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Yang J, Yue HR, Pan LY, Feng JX, Zhao S, Suwannarangsee S, Chempreda V, Liu CG, Zhao XQ. Fungal strain improvement for efficient cellulase production and lignocellulosic biorefinery: Current status and future prospects. BIORESOURCE TECHNOLOGY 2023:129449. [PMID: 37406833 DOI: 10.1016/j.biortech.2023.129449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Lignocellulosic biomass (LCB) has been recognized as a valuable carbon source for the sustainable production of biofuels and value-added biochemicals. Crude enzymes produced by fungal cell factories benefit economic LCB degradation. However, high enzyme production cost remains a great challenge. Filamentous fungi have been widely used to produce cellulolytic enzymes. Metabolic engineering of fungi contributes to efficient cellulase production for LCB biorefinery. Here the latest progress in utilizing fungal cell factories for cellulase production was summarized, including developing genome engineering tools to improve the efficiency of fungal cell factories, manipulating promoters, and modulating transcription factors. Multi-omics analysis of fungi contributes to identifying novel genetic elements for enhancing cellulase production. Furthermore, the importance of translation regulation of cellulase production are emphasized. Efficient development of fungal cell factories based on integrative strain engineering would benefit the overall bioconversion efficacy of LCB for sustainable bioproduction.
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Affiliation(s)
- Jie Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hou-Ru Yue
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li-Ya Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Surisa Suwannarangsee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Verawat Chempreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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2
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Li Y, Song W, Han X, Wang Y, Rao S, Zhang Q, Zhou J, Li J, Liu S, Du G. Recent progress in key lignocellulosic enzymes: Enzyme discovery, molecular modifications, production, and enzymatic biomass saccharification. BIORESOURCE TECHNOLOGY 2022; 363:127986. [PMID: 36126851 DOI: 10.1016/j.biortech.2022.127986] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 05/15/2023]
Abstract
Lignocellulose, the most prevalent biomass on earth, can be enzymatically converted into carbohydrates for bioethanol production and other uses. Among lignocellulosic enzymes, endoglucanase, xylanase, and laccase are the key enzymes, owing to their ability to disrupt the main structure of lignocellulose. Recently, new discovery methods have been established to obtain key lignocellulosic enzymes with excellent enzymatic properties. Molecular modification of enzymes to modulate their thermostability, catalytic activity, and substrate specificity has been performed with protein engineering technology. In addition, the enzyme expression has been effectively improved through expression element screening and host modification, as well as fermentation optimization. Immobilization of enzymes, use of surfactants, synergistic degradation, and optimization of reaction conditions have addressed the inefficiency of enzymatic saccharification. In this review, recent advances in key lignocellulosic enzymes are summarized, along with future prospects for the development of super-engineered strains and integrative technologies for enzymatic biomass saccharification.
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Affiliation(s)
- Yangyang Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Weiyan Song
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Xuyue Han
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yachan Wang
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Shengqi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou 214122, China
| | - Quan Zhang
- Dalian Research Institute of Petroleum and Petrochemicals, SINOPEC, Dalian 116000, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Song Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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3
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Promoter regulation and genetic engineering strategies for enhanced cellulase expression in Trichoderma reesei. Microbiol Res 2022; 259:127011. [DOI: 10.1016/j.micres.2022.127011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/18/2023]
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Madhavan A, Arun KB, Sindhu R, Alphonsa Jose A, Pugazhendhi A, Binod P, Sirohi R, Reshmy R, Kumar Awasthi M. Engineering interventions in industrial filamentous fungal cell factories for biomass valorization. BIORESOURCE TECHNOLOGY 2022; 344:126209. [PMID: 34715339 DOI: 10.1016/j.biortech.2021.126209] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 05/15/2023]
Abstract
Filamentous fungi possess versatile capabilities for synthesizing a variety of valuable bio compounds, including enzymes, organic acids and small molecule secondary metabolites. The advancements of genetic and metabolic engineering techniques and the availability of sequenced genomes discovered their potential as expression hosts for recombinant protein production. Remarkably, plant-biomass degrading filamentous fungi show the unique capability to decompose lignocellulose, an extremely recalcitrant biopolymer. The basic biochemical approaches have motivated several industrial processes for lignocellulose biomass valorisation into fermentable sugars and other biochemical for biofuels, biomolecules, and biomaterials. The review gives insight into current trends in engineering filamentous fungi for enzymes, fuels, and chemicals from lignocellulose biomass. This review describes the variety of enzymes and compounds that filamentous fungi produce, engineering of filamentous fungi for biomass valorisation with a special focus on lignocellulolytic enzymes and other bulk chemicals.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India.
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Anju Alphonsa Jose
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | | | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea; Centre for Energy & Environmental Sustainability, Lucknow 226001. Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, PR China
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Mondal S, Halder SK, Mondal KC. Tailoring in fungi for next generation cellulase production with special reference to CRISPR/CAS system. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2021; 2:113-129. [PMID: 38624901 PMCID: PMC8319711 DOI: 10.1007/s43393-021-00045-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022]
Abstract
Cellulose is the utmost plenteous source of biopolymer in our earth, and fungi are the most efficient and ubiquitous organism in degrading the cellulosic biomass by synthesizing cellulases. Tailoring through genetic manipulation has played a substantial role in constructing novel fungal strains towards improved cellulase production of desired traits. However, the traditional methods of genetic manipulation of fungi are time-consuming and tedious. With the availability of the full-genome sequences of several industrially relevant filamentous fungi, CRISPR-CAS (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) technology has come into the focus for the proficient development of manipulated strains of filamentous fungi. This review summarizes the mode of action of cellulases, transcription level regulation for cellulase expression, various traditional strategies of genetic manipulation with CRISPR-CAS technology to develop modified fungal strains for a preferred level of cellulase production, and the futuristic trend in this arena of research.
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Affiliation(s)
- Subhadeep Mondal
- Center for Life Sciences, Vidyasagar University, Midnapore, 721102 West Bengal India
| | - Suman Kumar Halder
- Department of Microbiology, Vidyasagar University, Midnapore, 721102 West Bengal India
| | - Keshab Chandra Mondal
- Department of Microbiology, Vidyasagar University, Midnapore, 721102 West Bengal India
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Yamashita M, Tsujikami M, Murata S, Kobayashi T, Shimizu M, Kato M. Artificial AmyR::XlnR transcription factor induces α-amylase production in response to non-edible xylan-containing hemicellulosic biomass. Enzyme Microb Technol 2021; 145:109762. [PMID: 33750542 DOI: 10.1016/j.enzmictec.2021.109762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/22/2021] [Accepted: 02/04/2021] [Indexed: 12/17/2022]
Abstract
Filamentous fungi belonging to the Aspergillus genus are one of the most favored microorganisms for industrial enzyme production because they can secrete large amounts of proteins into the culture medium. α-Amylase, an enzyme produced by Aspergillus species, is important for food and industrial applications. The production of α-amylase is induced by starch, mainly obtained from the edible biomass; however, the increasing demand for foods is limiting the application of the latter. Therefore, it is expected that using the non-edible biomass, such as rice straw, could improve the competition for industrial application starch containing resources. The transcription factor AmyR activates the transcription of amylolytic enzyme genes, while the transcription factor XlnR activates the transcription of xylanolytic enzyme genes in response to xylose. In this study, we aimed to construct an artificial AmyR::XlnR transcription factor (AXTF) by replacing the DNA-binding domain (1-159 amino acids) of XlnR with that (1-68 aa) of AmyR, which is capable of inducing amylolytic enzyme production in response to xylan-containing hemicellulosic biomass. The chimeric transcription factor AXTF was constructed and expressed using the gapA promoter in the amyR-deficient mutant strain SA1. When the AXTF strain was cultured in the minimal medium containing xylose as the carbon source, the amyB, amyF, agdB, and agdE transcription levels were 41.1-, 11.3-, 37.9-, and 23.7-fold higher, respectively, than those of the wild-type strain. The α-amylase and α-glucosidase activities in the culture supernatant of the AXTF strain grown with xylose for 48 h were 696.6 and 536.1 U/mL, respectively, while these activities were not detected in the culture supernatant of the wild-type and SA1 strains. When rice straw hydrolysate was used as a carbon source, the α-amylase and α-glucosidase activities were 590.2 and 362.7 U/mL, respectively. Thus, we successfully generated an Aspergillus nidulans strain showing amylolytic enzyme production in response to non-edible xylan-containing hemicellulosic biomass by transforming it with the chimeric transcription factor AXTF. Furthermore, the use of genes encoding engineered transcription factors is advantageous because introducing such genes into an industrial Aspergillus strain has similar simultaneous effects on multiple amylase genes controlled by AmyR.
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Affiliation(s)
- Miharu Yamashita
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Masaya Tsujikami
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Shunsuke Murata
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Tetsuo Kobayashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Masashi Kato
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan.
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Molecular engineering to improve lignocellulosic biomass based applications using filamentous fungi. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:73-109. [PMID: 33934853 DOI: 10.1016/bs.aambs.2020.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lignocellulosic biomass is an abundant and renewable resource, and its utilization has become the focus of research and biotechnology applications as a very promising raw material for the production of value-added compounds. Filamentous fungi play an important role in the production of various lignocellulolytic enzymes, while some of them have also been used for the production of important metabolites. However, wild type strains have limited efficiency in enzyme production or metabolic conversion, and therefore many efforts have been made to engineer improved strains. Examples of this are the manipulation of transcriptional regulators and/or promoters of enzyme-encoding genes to increase gene expression, and protein engineering to improve the biochemical characteristics of specific enzymes. This review provides and overview of the applications of filamentous fungi in lignocellulosic biomass based processes and the development and current status of various molecular engineering strategies to improve these processes.
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Hirasawa H, Shioya K, Mori K, Tashiro K, Aburatani S, Shida Y, Kuhara S, Ogasawara W. Cellulase productivity of Trichoderma reesei mutants developed in Japan varies with varying pH conditions. J Biosci Bioeng 2019; 128:264-273. [DOI: 10.1016/j.jbiosc.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 01/08/2023]
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Myco-Degradation of Lignocellulose: An Update on the Reaction Mechanism and Production of Lignocellulolytic Enzymes by Fungi. Fungal Biol 2019. [DOI: 10.1007/978-3-030-23834-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Zhang F, Bunterngsook B, Li JX, Zhao XQ, Champreda V, Liu CG, Bai FW. Regulation and production of lignocellulolytic enzymes from Trichoderma reesei for biofuels production. ADVANCES IN BIOENERGY 2019. [DOI: 10.1016/bs.aibe.2019.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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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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New Genomic Approaches to Enhance Biomass Degradation by the Industrial Fungus Trichoderma reesei. Int J Genomics 2018; 2018:1974151. [PMID: 30345291 PMCID: PMC6174759 DOI: 10.1155/2018/1974151] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/20/2018] [Accepted: 07/29/2018] [Indexed: 11/17/2022] Open
Abstract
The filamentous fungi Trichoderma reesei is one of the most well-studied cellulolytic microorganisms. It is the most important fungus for the industrial production of enzymes to biomass deconstruction being widely used in the biotechnology industry, mainly in the production of biofuels. Here, we performed an analytic review of the holocellulolytic system presented by T. reesei as well as the transcriptional and signaling mechanisms involved with holocellulase expression in this fungus. We also discuss new perspectives about control of secretion and cellulase expression based on RNA-seq and functional characterization data of T. reesei growth in different carbon sources, which comprise glucose, cellulose, sophorose, and sugarcane bagasse.
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