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Sveholm E, Mattila H, Aro N, Valkonen M, Paasela T, Pakula TM. Transcriptomic and metabolic changes in Trichoderma reesei caused by mutation in xylanase regulator 1 (xyr1). BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:106. [PMID: 39030601 PMCID: PMC11265206 DOI: 10.1186/s13068-024-02556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Trichoderma reesei is known for its ability to produce large amounts of extracellular proteins and is one of the most important industrially used filamentous fungus. Xylanase regulator 1 (XYR1) is the master regulator responsible for the activation of cellulase and hemicellulase gene expression under inducing conditions. It has been reported that strains with point mutations in certain areas of xyr1 bypass the need for inducing carbon source, allowing high (hemi)cellulase production even in the presence of glucose. These mutations also change the profile of produced proteins, shifting it more towards xylanase production, and increase the overall protein production in inducing conditions. However, how these mutations alter the metabolism and other cellular processes to cause these changes remains unclear. RESULTS In this study, we aimed to explore changes caused by a point mutation in xyr1 on transcriptomic and metabolic level to better understand the reasons behind the increased protein production in both repressing glucose and inducing lactose conditions. As expected, the expression of many carbohydrate-active enzyme (CAZy) genes was increased in the xyr1 mutant in both conditions. However, their induction was higher under inducing conditions. The xyr1 mutant strain built more biomass and produced more extracellular proteins during growth on lactose compared to the wild type xyr1 strain. Genes involved in oxidoreductive D-galactose catabolism pathway were upregulated in the xyr1 mutant strain, potentially contributing to the more efficient utilization of lactose. In addition to CAZy genes, clustering and enrichment analysis showed over-representation of mitochondria-related Gene Ontology terms in clusters where gene expression was higher in the xyr1 mutant, indicating that mitochondria play a role in the altered metabolic state associated with the xyr1 mutation. Metabolomics revealed that free tyrosine was more abundant in the xyr1 mutant strain in all measured timepoints, whereas multiple fatty acids were less abundant in the mutant strain on glucose. CONCLUSIONS The results contribute to more in-depth knowledge on T. reesei physiology growing under inducing and repressing carbon sources and gives new insights on the function of the master regulator XYR1. The vast data generated serve as a source for new targets for improved protein production.
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Affiliation(s)
- Emmi Sveholm
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Hans Mattila
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Nina Aro
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Mari Valkonen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Tanja Paasela
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland.
| | - Tiina M Pakula
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
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Zhu Z, Zou G, Chai S, Xiao M, Wang Y, Wang P, Zhou Z. The protein methyltransferase TrSAM inhibits cellulase gene expression by interacting with the negative regulator ACE1 in Trichoderma reesei. Commun Biol 2024; 7:375. [PMID: 38548869 PMCID: PMC10978942 DOI: 10.1038/s42003-024-06072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/19/2024] [Indexed: 04/01/2024] Open
Abstract
Protein methylation is a commonly posttranslational modification of transcriptional regulators to fine-tune protein function, however, whether this regulation strategy participates in the regulation of lignocellulase synthesis and secretion in Trichoderma reesei remains unexplored. Here, a putative protein methyltransferase (TrSAM) is screened from a T. reesei mutant with the ability to express heterologous β-glucosidase efficiently even under glucose repression. The deletion of its encoding gene trsam causes a significant increase of cellulase activities in all tested T. reesei strains, including transformants of expressing heterologous genes using cbh1 promotor. Further investigation confirms that TrSAM interacts with the cellulase negative regulator ACE1 via its amino acid residue Arg383, which causes a decrease in the ACE1-DNA binding affinity. The enzyme activity of a T. reesei strain harboring ACE1R383Q increases by 85.8%, whereas that of the strains with trsam or ace1 deletion increases by more than 100%. By contrast, the strain with ACE1R383K shows no difference to the parent strain. Taken together, our results demonstrate that TrSAM plays an important role in regulating the expression of cellulase and heterologous proteins initiated by cbh1 promotor through interacting with ACE1R383. Elimination and mutation of TrSAM and its downstream ACE1 alleviate the carbon catabolite repression (CCR) in expressing cellulase and heterologous protein in varying degrees. This provides a new solution for the exquisite modification of T. reesei chassis.
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Affiliation(s)
- Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, 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 Sciences, 300 FengLin Rd, Shanghai, 200032, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Science, 1000 Jinqi Rd, Shanghai, 201403, China
| | - Shunxing Chai
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinmei Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, 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 Sciences, 300 FengLin Rd, Shanghai, 200032, China.
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Adnan M, Liu G. Promoters and Synthetic Promoters in Trichoderma reesei. Methods Mol Biol 2024; 2844:47-68. [PMID: 39068331 DOI: 10.1007/978-1-0716-4063-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Trichoderma reesei holds immense promise for large-scale protein production, rendering it an excellent subject for deeper exploration using genetic engineering methods to achieve a comprehensive grasp of its cellular physiology. Understanding the genetic factors governing its intrinsic regulatory network is crucial, as lacking this knowledge could impede the expression of target genes. Prior and ongoing studies have concentrated on advancing new expression systems grounded in synthetic biology principles. These methodologies involve utilizing established potent promoters or engineered variations. Genomic and transcriptomic analyses have played a pivotal role in identifying robust promoters and expression systems, including light-responsive, copper-inducible, L-methionine-inducible, and Tet-On systems, among others. This chapter seeks to highlight various research endeavors focusing on tunable and constitutive promoters, the impact of different promoters on both native and foreign protein expression, the discovery of fresh promoters, and strategies conducive to future research aimed at refining and enhancing protein expression in T. reesei. Characterizing new promoters and adopting innovative expression systems hold the potential to significantly expand the molecular toolkit accessible for genetically engineering T. reesei strains. For instance, modifying potent inducible promoters such as Pcbh1 by replacing transcriptional repressors (cre1, ace1) with activators (xyr1, ace2, ace3, hap2/3/5) and integrating synthetic expression systems can result in increased production of crucial enzymes such as endoglucanases (EGLs), β-glucosidases (BGLs), and cellobiohydrolases (CBHs). Similarly, robust constitutive promoters such as Pcdna1 can be converted into synthetic hybrid promoters by incorporating activation elements from potent inducible promoters, facilitating cellulase induction and expression even under repressive conditions. Nevertheless, further efforts are necessary to uncover innovative promoters and devise novel expression strategies to enhance the production of desired proteins on an industrial scale.
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Affiliation(s)
- Muhammad Adnan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Gang Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.
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Maués DB, Maraschin JC, Duarte DÂ, Antoniêto ACC, Silva RN. Overexpression of the Transcription Factor Azf1 Reveals Novel Regulatory Functions and Impacts β-Glucosidase Production in Trichoderma reesei. J Fungi (Basel) 2023; 9:1173. [PMID: 38132774 PMCID: PMC10744372 DOI: 10.3390/jof9121173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The fungus Trichoderma reesei is an essential producer of enzymes that degrade lignocellulosic biomass to produce value-added bioproducts. The cellulolytic system of T. reesei is controlled by several transcription factors (TFs) that efficiently regulate the production of these enzymes. Recently, a new TF named Azf1 was identified as a positive regulator of cellulase expression. Here, we investigated novel regulatory functions of Azf1 by its overexpression. In the mutant strain OEazf1, overexpression of azf1 was achieved under both repression and induction conditions. Although azf1 was more abundant in transcript and protein, overexpression of this TF did not activate transcription of the cellulase gene in the presence of the repressor glucose, suggesting that Azf1 may be subject to posttranslational regulation. In cellulose, the expression of swo, encoding the accessory protein swollenin, and the β-glucosidases cel1a, cel1b, cel3b, and cel3g increases in the early stages of cultivation. The increased production of these β-glucosidases increases the hydrolysis rate of cellobiose and sophorose, which activates carbon catabolite repression (CCR) and causes repression of cellulase genes and the regulator Xyr1 in the later stages of cultivation. Moreover, overexpression of azf1 led to increased cellulase activity in T. reesei during long-term cultivation in cellulose and sugarcane bagasse. Our results provide new insights into the mechanisms regulating Azf1 and novel genes that are important targets of this TF. This work contributes to a better understanding of the complex mechanisms regulating cellulase expression in T. reesei. It will contribute to the development of strains with higher production of these essential enzymes.
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Affiliation(s)
| | | | | | | | - Roberto N. Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (D.B.M.); (J.C.M.); (D.Â.D.); (A.C.C.A.)
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Xu W, Ren Y, Xia Y, Liu L, Meng X, Chen G, Zhang W, Liu W. A novel transcriptional repressor specifically regulates xylanase gene 1 in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:161. [PMID: 37891680 PMCID: PMC10612264 DOI: 10.1186/s13068-023-02417-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND The well-known industrial fungus Trichoderma reesei has an excellent capability of secreting a large amount of cellulases and xylanases. The induced expression of cellulase and xylanase genes is tightly controlled at the transcriptional level. However, compared to the intensive studies on the intricate regulatory mechanism of cellulase genes, efforts to understand how xylanase genes are regulated are relatively limited, which impedes the further improvement of xylanase production by T. reesei via rational strain engineering. RESULTS To identify transcription factors involved in regulating xylanase gene expression in T. reesei, yeast one-hybrid screen was performed based on the promoters of two major extracellular xylanase genes xyn1 and xyn2. A putative transcription factor named XTR1 showing significant binding capability to the xyn1 promoter but not that of xyn2, was successfully isolated. Deletion of xtr1 significantly increased the transcriptional level of xyn1, but only exerted a minor promoting effect on that of xyn2. The xylanase activity was increased by ~ 50% with XTR1 elimination but the cellulase activity was hardly affected. Subcellular localization analysis of XTR1 fused to a green fluorescence protein demonstrated that XTR1 is a nuclear protein. Further analyses revealed the precise binding site of XTR1 and nucleotides critical for the binding within the xyn1 promoter. Moreover, competitive EMSAs indicated that XTR1 competes with the essential transactivator XYR1 for binding to the xyn1 promoter. CONCLUSIONS XTR1 represents a new transcriptional repressor specific for controlling xylanase gene expression. Isolation and functional characterization of this new factor not only contribute to further understanding the stringent regulatory network of xylanase genes, but also provide important clues for boosting xylanase biosynthesis in T. reesei.
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Affiliation(s)
- Wenqiang Xu
- State Key Laboratory of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, 266237, People's Republic of China
- Shandong Lishan Biotechnology Co., LTD, Jinan, China
| | - Yajing Ren
- State Key Laboratory of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Yuxiao Xia
- State Key Laboratory of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Lin Liu
- State Key Laboratory of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, 266237, People's Republic of China.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, No.72 Binhai Road, Qingdao, 266237, People's Republic of China
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Dong CD, Patel AK, Madhavan A, Chen CW, Singhania RR. Significance of glycans in cellulolytic enzymes for lignocellulosic biorefinery - A review. BIORESOURCE TECHNOLOGY 2023; 379:128992. [PMID: 37011847 DOI: 10.1016/j.biortech.2023.128992] [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: 02/15/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
Lignocellulosic (LC) biomass is the most abundant renewable resource for mankind gravitating society towards sustainable solution for energy that can reduce the carbon footprint. The economic feasibility of 'biomass biorefinery' depends upon the efficiency cellulolytic enzymes which is the main crux. Its high production cost and low efficiencies are the major limitations, that need to be resolved. As the complexity of the genome increases, so does the complexity of the proteome, further facilitated by protein post-translational modifications (PTMs). Glycosylation is regarded the major PTMs and hardly any recent work is focused on importance of glycosylation in cellulase. By modifying protein side chains and glycans, superior cellulases with improved stability and efficiency can be obtained. Functional proteomics relies heavily on PTMs because they regulate activity, localization, and interactions with protein, lipid, nucleic acid, and cofactor molecules. O- and N- glycosylation in cellulases influences its characteristics adding positive attributes to the enzymes.
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Affiliation(s)
- Cheng-Di Dong
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Anil Kumar Patel
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, India
| | - Aravind Madhavan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam, Kerala 690 525, India
| | - Chiu-Wen Chen
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Reeta Rani Singhania
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, India.
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7
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Christopher M, Sreeja-Raju A, Abraham A, Gokhale DV, Pandey A, Sukumaran RK. Early cellular events and potential regulators of cellulase induction in Penicillium janthinellum NCIM 1366. Sci Rep 2023; 13:5057. [PMID: 36977777 PMCID: PMC10050438 DOI: 10.1038/s41598-023-32340-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 03/26/2023] [Indexed: 03/30/2023] Open
Abstract
Cellulase production by fungi is tightly regulated in response to environmental cues, and understanding this mechanism is a key pre-requisite in the efforts to improve cellulase secretion. Based on UniProt descriptions of secreted Carbohydrate Active enZymes (CAZymes), 13 proteins of the cellulase hyper-producer Penicillium janthinellum NCIM 1366 (PJ-1366) were annotated as cellulases- 4 cellobiohydrolases (CBH), 7 endoglucanases (EG) and 2 beta glucosidases (BGL). Cellulase, xylanase, BGL and peroxidase activities were higher for cultures grown on a combination of cellulose and wheat bran, while EG was stimulated by disaccharides. Docking studies indicated that the most abundant BGL- Bgl2- has different binding sites for the substrate cellobiose and the product glucose, which helps to alleviate feedback inhibition, probably accounting for the low level of glucose tolerance exhibited. Out of the 758 transcription factors (TFs) differentially expressed on cellulose induction, 13 TFs were identified whose binding site frequencies on the promoter regions of the cellulases positively correlated with their abundance in the secretome. Further, correlation analysis of the transcriptional response of these regulators and TF-binding sites on their promoters indicated that cellulase expression is possibly preceded by up-regulation of 12 TFs and down-regulation of 16 TFs, which cumulatively regulate transcription, translation, nutrient metabolism and stress response.
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Affiliation(s)
- Meera Christopher
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - AthiraRaj Sreeja-Raju
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, 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, 226 001, Uttar Pradesh, India
- Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248 007, India
- Centre for Energy and Environmental Sustainability, Lucknow, 226 029, India
| | - Rajeev K Sukumaran
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram, Kerala, 695019, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
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Arai T, Ichinose S, Shibata N, Kakeshita H, Kodama H, Igarashi K, Takimura Y. Inducer-free cellulase production system based on the constitutive expression of mutated XYR1 and ACE3 in the industrial fungus Trichoderma reesei. Sci Rep 2022; 12:19445. [PMID: 36376415 PMCID: PMC9663580 DOI: 10.1038/s41598-022-23815-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Trichoderma reesei is a widely used host for producing cellulase and hemicellulase cocktails for lignocellulosic biomass degradation. Here, we report a genetic modification strategy for industrial T. reesei that enables enzyme production using simple glucose without inducers, such as cellulose, lactose and sophorose. Previously, the mutated XYR1V821F or XYR1A824V was known to induce xylanase and cellulase using only glucose as a carbon source, but its enzyme composition was biased toward xylanases, and its performance was insufficient to degrade lignocellulose efficiently. Therefore, we examined combinations of mutated XYR1V821F and constitutively expressed CRT1, BGLR, VIB1, ACE2, or ACE3, known as cellulase regulators and essential factors for cellulase expression to the T. reesei E1AB1 strain that has been highly mutagenized for improving enzyme productivity and expressing a ß-glucosidase for high enzyme performance. The results showed that expression of ACE3 to the mutated XYR1V821F expressing strain promoted cellulase expression. Furthermore, co-expression of these two transcription factors also resulted in increased productivity, with enzyme productivity 1.5-fold higher than with the conventional single expression of mutated XYR1V821F. Additionally, that productivity was 5.5-fold higher compared to productivity with an enhanced single expression of ACE3. Moreover, although the DNA-binding domain of ACE3 had been considered essential for inducer-free cellulase production, we found that ACE3 with a partially truncated DNA-binding domain was more effective in cellulase production when co-expressed with a mutated XYR1V821F. This study demonstrates that co-expression of the two transcription factors, the mutated XYR1V821F or XYR1A824V and ACE3, resulted in optimized enzyme composition and increased productivity.
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Affiliation(s)
- Toshiharu Arai
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Sakurako Ichinose
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Nozomu Shibata
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Hiroshi Kakeshita
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan.
| | - Hiroshi Kodama
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Kazuaki Igarashi
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
| | - Yasushi Takimura
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640‑8580, Japan
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Mattam AJ, Chaudhari YB, Velankar HR. Factors regulating cellulolytic gene expression in filamentous fungi: an overview. Microb Cell Fact 2022; 21:44. [PMID: 35317826 PMCID: PMC8939176 DOI: 10.1186/s12934-022-01764-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/27/2022] [Indexed: 12/19/2022] Open
Abstract
The growing demand for biofuels such as bioethanol has led to the need for identifying alternative feedstock instead of conventional substrates like molasses, etc. Lignocellulosic biomass is a relatively inexpensive feedstock that is available in abundance, however, its conversion to bioethanol involves a multistep process with different unit operations such as size reduction, pretreatment, saccharification, fermentation, distillation, etc. The saccharification or enzymatic hydrolysis of cellulose to glucose involves a complex family of enzymes called cellulases that are usually fungal in origin. Cellulose hydrolysis requires the synergistic action of several classes of enzymes, and achieving the optimum secretion of these simultaneously remains a challenge. The expression of fungal cellulases is controlled by an intricate network of transcription factors and sugar transporters. Several genetic engineering efforts have been undertaken to modulate the expression of cellulolytic genes, as well as their regulators. This review, therefore, focuses on the molecular mechanism of action of these transcription factors and their effect on the expression of cellulases and hemicellulases.
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Affiliation(s)
- Anu Jose Mattam
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India
| | - Yogesh Babasaheb Chaudhari
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India
| | - Harshad Ravindra Velankar
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India.
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10
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Promoter regulation and genetic engineering strategies for enhanced cellulase expression in Trichoderma reesei. Microbiol Res 2022; 259:127011. [DOI: 10.1016/j.micres.2022.127011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/18/2023]
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11
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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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Karuppiah V, Zhixiang L, Liu H, Murugappan V, Kumaran S, Perianaika Anahas AM, Chen J. Co-cultivation of T. asperellum GDFS1009 and B. amyloliquefaciens 1841: Strategy to regulate the production of ligno-cellulolytic enzymes for the lignocellulose biomass degradation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 301:113833. [PMID: 34592667 DOI: 10.1016/j.jenvman.2021.113833] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/21/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
The influence of fossil fuels on the environment focused on the development of new technology on biofuels. In this situation, lignocellulolytic hydrolysis enzymes such as Cellobiohydrolase, β-Glucosidase, Endoglucanase, cellulase and xylanase have broad applications in the biofuel production. The Trichoderma have used for the production of cellulase and xylanase to hydrolyze the lignocellulose. Hence, in the present study, co-culture has been employed to induce the production of polysaccharide hydrolyzing enzymes under both induction and repression conditions. The enzyme activity and its gene expression were induced by the co-culture of T. asperellum and B. amyloliquefaciens compared to the monoculture. Further, the co-culture upregulated the transcription regulatory genes and downregulated the repressor genes under both repressor and inducer conditions, respectively. The crude enzyme produced by the co-culture and monocultures using the optimized medium containing molasses, cornmeal and rice bran were further used to hydrolyze the pretreated corn Stover, rice straw, and wheat straw. These results indicate that the co-culture of T. asperellum and B. amyloliquefaciens is a promising and inexpensive method to advance the innovation on the continuous production of cellulase and xylanase under different circumstances for the bioconversion of lignocellulosic biomass into glucose for the bio-fuels.
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Affiliation(s)
- Valliappan Karuppiah
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Lu Zhixiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Hongyi Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Vallikkannu Murugappan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Subramanian Kumaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, 600119, India
| | | | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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Paul M, Mohapatra S, Kumar Das Mohapatra P, Thatoi H. Microbial cellulases - An update towards its surface chemistry, genetic engineering and recovery for its biotechnological potential. BIORESOURCE TECHNOLOGY 2021; 340:125710. [PMID: 34365301 DOI: 10.1016/j.biortech.2021.125710] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The inherent resistance of lignocellulosic biomass makes it impervious for industrially important enzymes such as cellulases to hydrolyze cellulose. Further, the competitive absorption behavior of lignin and hemicellulose for cellulases, due to their electron-rich surfaces augments the inappropriate utilization of these enzymes. Hence, modification of the surface charge of the cellulases to reduce its non-specific binding to lignin and enhance its affinity for cellulose is an urgent necessity. Further, maintaining the stability of cellulases by the preservation of their secondary structures using immobilization techniques will also play an integral role in its industrial production. In silico approaches for increasing the catalytic activity of cellulase enzymes is also significant along with a range of substrate specificity. In addition, enhanced productivity of cellulases by tailoring the related genes through the process of genetic engineering and higher cellulase recovery after saccharification seems to be promising areas for efficient and large-scale enzyme production concepts.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India
| | - Sonali Mohapatra
- Department of Biotechnology, College of Engineering & Technology, Bhubaneswar 751003, Odisha, India
| | - Pradeep Kumar Das Mohapatra
- Department of Microbiology, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India; PAKB Environment Conservation Centre, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India.
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Trichoderma reesei ACE4, a Novel Transcriptional Activator Involved in the Regulation of Cellulase Genes during Growth on Cellulose. Appl Environ Microbiol 2021; 87:e0059321. [PMID: 34047636 DOI: 10.1128/aem.00593-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The filamentous fungus Trichoderma reesei is a model strain for cellulase production. Cellulase gene expression in T. reesei is controlled by multiple transcription factors. Here, we identified by comparative genomic screening a novel transcriptional activator, ACE4 (activator of cellulase expression 4), that positively regulates cellulase gene expression on cellulose in T. reesei. Disruption of the ace4 gene significantly decreased expression of four main cellulase genes and the essential cellulase transcription factor-encoding gene ace3. Overexpression of ace4 increased cellulase production by approximately 22% compared to that in the parental strain. Further investigations using electrophoretic mobility shift assays, DNase I footprinting assays, and chromatin immunoprecipitation assays indicated that ACE4 directly binds to the promoter of cellulase genes by recognizing the two adjacent 5'-GGCC-3' sequences. Additionally, ACE4 directly binds to the promoter of ace3 and, in turn, regulates the expression of ACE3 to facilitate cellulase production. Collectively, these results demonstrate an important role for ACE4 in regulating cellulase gene expression, which will contribute to understanding the mechanism underlying cellulase expression in T. reesei. IMPORTANCE T. reesei is commonly utilized in industry to produce cellulases, enzymes that degrade lignocellulosic biomass for the production of bioethanol and bio-based products. T. reesei is capable of rapidly initiating the biosynthesis of cellulases in the presence of cellulose, which has made it useful as a model fungus for studying gene expression in eukaryotes. Cellulase gene expression is controlled through multiple transcription factors at the transcriptional level. However, the molecular mechanisms by which transcription is controlled remain unclear. In the present study, we identified a novel transcription factor, ACE4, which regulates cellulase expression on cellulose by binding to the promoters of cellulase genes and the cellulase activator gene ace3. Our study not only expands the general functional understanding of the novel transcription factor ACE4 but also provides evidence for the regulatory mechanism mediating gene expression in T. reesei.
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15
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Ammonium Ions Induce Cellulase Synthesis in Trichoderma koningii. Curr Microbiol 2021; 78:3201-3211. [PMID: 34213616 DOI: 10.1007/s00284-021-02568-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
Cellulase plays an important role in addressing the issue of the energy crisis. However, the yield and degradation efficiency of cellulase remain a major challenge. In the present study, we aimed to verify whether ammonium ion (NH4+) could induce cellulase synthesis from T. koningii AS3.2774 and to explore new functional genes related to the cellulase production. Our results indicated that NH4+ induces cellulase production in a way different from nitrogen sources. NH4+-mediated mycelia displayed a significant increase in transport vesicles. Under NH4+ mediation, CBHI, CBHII, glycoside hydrolase family 5 proteins, Hap2/3/5 complexes, "ribosome biogenesis", and "heme binding" were significantly up-regulated, and differentially expressed genes (DEGs) were mainly involved in "Metabolism". Collectively, our findings illustrated that NH4+ induced the cellulase production at morphological and gene expression levels, which might be related to the Hap2/3/5 complex, ribosomes, and genes involved in various amino acid metabolism, pyruvate metabolism, and glycolysis/gluconeogenesis. Taken together, our results provided valuable insights into the regulatory network of cellulase gene expression in filamentous fungi.
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Karuppiah V, Zhixiang L, Liu H, Vallikkannu M, Chen J. Co-culture of Vel1-overexpressed Trichoderma asperellum and Bacillus amyloliquefaciens: An eco-friendly strategy to hydrolyze the lignocellulose biomass in soil to enrich the soil fertility, plant growth and disease resistance. Microb Cell Fact 2021; 20:57. [PMID: 33653343 PMCID: PMC7927390 DOI: 10.1186/s12934-021-01540-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background Retention of agricultural bio-mass residues without proper treatment could affect the subsequent plant growth. In the present investigation, the co-cultivation of genetically engineered T. asperellum and B. amyloliquefaciens has been employed for multiple benefits including the enrichment of lignocellulose biodegradation, plant growth, defense potential and disease resistance. Results The Vel1 gene predominantly regulates the secondary metabolites, sexual and asexual development as well as cellulases and polysaccharide hydrolases productions. Overexpression mutant of the Trichoderma asperellum Vel1 locus (TA OE-Vel1) enhanced the activity of FPAase, CMCase, PNPCase, PNPGase, xylanase I, and xylanase II through the regulation of transcription regulating factors and the activation of cellulase and xylanase encoding genes. Further, these genes were induced upon co-cultivation with Bacillus amyloliquefaciens (BA). The co-culture of TA OE-Vel1 + BA produced the best composition of enzymes and the highest biomass hydrolysis yield of 89.56 ± 0.61%. The co-culture of TA OE-Vel1 + BA increased the corn stover degradation by the secretion of cellulolytic enzymes and maintained the C/N ratio of the corn stover amended soil. Moreover, the TA OE-Vel1 + BA increased the maize plant growth, expression of defense gene and disease resistance against Fusarium verticillioides and Cohilohorus herostrophus. Conclusion The co-cultivation of genetically engineered T. asperellum and B. amyloliquefaciens could be utilized as a profound and meaningful technique for the retention of agro residues and subsequent plant growth.
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Affiliation(s)
- Valliappan Karuppiah
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Lu Zhixiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Hongyi Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Murugappan Vallikkannu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China. .,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China.
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Effects of the Transcription Factor Ace2 from Trichoderma reesei on Cellulase and Hemicellulase Expression in Trichoderma orientalis EU7-22. Appl Biochem Biotechnol 2021; 193:2098-2109. [PMID: 33608806 DOI: 10.1007/s12010-021-03529-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
Trichoderma orientalis (T. orientalis) EU7-22 has a complete cellulase system and shows a remarkable enzyme activity with high potential in the industry. Ace2 is an important transcriptional factor for cellulase and hemicellulase expression in Trichoderma reesei (T. reesei). However, the ace2 gene cannot be found in the genome of T. orientalis. Researches show that the mechanism of cellulase transcriptional regulation in T. orientalis keeps high similarity with T. reesei up till now. So, in this study, the ace2 of Trichoderma reesei QM9414 was heterologous expressed in T. orientalis EU7-22. As a result, xylanase activity and β-glucosidase activity of ace2 heterogeneous expression strains are improved and total cellulase activity is decreased. The result of qPCR is in accordance with enzyme activities. This study provides a reference for an in-depth study on transcriptional regulation mechanisms of T. orientalis.
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Daranagama ND, Suzuki Y, Shida Y, Ogasawara W. Involvement of Xyr1 and Are1 for Trichodermapepsin Gene Expression in Response to Cellulose and Galactose in Trichoderma reesei. Curr Microbiol 2020; 77:1506-1517. [DOI: 10.1007/s00284-020-01955-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/18/2020] [Indexed: 10/24/2022]
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19
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Protein phosphatases regulate growth, development, cellulases and secondary metabolism in Trichoderma reesei. Sci Rep 2019; 9:10995. [PMID: 31358805 PMCID: PMC6662751 DOI: 10.1038/s41598-019-47421-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/03/2019] [Indexed: 12/15/2022] Open
Abstract
Trichoderma reesei represents one of the most prolific producers of plant cell wall degrading enzymes. Recent research showed broad regulation by phosphorylation in T. reesei, including important transcription factors involved in cellulase regulation. To evaluate factors crucial for changes in these phosphorylation events, we studied non-essential protein phosphatases (PPs) of T. reesei. Viable deletion strains were tested for growth on different carbon sources, osmotic and oxidative stress response, asexual and sexual development, cellulase and protease production as well as secondary metabolism. Six PPs were found to be positive or negative regulators for cellulase production. A correlation of the effects of PPs on protease activities and cellulase activities was not detected. Hierarchical clustering of regulation patterns and phenotypes of deletion indicated functional specialization within PP classes and common as well as variable effects. Our results confirmed the central role of catalytic and regulatory subunits of PP2A which regulates several aspects of cell growth and metabolism. Moreover we show that the additional homologue of PPH5 in Trichoderma spp., PPH5-2 assumes distinct functions in metabolism, development and stress response, different from PPH5. The influence of PPs on both cellulase gene expression and secondary metabolite production support an interrelationship in the underlying regulation mechanisms.
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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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21
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Zhang J, Wu C, Wang W, Wang W, Wei D. Construction of enhanced transcriptional activators for improving cellulase production in Trichoderma reesei RUT C30. BIORESOUR BIOPROCESS 2018; 5:40. [PMID: 32288986 PMCID: PMC7101855 DOI: 10.1186/s40643-018-0226-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 08/14/2018] [Indexed: 11/21/2022] Open
Abstract
Enhancing cellulase production in Trichoderma reesei is of great interest for an economical biorefinery. Artificial transcription factors are a potentially powerful molecular strategy for improving cellulase production in T. reesei. In this study, enhanced transcriptional activators XYR1VP, ACE2VP, and ACE1VP were constructed by linking the C terminus of XYR1, ACE2, or ACE1 with an activation domain of herpes simplex virus protein VP16. T. reesei transformants TXYR1VP, TACE2VP, and TACE1VP showed improved cellulase and/or xylanase production. TXYR1VP has a cellulase-free phenotype but with significantly elevated xylanase production. Xylanase I and xylanase II activities [U/(mg biomass)] increased by 51% and 80%, respectively, in TXYR1VP in comparison with parental strain RUT C30. The filter paper activity of TACE2VP in the Avicel-based medium increased by 52% compared to that of RUT C30. In the Avicel-based medium, TACE1VP manifested an 80% increase in FPase activity and a 50% increase in xylanase activity as compared to those of RUT C30. Additionally, when pretreated corn stover was hydrolyzed, crude enzymes produced from TACE1VP yielded a greater glucose release than did the enzymes produced by parental strain RUT C30.![]()
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Affiliation(s)
- Jiajia Zhang
- 1New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237 China
| | - Chuan Wu
- 1New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237 China
| | - Wei Wang
- 2State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Wei Wang
- 1New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237 China
| | - Dongzhi Wei
- 1New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237 China
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Zhang J, Wu C, Wang W, Wang W, Wei D. A versatile Trichoderma reesei expression system for the production of heterologous proteins. Biotechnol Lett 2018; 40:965-972. [PMID: 29644559 DOI: 10.1007/s10529-018-2548-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
Abstract
OBJECTIVES To develop a versatile Trichoderma reesei (teleomorph Hypocrea jecorina) expression system for the high-purity production of heterologous proteins. RESULTS The versatile T. reesei expression system is based on xyn1 and xyn2 promoters, A824V transition in XYRI, and a bicomponent carbon source strategy. Red fluorescent protein gene rfp and alkaline endoglucanase EGV gene egv3 from Humicola insolens were used as reporter genes to test our versatile expression system CONCLUSIONS: The versatile T. reesei expression system can be applied to produce heterologous proteins with high purity and high yield.
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Affiliation(s)
- Jiajia Zhang
- New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237, China
| | - Chuan Wu
- New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wei Wang
- New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237, China.
| | - Dongzhi Wei
- New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237, China
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Zhang J, Zhang G, Wang W, Wang W, Wei D. Enhanced cellulase production in Trichoderma reesei RUT C30 via constitution of minimal transcriptional activators. Microb Cell Fact 2018; 17:75. [PMID: 29773074 PMCID: PMC5956553 DOI: 10.1186/s12934-018-0926-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 05/11/2018] [Indexed: 01/06/2023] Open
Abstract
Background Cellulase can convert lignocellulosic feedstocks into fermentable sugars, which can be used for the industrial production of biofuels and chemicals. The high cost of cellulase production remains a challenge for lignocellulose breakdown. Trichoderma reesei RUT C30 serves as a well-known industrial workhorse for cellulase production. Therefore, the enhancement of cellulase production by T. reesei RUT C30 is of great importance. Results Two sets of novel minimal transcriptional activators (DBDace2-VP16 and DBDcre1-VP16) were designed and expressed in T. reesei RUT C30. Expression of DBDace2-VP16 and DBDcre1-VP16 improved cellulase production under induction (avicel or lactose) and repression (glucose) conditions, respectively. The strain TMTA66 under avicel and TMTA139 under glucose with the highest cellulase activities outperformed other transformants and the parental strain under the corresponding conditions. For TMTA66 strains, the highest FPase activity was approximately 1.3-fold greater than that of the parental strain RUT C30 at 120 h of cultivation in a shake flask using avicel as the sole carbon source. The FPase activity (U/mg biomass) in TMTA139 strains was approximately 26.5-fold higher than that of the parental strain RUT C30 at 72 h of cultivation in a shake flask using glucose as the sole carbon source. Furthermore, the crude enzymes produced in the 7-L fermenter from TMTA66 and TMTA139 supplemented with commercial β-glucosidase hydrolyzed pretreated corn stover effectively. Conclusions These results show that replacing natural transcription factors with minimal transcriptional activators is a powerful strategy to enhance cellulase production in T. reesei. Our current study also offers an alternative genetic engineering strategy for the enhanced production of industrial products by other fungi. Electronic supplementary material The online version of this article (10.1186/s12934-018-0926-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiajia Zhang
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B. 311, Shanghai, 200237, China
| | - Guoxiu Zhang
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B. 311, Shanghai, 200237, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B. 311, Shanghai, 200237, China.
| | - Dongzhi Wei
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, P.O.B. 311, Shanghai, 200237, China
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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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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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Shida Y, Furukawa T, Ogasawara W. Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei, the hyper-cellulolytic filamentous fungus. Biosci Biotechnol Biochem 2016; 80:1712-29. [DOI: 10.1080/09168451.2016.1171701] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Abstract
The filamentous fungus Trichoderma reesei is a potent cellulase producer and the best-studied cellulolytic fungus. A lot of investigations not only on glycoside hydrolases produced by T. reesei, but also on the machinery controlling gene expression of these enzyme have made this fungus a model organism for cellulolytic fungi. We have investigated the T. reesei strain including mutants developed in Japan in detail to understand the molecular mechanisms that control the cellulase gene expression, the biochemical and morphological aspects that could favor this phenotype, and have attempted to generate novel strains that may be appropriate for industrial use. Subsequently, we developed recombinant strains by combination of these insights and the heterologous-efficient saccharifing enzymes. Resulting enzyme preparations were highly effective for saccharification of various biomass. In this review, we present some of the salient findings from the recent biochemical, morphological, and molecular analyses of this remarkable cellulase hyper-producing fungus.
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Affiliation(s)
- Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takanori Furukawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
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Chen L, Zou G, Wang J, Wang J, Liu R, Jiang Y, Zhao G, Zhou Z. Characterization of the Ca2+-responsive signaling pathway in regulating the expression and secretion of cellulases inTrichoderma reeseiRut-C30. Mol Microbiol 2016; 100:560-75. [DOI: 10.1111/mmi.13334] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Ling Chen
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Gen Zou
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Jingzhi Wang
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Jin Wang
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Rui Liu
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Yanping Jiang
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
| | - Zhihua Zhou
- Key Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Shanghai 200032 China
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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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Derntl C, Rassinger A, Srebotnik E, Mach RL, Mach-Aigner AR. Xpp1 regulates the expression of xylanases, but not of cellulases in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:112. [PMID: 26246855 PMCID: PMC4526299 DOI: 10.1186/s13068-015-0298-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/24/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND The ascomycete Trichoderma reesei is industrially used for the production of cellulases. During the production process xylanases are co-secreted, which uses energy and nutrients. Cellulases and xylanases share the same main regulators, which makes a knowledge-based strain design difficult. However, previously a cis-element in the promoter of the main xylanase-encoding gene was identified as binding site for a putative repressor. Subsequently, three candidate repressors were identified in a pull-down approach. The expression of the most promising candidate, Xpp1 (Xylanase promoter-binding protein 1), was reported to be up-regulated on the repressing carbon source d-glucose and to bind the cis-element in vitro. RESULTS In this study, Xpp1 was deleted and over-expressed in T. reesei. An in vivo DNA-footprint assay indicated that Xpp1 binds a palindromic sequence in the xyn2 promoter. Comparison of the deletion, the over-expression, and the parent strain demonstrated that Xpp1 regulates gene expression of xylanolytic enzymes at later cultivation stages. Xpp1 expression was found to be up-regulated, additionally to d-glucose, by high d-xylose availability. These findings together with the observed xyn2 transcript levels during growth on xylan suggest that Xpp1 is the mediator of a feedback mechanism. Notably, Xpp1 has neither influence on the d-xylose metabolism nor on the expression of cellulases. CONCLUSIONS Xpp1 as regulator acting on the expression of xylanases, but not cellulases, is a highly promising candidate for knowledge-based strain design to improve the cellulases-to-xylanases ratio during industrial cellulase production.
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Affiliation(s)
- Christian Derntl
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Alice Rassinger
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Ewald Srebotnik
- />Department of Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Robert L Mach
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Astrid R Mach-Aigner
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
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Trichoderma atroviride transcriptional regulator Xyr1 supports the induction of systemic resistance in plants. Appl Environ Microbiol 2014; 80:5274-81. [PMID: 24951787 DOI: 10.1128/aem.00930-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
As a result of a transcriptome-wide analysis of the ascomycete Trichoderma atroviride, mycoparasitism-related genes were identified; of these, 13 genes were further investigated for differential expression. In silico analysis of the upstream regulatory regions of these genes pointed to xylanase regulator 1 (Xyr1) as a putatively involved regulatory protein. Transcript analysis of the xyr1 gene of T. atroviride in confrontation with other fungi allowed us to determine that xyr1 levels increased during mycoparasitism. To gain knowledge about the precise role of Xyr1 in the mycoparasitic process, the corresponding gene was deleted from the T. atroviride genome. This resulted in strong reductions in the transcript levels of axe1 and swo1, which encode accessory cell wall-degrading enzymes considered relevant for mycoparasitism. We also analyzed the role of Xyr1 in the Trichoderma-Arabidopsis interaction, finding that the plant response elicited by T. atroviride is delayed if Xyr1 is missing in the fungus.
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Gorsche R, Jovanovic B, Gudynaite-Savitch L, Mach RL, Mach-Aigner AR. A highly sensitive in vivo footprinting technique for condition-dependent identification of cis elements. Nucleic Acids Res 2013; 42:e1. [PMID: 24097437 PMCID: PMC3874196 DOI: 10.1093/nar/gkt883] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Knowing which regions of a gene are targeted by transcription factors during induction or repression is essential for understanding the mechanisms responsible for regulation. Therefore, we re-designed the traditional in vivo footprinting method to obtain a highly sensitive technique, which allows identification of the cis elements involved in condition-dependent gene regulation. Data obtained through DMS methylation, HCl DNA cleavage and optimized ligation-mediated PCR using fluorescent labelling followed by capillary gel electrophoresis are analysed by ivFAST. In this work we have developed this command line-based program, which is designed to ensure automated and fast data processing and visualization. The new method facilitates a quantitative, high-throughput approach because it enables the comparison of any number of in vivo footprinting results from different conditions (e.g. inducing, repressing, de-repressing) to one another by employing an internal standard. For validation of the method the well-studied upstream regulatory region of the Trichoderma reesei xyn1 (endoxylanase 1) gene was used. Applying the new method we could identify the motives involved in condition-dependent regulation of the cbh2 (cellobiohydrolase 2) and xyn2 (endoxylanase 2) genes.
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Affiliation(s)
- Rita Gorsche
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Str. 1 a, A-1060 Vienna, Austria and Department of Biology, University of Ottawa, Gendron Hall, 30 Marie Curie, Ottawa, ON, K1N6N5, Canada
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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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RETRACTED ARTICLE: The effects of each beta-glucosidase gene deletion on cellulase gene regulation in Neurospora crassa (online publication: DOI 10.1007/s10482-013- 9972-7). Antonie Van Leeuwenhoek 2013; 105:269. [PMID: 24000093 DOI: 10.1007/s10482-013-9972-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 07/09/2013] [Indexed: 11/26/2022]
Abstract
Takao Kasuga and Zhiliang Fan were listed as co-authors without their acknowledgement and would like to be removed from the authors list. This article is retracted on request of Weihua Wu due to inconsistent errors of intracellular and total beta-glucosidase activities assay and the mycelia weight measurement in this paper. These errors led to inaccurate results of total and intracellular beta-glucosidase activities, and the normalized endoglucanases and exoglucanases activities and therefore compromise the partial conclusions of this publication.
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Wang M, Zhao Q, Yang J, Jiang B, Wang F, Liu K, Fang X. A mitogen-activated protein kinase Tmk3 participates in high osmolarity resistance, cell wall integrity maintenance and cellulase production regulation in Trichoderma reesei. PLoS One 2013; 8:e72189. [PMID: 23991059 PMCID: PMC3753334 DOI: 10.1371/journal.pone.0072189] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/07/2013] [Indexed: 01/09/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK) pathways are important signal transduction pathways conserved in essentially all eukaryotes, but haven't been subjected to functional studies in the most important cellulase-producing filamentous fungus Trichoderma reesei. Previous reports suggested the presence of three MAPKs in T. reesei: Tmk1, Tmk2, and Tmk3. By exploring the phenotypic features of T. reesei Δtmk3, we first showed elevated NaCl sensitivity and repressed transcription of genes involved in glycerol/trehalose biosynthesis under higher osmolarity, suggesting Tmk3 participates in high osmolarity resistance via derepression of genes involved in osmotic stabilizer biosynthesis. We also showed significant downregulation of genes encoding chitin synthases and a β-1,3-glucan synthase, decreased chitin content, ‘budded’ hyphal appearance typical to cell wall defective strains, and increased sensitivity to calcofluor white/Congo red in the tmk3 deficient strain, suggesting Tmk3 is involved in cell wall integrity maintenance in T. reesei. We further observed the decrease of cellulase transcription and production in T. reesei Δtmk3 during submerged cultivation, as well as the presence of MAPK phosphorylation sites on known transcription factors involved in cellulase regulation, suggesting Tmk3 is also involved in the regulation of cellulase production. Finally, the expression of cell wall integrity related genes, the expression of cellulase coding genes, cellulase production and biomass accumulation were compared between T. reesei Δtmk3 grown in solid state media and submerged media, showing a strong restoration effect in solid state media from defects resulted from tmk3 deletion. These results showed novel physiological processes that fungal Hog1-type MAPKs are involved in, and present the first experimental investigation of MAPK signaling pathways in T. reesei. Our observations on the restoration effect during solid state cultivation suggest that T. reesei is evolved to favor solid state growth, bringing up the proposal that the submerged condition normally used during investigations on fungal physiology might be misleading.
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Affiliation(s)
- Mingyu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- National Glycoengineering Research Center, Shandong University, Jinan, China
| | - Qiushuang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Jinghua Yang
- Department of Surgery, VA Boston Healthcare System, Boston University, Boston, Massachusetts, United States of America
- Cancer Research Center, Shandong University School of Medicine, Jinan, China
| | - Baojie Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Fangzhong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Kuimei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- National Glycoengineering Research Center, Shandong University, Jinan, China
- * E-mail:
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Wang S, Liu G, Wang J, Yu J, Huang B, Xing M. Enhancing cellulase production in Trichoderma reesei RUT C30 through combined manipulation of activating and repressing genes. ACTA ACUST UNITED AC 2013; 40:633-41. [DOI: 10.1007/s10295-013-1253-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 02/22/2013] [Indexed: 10/27/2022]
Abstract
Abstract
To investigate whether enzyme production can be enhanced in the Trichoderma reesei industrial hyperproducer strain RUT C30 by manipulation of cellulase regulation, the positive regulator Xyr1 was constitutively expressed under the control of the strong T. reesei pdc promoter, resulting in significantly enhanced cellulase activity in the transformant during growth on cellulose. In addition, constitutive expression of xyr1 combined with downregulation of the negative regulator encoding gene ace1 further increased cellulase and xylanase activities. Compared with RUT C30, the resulting transformant exhibited 103, 114, and 134 % greater total secreted protein levels, filter paper activity, and CMCase activity, respectively. Surprisingly, strong increases in xyr1 basal expression levels resulted in very high levels of CMCase activity during growth on glucose. These findings demonstrate the feasibility of improving cellulase production by modifying regulator expression, and suggest an attractive new single-step approach for increasing total cellulase productivity in T. reesei.
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Affiliation(s)
- Shaowen Wang
- grid.263488.3 0000000104729649 Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences Shenzhen University 518060 Shenzhen China
- grid.27446.33 0000000417899163 School of Life Sciences Northeast Normal University 130024 Changchun China
| | - Gang Liu
- grid.263488.3 0000000104729649 Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences Shenzhen University 518060 Shenzhen China
| | - Juan Wang
- grid.263488.3 0000000104729649 Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences Shenzhen University 518060 Shenzhen China
| | - Jianteng Yu
- Department of Marine Biology Shenzhen Key Laboratory of Marine Biotechnology and Ecology 518060 Shenzhen China
| | - Baiqu Huang
- grid.27446.33 0000000417899163 School of Life Sciences Northeast Normal University 130024 Changchun China
| | - Miao Xing
- grid.263488.3 0000000104729649 Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences Shenzhen University 518060 Shenzhen China
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Amore A, Giacobbe S, Faraco V. Regulation of cellulase and hemicellulase gene expression in fungi. Curr Genomics 2013; 14:230-49. [PMID: 24294104 PMCID: PMC3731814 DOI: 10.2174/1389202911314040002] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 11/22/2022] Open
Abstract
Research on regulation of cellulases and hemicellulases gene expression may be very useful for increasing the production of these enzymes in their native producers. Mechanisms of gene regulation of cellulase and hemicellulase expression in filamentous fungi have been studied, mainly in Aspergillus and Trichoderma. The production of these extracellular enzymes is an energy-consuming process, so the enzymes are produced only under conditions in which the fungus needs to use plant polymers as an energy and carbon source. Moreover, production of many of these enzymes is coordinately regulated, and induced in the presence of the substrate polymers. In addition to induction by mono- and oligo-saccharides, genes encoding hydrolytic enzymes involved in plant cell wall deconstruction in filamentous fungi can be repressed during growth in the presence of easily metabolizable carbon sources, such as glucose. Carbon catabolite repression is an important mechanism to repress the production of plant cell wall degrading enzymes during growth on preferred carbon sources. This manuscript reviews the recent advancements in elucidation of molecular mechanisms responsible for regulation of expression of cellulase and hemicellulase genes in fungi.
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Affiliation(s)
- Antonella Amore
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, via Cintia, 4 80126 Naples, Italy
| | - Simona Giacobbe
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, via Cintia, 4 80126 Naples, Italy
| | - Vincenza Faraco
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, via Cintia, 4 80126 Naples, Italy
- School of Biotechnological Sciences, University of Naples “Federico II” Italy
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Controlled preparation of cellulases with xylanolytic enzymes from Trichoderma reesei (Hypocrea jecorina) by continuous-feed cultivation using soluble sugars. Biosci Biotechnol Biochem 2013; 77:161-6. [PMID: 23291768 DOI: 10.1271/bbb.120696] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The objective of this study was to develop an efficient production system for cellulase preparation with a high level of xylanolytic enzymes using soluble carbon sources. When xylose and arabinose were simultaneously fed with glucose and cellobiose, a mutant of Trichoderma reesei, M3-1, showed sufficient levels of cellulolytic and xylanolytic activities, indicating that xylose and arabinose are good inducers for the production of xylanolytic enzymes. In a continuous feeding experiment using glucose/cellobiose and glucose/xylose/cellobiose, cellulase preparations with various levels of xylanolytic enzymes were obtained by altering the feeding solutions and the timing of their addition. The volumetric production rates for xylanolytic activities at the glucose/xylose/cellobiose-feeding phase were significantly higher than at the glucose/cellobiose-feeding phase, while those for cellulolytic activities were comparable under the two conditions. Thus the composition of the enzyme preparation produced by the mutant was readily controlled by varying the inducers and the pattern of their addition, facilitating the tailored production of enzymes in a diversity of bioconversion processes.
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Functional analysis of the degradation of cellulosic substrates by a Chaetomium globosum endophytic isolate. Appl Environ Microbiol 2012; 78:3693-705. [PMID: 22389369 DOI: 10.1128/aem.00124-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most photosynthetically fixed carbon is contained in cell wall polymers present in plant biomasses, the largest organic carbon source in the biosphere. The degradation of these polymers for biotechnological purposes requires the combined action of several enzymes. To identify new activities, we examined which enzymes are activated by an endophytic strain of Chaetomium globosum to degrade cellulose-containing substrates. After biochemical analyses of the secretome of the fungus grown on cellulose or woody substrates, we took advantage of the available genomic data to identify potentially involved genes. After in silico identification of putative genes encoding either proteins able to bind to cellulose or glycohydrolases (GHs) of family 7, we investigated their transcript levels by reverse transcription-quantitative PCR (RT-qPCR). Our data suggest that eight genes compose the core of the cellulose-degrading system of C. globosum. Notably, the related enzymes belong structurally to the well-described GH families 5, 6, 7, 16, and 45, which are known to be the core of the cellulose degradation systems of several ascomycetes. The high expression levels of cellobiose dehydrogenase and two GH 61 enzymes suggest the involvement of this oxidoreductive synergic system in C. globosum. Transcript analysis along with relevant coding sequence (CDS) isolation and expression of recombinant proteins proved to be a key strategy for the determination of the features of two endoglucanases used by C. globosum for the first attack of crystalline cellulose. Finally, the possible involvement of transcriptional regulators described for other ascomycetes is discussed.
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Roles of protein kinase A and adenylate cyclase in light-modulated cellulase regulation in Trichoderma reesei. Appl Environ Microbiol 2012; 78:2168-78. [PMID: 22286997 DOI: 10.1128/aem.06959-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cyclic AMP (cAMP) pathway represents a central signaling cascade with crucial functions in all organisms. Previous studies of Trichoderma reesei (anamorph of Hypocrea jecorina) suggested a function of cAMP signaling in regulation of cellulase gene expression. We were therefore interested in how the crucial components of this pathway, adenylate cyclase (ACY1) and cAMP-dependent protein kinase A (PKA), would affect cellulase gene expression. We found that both ACY1 and PKA catalytic subunit 1 (PKAC1) are involved in regulation of vegetative growth but are not essential for sexual development. Interestingly, our results showed considerably increased transcript abundance of cellulase genes in darkness compared to light (light responsiveness) upon growth on lactose. This effect is strongly enhanced in mutant strains lacking PKAC1 or ACY1. Comparison to the wild type showed that ACY1 has a consistently positive effect on cellulase gene expression in light and darkness, while PKAC1 influences transcript levels of cellulase genes positively in light but negatively in darkness. A function of PKAC1 in light-modulated cellulase gene regulation is also reflected by altered complex formation within the cel6a/cbh2 promoter in light and darkness and in the absence of pkac1. Analysis of transcript levels of cellulase regulator genes indicates that the regulatory output of the cAMP pathway may be established via adjustment of XYR1 abundance. Consequently, both adenylate cyclase and protein kinase A are involved in light-modulated cellulase gene expression in T. reesei and have a dampening effect on the light responsiveness of this process.
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Seiboth B, Herold S, Kubicek CP. Metabolic engineering of inducer formation for cellulase and hemicellulase gene expression in Trichoderma reesei. Subcell Biochem 2012; 64:367-90. [PMID: 23080260 DOI: 10.1007/978-94-007-5055-5_18] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The filamentous fungus T. reeseiis today a paradigm for the commercial scale production of different plant cell wall degrading enzymes mainly cellulases and hemicellulases. Its enzymes have a long history of safe use in industry and well established applications are found within the pulp, paper, food, feed or textile processing industries. However, when these enzymes are to be used for the saccharification of cellulosic plant biomass to simple sugars which can be further converted to biofuels or other biorefinery products, and thus compete with chemicals produced from fossil sources, additional efforts are needed to reduce costs and maximize yield and efficiency of the produced enzyme mixtures. One approach to this end is the use of genetic engineering to manipulate the biochemical and regulatory pathways that operate during enzyme production and control enzyme yield. This review aims at a description of the state of art in this area.
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Affiliation(s)
- Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, 166-5, A-1060, Vienna, Austria
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Steiger MG, Mach-Aigner AR, Gorsche R, Rosenberg EE, Mihovilovic MD, Mach RL. Synthesis of an antiviral drug precursor from chitin using a saprophyte as a whole-cell catalyst. Microb Cell Fact 2011; 10:102. [PMID: 22141613 PMCID: PMC3245449 DOI: 10.1186/1475-2859-10-102] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 12/05/2011] [Indexed: 11/25/2022] Open
Abstract
Background Recent incidents, such as the SARS and influenza epidemics, have highlighted the need for readily available antiviral drugs. One important precursor currently used for the production of Relenza, an antiviral product from GlaxoSmithKline, is N-acetylneuraminic acid (NeuNAc). This substance has a considerably high market price despite efforts to develop cost-reducing (biotechnological) production processes. Hypocrea jecorina (Trichoderma reesei) is a saprophyte noted for its abundant secretion of hydrolytic enzymes and its potential to degrade chitin to its monomer N-acetylglucosamine (GlcNAc). Chitin is considered the second most abundant biomass available on earth and therefore an attractive raw material. Results In this study, we introduced two enzymes from bacterial origin into Hypocrea, which convert GlcNAc into NeuNAc via N-acetylmannosamine. This enabled the fungus to produce NeuNAc from the cheap starting material chitin in liquid culture. Furthermore, we expressed the two recombinant enzymes as GST-fusion proteins and developed an enzyme assay for monitoring their enzymatic functionality. Finally, we demonstrated that Hypocrea does not metabolize NeuNAc and that no NeuNAc-uptake by the fungus occurs, which are important prerequisites for a potential production strategy. Conclusions This study is a proof of concept for the possibility to engineer in a filamentous fungus a bacterial enzyme cascade, which is fully functional. Furthermore, it provides the basis for the development of a process for NeuNAc production as well as a general prospective design for production processes that use saprophytes as whole-cell catalysts.
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Affiliation(s)
- Matthias G Steiger
- Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Str. 1a, A-1060 Wien, Austria
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Differential regulation of the cellulase transcription factors XYR1, ACE2, and ACE1 in Trichoderma reesei strains producing high and low levels of cellulase. EUKARYOTIC CELL 2010; 10:262-71. [PMID: 21169417 DOI: 10.1128/ec.00208-10] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Due to its capacity to produce large amounts of cellulases, Trichoderma reesei is increasingly being investigated for second-generation biofuel production from lignocellulosic biomass. The induction mechanisms of T. reesei cellulases have been described recently, but the regulation of the genes involved in their transcription has not been studied thoroughly. Here we report the regulation of expression of the two activator genes xyr1 and ace2, and the corepressor gene ace1, during the induction of cellulase biosynthesis by the inducer lactose in T. reesei QM 9414, a strain producing low levels of cellulase (low producer). We show that all three genes are induced by lactose. xyr1 was also induced by d-galactose, but this induction was independent of d-galactose metabolism. Moreover, ace1 was carbon catabolite repressed, whereas full induction of xyr1 and ace2 in fact required CRE1. Significant differences in these regulatory patterns were observed in the high-producer strain RUT C30 and the hyperproducer strain T. reesei CL847. These observations suggest that a strongly elevated basal transcription level of xyr1 and reduced upregulation of ace1 by lactose may have been important for generating the hyperproducer strain and that thus, these genes are major control elements of cellulase production.
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Mach-Aigner AR, Grosstessner-Hain K, Poças-Fonseca MJ, Mechtler K, Mach RL. From an electrophoretic mobility shift assay to isolated transcription factors: a fast genomic-proteomic approach. BMC Genomics 2010; 11:644. [PMID: 21087492 PMCID: PMC3012607 DOI: 10.1186/1471-2164-11-644] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 11/18/2010] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Hypocrea jecorina (anamorph Trichoderma reesei) is a filamentous ascomycete of industrial importance due to its hydrolases (e.g., xylanases and cellulases). The regulation of gene expression can influence the composition of the hydrolase cocktail, and thus, transcription factors are a major target of current research. Here, we design an approach for identifying a repressor of a xylanase-encoding gene. RESULTS We used streptavidin affinity chromatography to isolate the Xylanase promoter-binding protein 1 (Xpp1). The optimal conditions and templates for the chromatography step were chosen according to the results of an electrophoretic mobility shift assay performed under repressing conditions, which yielded a DNA-protein complex specific to the AGAA-box (the previously identified, tetranucleotide cis-acting element). After isolating AGAA-box binding proteins, the eluted proteins were identified with Nano-HPLC/tandem MS-coupled detection. We compared the identified peptides to sequences in the H. jecorina genome and predicted in silico the function and DNA-binding ability of the identified proteins. With the results from these analyses, we eliminated all but three candidate proteins. We verified the transcription of these candidates and tested their ability to specifically bind the AGAA-box. In the end, only one candidate protein remained. We generated this protein with in vitro translation and used an EMSA to demonstrate the existence of an AGAA-box-specific protein-DNA complex. We found that the expression of this gene is elevated under repressing conditions relative to de-repressing or inducing conditions. CONCLUSIONS We identified a putative transcription factor that is potentially involved in repressing xylanase 2 expression. We also identified two additional potential regulatory proteins that bind to the xyn2 promoter. Thus, we succeeded in identifying novel, putative transcription factors for the regulation of xylanase expression in H. jecorina.
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Affiliation(s)
- Astrid R Mach-Aigner
- Department of Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Wien, Austria.
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Steiger MG, Mach RL, Mach-Aigner AR. An accurate normalization strategy for RT-qPCR in Hypocrea jecorina (Trichoderma reesei). J Biotechnol 2010; 145:30-7. [PMID: 19861137 DOI: 10.1016/j.jbiotec.2009.10.012] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 10/12/2009] [Accepted: 10/16/2009] [Indexed: 11/24/2022]
Abstract
Hypocrea jecorina is an important, filamentous fungus due to its effective production of hydrolytic enzymes. Gene expression studies provide deeper insight into environment sensing and cellular response mechanisms. Reverse transcription-quantitative PCR is a gene-specific and powerful tool to measure even minor changes in mRNA composition. An accurate normalization strategy is absolutely necessary for appropriate interpretation of reverse transcription-quantitative PCR results. One frequently applied strategy is the usage of a reference gene. Adequate reference genes for Hypocrea have not been published so far. By using the NormFinder and geNorm softwares, we evaluated the most stable genes amongst six potential reference genes in 34 samples from diverse cultivation conditions. Under those experimental conditions, sar1 encoding for a small GTPase was found to be the most stable gene, whereas act encoding for actin was not amongst the best validated ones. The influence of the reference system on the expression data is demonstrated by analysis of two target genes, encoding for the Xylanase regulator 1 and for Xylanase II. We further validated obtained xylanase 2 transcription rates with the corresponding enzyme activity.
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45
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D-Xylose as a repressor or inducer of xylanase expression in Hypocrea jecorina (Trichoderma reesei). Appl Environ Microbiol 2010; 76:1770-6. [PMID: 20097821 DOI: 10.1128/aem.02746-09] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For Hypocrea jecorina (anamorph Trichoderma reesei), a filamentous fungus used for hydrolase production in different industries, it has been a long-term practice to use d-xylose as an inducing substance. We demonstrate in this study that the degree of xylanase-encoding gene induction strictly depends on the concentration of d-xylose, which was found to be optimal from 0.5 to 1 mM for 3 h of cultivation. At higher concentrations of d-xylose, a reduced level of xylanase gene expression was observed. In the present study, we also provide evidence that the d-xylose concentration-dependent induction is antagonized by carbon catabolite repressor 1. This repressor mediates its influence on d-xylose indirectly, by reducing the expression of xylanase regulator 1, the main activator of most hydrolase-encoding genes. Additionally, a direct influence of the repressor on xylanase 1 expression in the presence of d-xylose was found. Furthermore, we show that d-xylose reductase 1 is needed to metabolize d-xylose to achieve full induction of xylanase expression. Finally, a strain which expresses xylanase regulator 1 at a constant level was used to partially overcome the negative influence exerted by carbon catabolite repressor 1 on d-xylose.
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46
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Guangtao Z, Seiboth B, Wen C, Yaohua Z, Xian L, Wang T. A novel carbon source-dependent genetic transformation system for the versatile cell factory Hypocrea jecorina (anamorph Trichoderma reesei). FEMS Microbiol Lett 2009; 303:26-32. [PMID: 20002748 DOI: 10.1111/j.1574-6968.2009.01851.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Genetic transformation is an indispensable tool for basic fungal research, as well as a useful technique for directed improvement of industrial strains. Here we describe a simple and reproducible transformation system for the filamentous fungus Hypocrea jecorina. The system is based on hxk1 (encoding hexokinase) as selectable marker, a hexokinase-negative strain and D-mannitol, which is used as selective carbon source and osmotic stabilizer. Following transformation with the hxk1 gene, the obtained transformants were able to grow on D-mannitol as sole carbon source. Transformation efficiency achieved using D-mannitol as carbon source and osmotic stabilizer was roughly five times higher than that using D-sorbitol. The utility of this system was further demonstrated by transformation of H. jecorina with the egfp (encoding the enhanced green fluorescent protein) gene. Fluorescence microscopy revealed EGFP fluorescence in positive transformants. Our results demonstrated the feasibility of exploiting a carbon source metabolic pathway for the development of promising fungal transformation systems, which provides a new molecular toolbox for genetic modifications of the cell factory H. jecorina.
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Affiliation(s)
- Zhang Guangtao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan Shandong, China
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Kubicek CP, Mikus M, Schuster A, Schmoll M, Seiboth B. Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina. BIOTECHNOLOGY FOR BIOFUELS 2009; 2:19. [PMID: 19723296 PMCID: PMC2749017 DOI: 10.1186/1754-6834-2-19] [Citation(s) in RCA: 244] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2009] [Accepted: 09/01/2009] [Indexed: 05/05/2023]
Abstract
Hypocrea jecorina (= Trichoderma reesei) is the main industrial source of cellulases and hemicellulases used to depolymerise plant biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. Cellulases are formed adaptively, and several positive (XYR1, ACE2, HAP2/3/5) and negative (ACE1, CRE1) components involved in this regulation are now known. In addition, its complete genome sequence has been recently published, thus making the organism susceptible to targeted improvement by metabolic engineering. In this review, we summarise current knowledge about how cellulase biosynthesis is regulated, and outline recent approaches and suitable strategies for facilitating the targeted improvement of cellulase production by genetic engineering.
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Affiliation(s)
- Christian P Kubicek
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
| | - Marianna Mikus
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
| | - André Schuster
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
| | - Monika Schmoll
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
| | - Bernhard Seiboth
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
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Furukawa T, Shida Y, Kitagami N, Mori K, Kato M, Kobayashi T, Okada H, Ogasawara W, Morikawa Y. Identification of specific binding sites for XYR1, a transcriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei. Fungal Genet Biol 2009; 46:564-74. [PMID: 19393758 DOI: 10.1016/j.fgb.2009.04.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Revised: 04/15/2009] [Accepted: 04/15/2009] [Indexed: 11/20/2022]
Abstract
The transcriptional activator XYR1 is the central regulator that governs cellulolytic and xylanolytic gene expression in Trichoderma reesei. However, despite its biological importance, relatively little is known about its functional binding sequences. In the present study, we investigated the binding characteristics and specific target for XYR1 by using DNase I footprinting analysis and electrophoretic mobility shift assays. We demonstrate that XYR1 can interact not only with the 5'-GGCTAA-3' motif but also with several 5'-GGC(A/T)(3)-3' motifs. In silico analysis revealed that the 5'-GGC(A/T)(3)-3' motifs are widespread as single site in 5'-upstream region of all the XYR1-regulated genes. Furthermore, we defined the important nucleotides within the binding site that contribute to specific interaction with XYR1. Our results suggest that, together with the inverted repeat motifs, the single 5'-GGC(A/T)(4)-3' motifs play important roles as functional XYR1-binding sites in the regulation of cellulase and xylanase gene expression in T. reesei.
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Affiliation(s)
- Takanori Furukawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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Transcriptional regulation of xyr1, encoding the main regulator of the xylanolytic and cellulolytic enzyme system in Hypocrea jecorina. Appl Environ Microbiol 2008; 74:6554-62. [PMID: 18791032 DOI: 10.1128/aem.01143-08] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Hypocrea jecorina, Xyr1 (xylanase regulator 1) is the main transcription activator of hydrolase-encoding genes, such as xyn1, xyn2, bxl1, cbh1, cbh2, egl1, and bgl1. Even though Xyr1 mediates the induction signal for all these genes derived from various inducing carbon sources and compounds, xyr1 transcription itself is not inducible by any of these substances. However, cultivation on glucose as the carbon source provokes carbon catabolite repression of xyr1 transcription mediated by Cre1. In addition, xyr1 transcription is repressed by the specific transcription factor Ace1. Moreover, Xyr1 is permanently available in the cell, and no de novo synthesis of this factor is needed for a first induction of xyn1 transcription. The constitutive expression of xyr1 leads to a significant elevation/deregulation of the xyn1, xyn2, and bxl1 transcription compared to what is seen for the parental strain. Overall, the corresponding xylanolytic enzyme activities are clearly elevated in a constitutively xyr1-expressing strain, emphasizing this factor as an auspicious target for genetically engineered strain improvement.
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Furukawa T, Shida Y, Kitagami N, Ota Y, Adachi M, Nakagawa S, Shimada R, Kato M, Kobayashi T, Okada H, Ogasawara W, Morikawa Y. Identification of the cis-acting elements involved in regulation of xylanase III gene expression in Trichoderma reesei PC-3-7. Fungal Genet Biol 2008; 45:1094-102. [DOI: 10.1016/j.fgb.2008.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 10/22/2022]
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