identified previously. Additionally, seven other promoters (for cel7b, cel61a, cel61b, cel3c, cel3d, xyn3 and swo genes) presented a putative XYR1-binding site, and strong sites for CRE1 were found at the xyr1 and cel7b promoters. Using the cis-regulatory architectures nearly defined for XYR1 and CRE1, we performed genome-wide identification of potential targets for direct regulation by both proteins and important differences on their functional regulons were elucidated. Finally, we performed binding site mapping on the promoters of differentially expressed genes found in T. reesei mutant strains lacking xyr1 or cre1 and found that indirect regulation plays a key role on their signalling pathways. Taken together, the data provided here sheds new light on the mechanisms for signal integration mediated by XYR1 and CRE1 at cellulase promoters.
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Affiliation(s)
- Rafael Silva-Rocha
- Department of Biochemistry and Immunology, FMRP - University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Lilian dos Santos Castro
- Department of Biochemistry and Immunology, FMRP - University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | | | | | - Gabriela Felix Persinoti
- Department of Biochemistry and Immunology, FMRP - University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, FMRP - University of São Paulo, Ribeirao Preto, São Paulo, Brazil
- * E-mail:
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Li J, Lin L, Li H, Tian C, Ma Y. Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:31. [PMID: 24581151 PMCID: PMC4015282 DOI: 10.1186/1754-6834-7-31] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/14/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND D-glucose, D-xylose and L-arabinose are the three major monosaccharides in plant cell walls. Complete utilization of all three sugars is still a bottleneck for second-generation cellulolytic bioethanol production, especially for L-arabinose. However, little is known about gene expression profiles during L-arabinose utilization in fungi and a comparison of the genome-wide fungal response to these three major monosaccharides has not yet been reported. RESULTS Using next-generation sequencing technology, we have analyzed the transcriptome of N. crassa grown on L-arabinose versus D-xylose, with D-glucose as the reference. We found that the gene expression profiles on L-arabinose were dramatically different from those on D-xylose. It appears that L-arabinose can rewire the fungal cell metabolic pathway widely and provoke the expression of many kinds of sugar transporters, hemicellulase genes and transcription factors. In contrast, many fewer genes, mainly related to the pentose metabolic pathway, were upregulated on D-xylose. The rewired metabolic response to L-arabinose was significantly different and wider than that under no carbon conditions, although the carbon starvation response was initiated on L-arabinose. Three novel sugar transporters were identified and characterized for their substrates here, including one glucose transporter GLT-1 (NCU01633) and two novel pentose transporters, XAT-1 (NCU01132), XYT-1 (NCU05627). One transcription factor associated with the regulation of hemicellulase genes, HCR-1 (NCU05064) was also characterized in the present study. CONCLUSIONS We conducted the first transcriptome analysis of Neurospora crassa grown on L-arabinose and performed a comparative analysis with cells grown on D-xylose and D-glucose, which deepens the understanding of the utilization of L-arabinose and D-xylose in filamentous fungi. The dataset generated by this research will be useful for mining target genes for D-xylose and L-arabinose utilization engineering and the novel sugar transportes identified are good targets for pentose untilization and biofuels production. Moreover, hemicellulase production by fungi could be improved by modifying the hemicellulase regulator discovered here.
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Affiliation(s)
- Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangcai Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Huiyan Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Castro LDS, Antoniêto ACC, Pedersoli WR, Silva-Rocha R, Persinoti GF, Silva RN. Expression pattern of cellulolytic and xylanolytic genes regulated by transcriptional factors XYR1 and CRE1 are affected by carbon source in Trichoderma reesei. Gene Expr Patterns 2014; 14:88-95. [PMID: 24480777 DOI: 10.1016/j.gep.2014.01.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 12/09/2013] [Accepted: 01/07/2014] [Indexed: 01/28/2023]
Abstract
Trichoderma reesei is the most important fungus for the industrial production of enzymes to biomass deconstruction. Most of the genes encoding cellulases and hemicellulases are regulated by the transcription factors CRE1 and XYR1. In this work, the regulation of 22 genes of cellulases and xylanases by these transcription factors was investigated under three different carbon sources. Analysis of gene expression and enzymatic profiles of CMCase, β-glucosidase, and xylanases showed different regulation that was depended of the carbon source in both Δxyr1 and Δcre1 mutants. In the presence of glucose, the majority of genes evaluated (82%) showed increased expression levels in the Δcre1 mutant compared to the parental QM9414 strain. In the Δxyr1 mutant, it was observed that expression of cellulase and xylanase genes was reduced compared to the parental QM9414 strain, when cultured in the presence of cellulose or sophorose. Interesting, in the presence of glucose, approximately 60% of the analyzed genes had increased expression in the Δxyr1 mutant compared to parental strain. Furthermore, no correlation between gene expression and the number of putative binding sites of XYR1 and CRE1 to promoter region of cellulolytic and xylanolytic studied genes was observed. Therefore, these results demonstrated that the regulation of cellulase and xylanase by the transcription factors CRE1 and XYR1 is influenced by different carbon sources.
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Affiliation(s)
- Lilian dos Santos Castro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Wellington Ramos Pedersoli
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Rafael Silva-Rocha
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Gabriela F Persinoti
- Department of Genetic, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, 14049-900 Ribeirão Preto, SP, Brazil.
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Novello M, Vilasboa J, Schneider WDH, Reis LD, Fontana RC, Camassola M. Enzymes for second generation ethanol: exploring new strategies for the use of xylose. RSC Adv 2014. [DOI: 10.1039/c4ra00909f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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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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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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