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Salazar-Cerezo S, de Vries RP, Garrigues S. Strategies for the Development of Industrial Fungal Producing Strains. J Fungi (Basel) 2023; 9:834. [PMID: 37623605 PMCID: PMC10455633 DOI: 10.3390/jof9080834] [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: 06/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.
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Affiliation(s)
- Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, VLC, Spain
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Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
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Baldin C, Kühbacher A, Merschak P, Wagener J, Gsaller F. Modular Inducible Multigene Expression System for Filamentous Fungi. Microbiol Spectr 2022; 10:e0367022. [PMID: 36350143 PMCID: PMC9769661 DOI: 10.1128/spectrum.03670-22] [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: 09/11/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Inducible promoters are indispensable elements when considering the possibility to modulate gene expression on demand. Desirable traits of conditional expression systems include their capacity for tight downregulation, high overexpression, and in some instances for fine-tuning, to achieve a desired product's stoichiometry. Although the number of inducible systems is slowly increasing, suitable promoters comprising these features are rare. To date, the concomitant use of multiple regulatable promoter platforms for controlled multigene expression has been poorly explored. This work provides pioneer work in the human pathogenic fungus Aspergillus fumigatus, wherein we investigated different inducible systems, elucidated three candidate promoters, and proved for the first time that up to three systems can be used simultaneously without interfering with each other. Proof of concept was obtained by conditionally expressing three antifungal drug targets within the ergosterol biosynthetic pathway under the control of the xylose-inducible PxylP system, the tetracycline-dependent Tet-On system, and the thiamine-repressible PthiA system. IMPORTANCE In recent years, inducible promoters have gained increasing interest for industrial or laboratory use and have become key instruments for protein expression, synthetic biology, and metabolic engineering. Constitutive, high-expressing promoters can be used to achieve high expression yields; however, the continuous overexpression of specific proteins can lead to an unpredictable metabolic burden. To prevent undesirable effects on the expression host's metabolism, the utilization of tunable systems that allow expression of a gene product on demand is indispensable. Here, we elucidated several excellent tunable promoter systems and verified that each can be independently induced in a single strain to ultimately develop a unique conditional multigene expression system. This highly efficient, modular toolbox has the potential to significantly advance applications in fundamental as well as applied research in which regulatable expression of several genes is a key requirement.
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Affiliation(s)
- Clara Baldin
- Institute of Molecular Biology, Biocenter Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander Kühbacher
- Institute of Molecular Biology, Biocenter Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Petra Merschak
- Institute of Molecular Biology, Biocenter Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Wagener
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Fabio Gsaller
- Institute of Molecular Biology, Biocenter Innsbruck, Medical University of Innsbruck, Innsbruck, Austria
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Markova EA, Shaw RE, Reynolds CR. Prediction of strain engineerings that amplify recombinant protein secretion through the machine learning approach MaLPHAS. ENGINEERING BIOLOGY 2022; 6:82-90. [PMID: 36968340 PMCID: PMC9995161 DOI: 10.1049/enb2.12025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022] Open
Abstract
This article presents a discussion of the process of precision fermentation (PF), describing the history of the space, the expected 70% growth over the next 5 years, various applications of precision fermented products, and the markets available to be disrupted by the technology. A range of prokaryotic and eukaryotic host organisms used for PF are described, with the advantages, disadvantages and applications of each. The process of setting up PF and strain engineering is described, as well as various ways that computational analysis and design techniques can be employed to assist PF engineering. The article then describes the design and implementation of a machine learning method, machine learning predictions having amplified secretion (MaLPHAS) to predict strain engineerings, which optimise the secretion of a recombinant protein. This approach showed an in silico cross-validated R 2 accuracy on the training data of up to 46.6% and in an in vitro test on a Komagataella phaffii strain, identified one gene engineering out of five predicted, which was shown to double the secretion of a heterologous protein and outperform three of the best-known edits from the literature for improving secretion in K. phaffii.
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Khatami SH, Vakili O, Movahedpour A, Ghesmati Z, Ghasemi H, Taheri-Anganeh M. Laccase: Various types and applications. Biotechnol Appl Biochem 2022; 69:2658-2672. [PMID: 34997643 DOI: 10.1002/bab.2313] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/03/2022] [Indexed: 12/27/2022]
Abstract
Laccase belongs to the polyphenol oxidase family and is very important in removing environmental pollutants due to its structural and functional properties. Recently, the ability of laccase to oxidize phenolic and nonphenolic substances has been considered by many researchers. This enzyme's application scope includes a broad range of chemical processes and industrial usages, such as bioremediation, nanobiotechnology, woodworking industries, bleaching of paper pulp, dyeing in the textile industry, biotechnological uses in food industries, biorefining, detoxification from wastewater, production of organic matter from phenolic and amine substrates, and biofuels. Although filamentous fungi produce large amounts of laccase, high-yield industrial-scale production of laccase is still faced with many problems. At present, researchers are trying to increase the efficiency and productivity and reduce the final price of laccase by finding suitable microorganisms and improving the process of production and purification of laccase. This article reviews the introduction of laccase, its properties, production processes, and the effect of various factors on the enzyme's stability and activity, and some of its applications in various industries.
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Affiliation(s)
- Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Zeinab Ghesmati
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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Pang AP, Luo Y, Hu X, Zhang F, Wang H, Gao Y, Durrani S, Li C, Shi X, Wu FG, Li BZ, Lu Z, Lin F. Transmembrane transport process and endoplasmic reticulum function facilitate the role of gene cel1b in cellulase production of Trichoderma reesei. Microb Cell Fact 2022; 21:90. [PMID: 35590356 PMCID: PMC9118834 DOI: 10.1186/s12934-022-01809-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background A total of 11 β-glucosidases are predicted in the genome of Trichoderma reesei, which are of great importance for regulating cellulase biosynthesis. Nevertheless, the relevant function and regulation mechanism of each β-glucosidase remained unknown. Results We evidenced that overexpression of cel1b dramatically decreased cellulase synthesis in T. reesei RUT-C30 both at the protein level and the mRNA level. In contrast, the deletion of cel1b did not noticeably affect cellulase production. Protein CEL1B was identified to be intracellular, being located in vacuole and cell membrane. The overexpression of cel1b reduced the intracellular pNPGase activity and intracellular/extracellular glucose concentration without inducing carbon catabolite repression. On the other hand, RNA-sequencing analysis showed the transmembrane transport process and endoplasmic reticulum function were affected noticeably by overexpressing cel1b. In particular, some important sugar transporters were notably downregulated, leading to a compromised cellular uptake of sugars including glucose and cellobiose. Conclusions Our data suggests that the cellulase inhibition by cel1b overexpression was not due to the β-glucosidase activity, but probably the dysfunction of the cellular transport process (particularly sugar transport) and endoplasmic reticulum (ER). These findings advance the knowledge of regulation mechanism of cellulase synthesis in filamentous fungi, which is the basis for rationally engineering T. reesei strains to improve cellulase production in industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01809-1.
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Affiliation(s)
- Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yongsheng Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Funing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yichen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Chengcheng Li
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaotong Shi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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Strong PJ, Self R, Allikian K, Szewczyk E, Speight R, O'Hara I, Harrison MD. Filamentous fungi for future functional food and feed. Curr Opin Biotechnol 2022; 76:102729. [PMID: 35525176 DOI: 10.1016/j.copbio.2022.102729] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 11/19/2022]
Abstract
In this review, we offer our opinion of current and expected trends regarding the use of mushrooms and mycelia in food and feed. Mushrooms have provided food for millennia and production methods and species diversity have recently expanded. Beyond mushrooms, cultured fungal mycelia are now harvested as a primary product for food. Mushrooms and mycelia provide dietary protein, lipids and fatty acids, vitamins, fibre, and flavour, and can improve the organoleptic properties of processed foods (including meat analogues). Further, they are often key ingredients in nutritional or therapeutic supplements because of diverse specialised metabolites. Mycelia can also improve feed conversion efficiency, gut health, and wellbeing in livestock. New molecular tools, coupled with quality genetic data, are improving production technologies, enabling the synthesis of specialised metabolites, and creating new processing and valorisation opportunities. Production systems for submerged culture are capital intensive, but investment is required considering the scale of the protein market.
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Affiliation(s)
- Peter James Strong
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia.
| | - Rachel Self
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia
| | - Kathrine Allikian
- Nourish Ingredients, Unit 2, 6 Pelle Street, Mitchell, Canberra, Australian Capital Territory 2911, Australia
| | - Edyta Szewczyk
- Bolt Threads, 5858 Horton St, Suite 400, Emeryville, CA 94608, United States
| | - Robert Speight
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Ian O'Hara
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia
| | - Mark D Harrison
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia
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Yan Q, Han L, Liu X, You C, Zhou S, Zhou Z. Development of an auto-inducible expression system by nitrogen sources switching based on the nitrogen catabolite repression regulation. Microb Cell Fact 2022; 21:73. [PMID: 35484589 PMCID: PMC9047365 DOI: 10.1186/s12934-022-01794-5] [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: 02/24/2022] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The construction of protein expression systems is mainly focused on carbon catabolite repression and quorum-sensing systems. However, each of these regulatory modes has an inherent flaw, which is difficult to overcome. Organisms also prioritize using different nitrogen sources, which is called nitrogen catabolite repression. To date, few gene regulatory systems based on nitrogen catabolite repression have been reported. RESULTS In this study, we constructed a nitrogen switching auto-inducible expression system (NSAES) based on nitrogen catabolite regulation and nitrogen utilization in Aspergillus nidulans. The PniaD promoter that is highly induced by nitrate and inhibition by ammonia was used as the promoter. Glucuronidase was the reporter protein. Glucuronidase expression occurred after ammonium was consumed in an ammonium and nitrate compounding medium, achieving stage auto-switching for cell growth and gene expression. This system maintained a balance between cell growth and protein production to maximize stress products. Expressions of glycosylated and secretory proteins were successfully achieved using this auto-inducible system. CONCLUSIONS We described an efficient auto-inducible protein expression system based on nitrogen catabolite regulation. The system could be useful for protein production in the laboratory and industrial applications. Simultaneously, NSAES provides a new auto-inducible expression regulation mode for other filamentous fungi.
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Affiliation(s)
- Qin Yan
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xinyue Liu
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Cuiping You
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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Lübeck M, Lübeck PS. Fungal Cell Factories for Efficient and Sustainable Production of Proteins and Peptides. Microorganisms 2022; 10:microorganisms10040753. [PMID: 35456803 PMCID: PMC9025306 DOI: 10.3390/microorganisms10040753] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 01/12/2023] Open
Abstract
Filamentous fungi are a large and diverse taxonomically group of microorganisms found in all habitats worldwide. They grow as a network of cells called hyphae. Since filamentous fungi live in very diverse habitats, they produce different enzymes to degrade material for their living, for example hydrolytic enzymes to degrade various kinds of biomasses. Moreover, they produce defense proteins (antimicrobial peptides) and proteins for attaching surfaces (hydrophobins). Many of them are easy to cultivate in different known setups (submerged fermentation and solid-state fermentation) and their secretion of proteins and enzymes are often much larger than what is seen from yeast and bacteria. Therefore, filamentous fungi are in many industries the preferred production hosts of different proteins and enzymes. Edible fungi have traditionally been used as food, such as mushrooms or in fermented foods. New trends are to use edible fungi to produce myco-protein enriched foods. This review gives an overview of the different kinds of proteins, enzymes, and peptides produced by the most well-known fungi used as cell factories for different purposes and applications. Moreover, we describe some of the challenges that are important to consider when filamentous fungi are optimized as efficient cell factories.
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Naeem M, Manzoor S, Abid MUH, Tareen MBK, Asad M, Mushtaq S, Ehsan N, Amna D, Xu B, Hazafa A. Fungal Proteases as Emerging Biocatalysts to Meet the Current Challenges and Recent Developments in Biomedical Therapies: An Updated Review. J Fungi (Basel) 2022; 8:jof8020109. [PMID: 35205863 PMCID: PMC8875690 DOI: 10.3390/jof8020109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 02/07/2023] Open
Abstract
With the increasing world population, demand for industrialization has also increased to fulfill humans' living standards. Fungi are considered a source of essential constituents to produce the biocatalytic enzymes, including amylases, proteases, lipases, and cellulases that contain broad-spectrum industrial and emerging applications. The present review discussed the origin, nature, mechanism of action, emerging aspects of genetic engineering for designing novel proteases, genome editing of fungal strains through CRISPR technology, present challenges and future recommendations of fungal proteases. The emerging evidence revealed that fungal proteases show a protective role to many environmental exposures and discovered that an imbalance of protease inhibitors and proteases in the epithelial barriers leads to the protection of chronic eosinophilic airway inflammation. Moreover, mitoproteases recently were found to execute intense proteolytic processes that are crucial for mitochondrial integrity and homeostasis function, including mitochondrial biogenesis, protein synthesis, and apoptosis. The emerging evidence revealed that CRISPR/Cas9 technology had been successfully developed in various filamentous fungi and higher fungi for editing of specific genes. In addition to medical importance, fungal proteases are extensively used in different industries such as foods to prepare butter, fruits, juices, and cheese, and to increase their shelf life. It is concluded that hydrolysis of proteins in industries is one of the most significant applications of fungal enzymes that led to massive usage of proteomics.
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Affiliation(s)
- Muhammad Naeem
- College of Life Science, Hebei Normal University, Shijiazhuang 050025, China;
| | - Saba Manzoor
- Department of Zoology, University of Sialkot, Sialkot 51310, Pakistan;
| | | | | | - Mirza Asad
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Sajida Mushtaq
- Department of Zoology, Government College Women University, Sialkot 51040, Pakistan;
| | - Nazia Ehsan
- Department of Zoology, Wildlife and Fisheries, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Dua Amna
- Institute of Food Science & Nutrition, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Baojun Xu
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University (BNU-HKBU) United International College, Zhuhai 519087, China
- Correspondence: (B.X.); (A.H.)
| | - Abu Hazafa
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
- Correspondence: (B.X.); (A.H.)
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11
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Chai S, Zhu Z, Tian E, Xiao M, Wang Y, Zou G, Zhou Z. Building a Versatile Protein Production Platform Using Engineered Trichoderma reesei. ACS Synth Biol 2022; 11:486-496. [PMID: 34928572 DOI: 10.1021/acssynbio.1c00570] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trichoderma reesei has an extremely high capacity for synthesizing and secreting proteins, thus exhibiting promise as an expression platform for heterologous proteins. However, T. reesei secretes large amounts of native proteins, which hinders its widespread application for heterologous protein production. Here, we designed and built a series of T. reesei chassis using an iterative gene deletion approach based on an efficient genome editing system. Donor DNAs with specially designed construct facilitated screening of positive deletion strains without ectopic insertion. Finally, marker-free T. reesei chassis with lower rates of native protein secretion and low levels of extracellular protease activity were constructed after 11 consecutive rounds of gene deletion. Higher production levels of three heterologous proteins─a bacterial xylanase XYL7, a fungal immunomodulatory protein LZ8, and the human serum albumin HSA─were achieved with these chassis using the cbh1 promoter. It is possible that diverse high-value proteins might be produced at a high yield using this engineered platform.
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Affiliation(s)
- 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, 19(A) Yuquan Rd, Beijing 100049, China
| | - 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, 19(A) Yuquan Rd, Beijing 100049, China
| | - Ernuo Tian
- 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
| | - 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, 19(A) Yuquan Rd, Beijing 100049, China
| | - Yan 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
| | - 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 Sciences, 1000 Jinqi Rd, Shanghai 201403, 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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Sun Y, Qian Y, Zhang J, Yao C, Wang Y, Liu H, Zhong Y. Development of a novel expression platform for heterologous protein production via deleting the p53-like regulator Vib1 in Trichoderma reesei. Enzyme Microb Technol 2022; 155:109993. [DOI: 10.1016/j.enzmictec.2022.109993] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/03/2022] [Accepted: 01/11/2022] [Indexed: 02/06/2023]
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Li X, Dilokpimol A, Kabel MA, de Vries RP. Fungal xylanolytic enzymes: Diversity and applications. BIORESOURCE TECHNOLOGY 2022; 344:126290. [PMID: 34748977 DOI: 10.1016/j.biortech.2021.126290] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 05/26/2023]
Abstract
As important polysaccharide degraders in nature, fungi can diversify their extensive set of carbohydrate-active enzymes to survive in ecological habitats of various composition. Among these enzymes, xylanolytic ones can efficiently and sustainably degrade xylans into (fermentable) monosaccharides to produce valuable chemicals or fuels from, for example relevant for upgrading agro-food industrial side streams. Moreover, xylanolytic enzymes are being used in various industrial applications beyond biomass saccharification, e.g. food, animal feed, biofuel, pulp and paper. As a reference for researchers working in related areas, this review summarized the current knowledge on substrate specificity of xylanolytic enzymes from different families of the Carbohydrate-Active enZyme database. Additionally, the diversity of enzyme sets in fungi were discussed by comparing the number of genes encoding xylanolytic enzymes in selected fungal genomes. Finally, to support bio-economy, the current applications of fungal xylanolytic enzymes in industry were reviewed.
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Affiliation(s)
- Xinxin Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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14
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Kislitsin VY, Chulkin AM, Zorov IN, Shashkov IA, Satrutdinov AD, Sinitsyn AP, Rozhkova AM. Influence of Mono- and Oligosaccharides on cbh1 Gene Transcription in the Filamentous Fungus Penicillium verruculosum. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821090040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Sinitsyn AP, Sinitsyna OA, Rozhkova AM. Production of Industrial Enzymes Based on the Expression System of the Fungus Penicillium verruculosum. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821080068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Mittermair S, Lakatos G, Nicoletti C, Ranglová K, Manoel JC, Grivalský T, Kozhan DM, Masojídek J, Richter J. Impact of glgA1, glgA2 or glgC overexpression on growth and glycogen production in Synechocystis sp. PCC 6803. J Biotechnol 2021; 340:47-56. [PMID: 34481001 DOI: 10.1016/j.jbiotec.2021.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Low production rates are still one limiting factor for the industrial climate-neutral production of biovaluable compounds in cyanobacteria. Next to optimized cultivation conditions, new production strategies are required. Hence, the use of established molecular tools could lead to increased product yields in the cyanobacterial model organism Synechocystis sp. PCC6803. Its main storage compound glycogen was chosen to be increased by the use of these tools. In this study, the three genes glgC, glgA1 and glgA2, which are part of the glycogen synthesis pathway, were combined with the Pcpc560 promoter and the neutral cloning site NSC1. The complete genome integration, protein formation, biomass production and glycogen accumulation were determined to select the most productive transformants. The overexpression of glgA2 did not increase the biomass or glycogen production in short-term trials compared to the other two genes but caused transformants death in long-term trials. The transformants glgA1_11 and glgC_2 showed significantly increased biomass (1.6-fold - 1.7-fold) and glycogen production (3.5-fold - 4-fold) compared to the wild type after 96 h making them a promising energy source for further applications. Those could include for example a two-stage production process, with first energy production (glycogen) and second increased product formation (e.g. ethanol).
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Affiliation(s)
- Sandra Mittermair
- Department of Biology and Chemistry, AG Biosciences, University of Applied Sciences Upper Austria, Roseggerstraße 15, 4600 Wels, Austria
| | - Gergely Lakatos
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Cecilia Nicoletti
- Department of Biology and Chemistry, AG Biosciences, University of Applied Sciences Upper Austria, Roseggerstraße 15, 4600 Wels, Austria
| | - Karolína Ranglová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - João Câmara Manoel
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Tomáš Grivalský
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Daniyar Malikuly Kozhan
- Al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, 71 Al-Farabi Ave., Almaty 050040, Kazakhstan
| | - Jiří Masojídek
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Juliane Richter
- Department of Biology and Chemistry, AG Biosciences, University of Applied Sciences Upper Austria, Roseggerstraße 15, 4600 Wels, Austria.
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17
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Miao Y, Xia Y, Kong Y, Zhu H, Mei H, Li P, Feng H, Xun W, Xu Z, Zhang N, Liu D, Shen Q, Zhang R. Overcoming diverse homologous recombinations and single chimeric guide RNA competitive inhibition enhances Cas9-based cyclical multiple genes coediting in filamentous fungi. Environ Microbiol 2021; 23:2937-2954. [PMID: 33754479 DOI: 10.1111/1462-2920.15477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/18/2021] [Indexed: 12/26/2022]
Abstract
Deciphering the complex cellular behaviours and advancing the biotechnology applications of filamentous fungi increase the requirement for genetically manipulating a large number of target genes. The current strategies cannot cyclically coedit multiple genes simultaneously. In this study, we firstly revealed the existence of diverse homologous recombination (HR) types in marker-free editing of filamentous fungi, and then, demonstrated that sgRNA efficiency-mediated competitive inhibition resulted in the low integration of multiple genetic sites during coediting, which are the two major obstacles to limit the efficiency of cyclically coediting of multiple genes. To overcome these obstacles, we developed a biased cutting strategy by Cas9 to greatly enhance the desired HR type and applied a new selection marker labelling strategy for multiple donor DNAs, in which only the donor DNA with the lowest sgRNA efficiency was labelled. Combined with these strategies, we successfully developed a convenient method for cyclically coediting multiple genes in different filamentous fungi. In addition, diverse HRs resulted in a useful and convenient one-step approach for gene functional study combining both gene disruption and complementation. This research provided both a useful one-step approach for gene functional study and an efficient strategy for cyclically coediting multiple genes in filamentous fungi.
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Affiliation(s)
- Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanwei Xia
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanqiong Kong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Han Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huiling Mei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pan Li
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haichao Feng
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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18
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Accelerated glucose metabolism in hyphae-dispersed Aspergillus oryzae is suitable for biological production. J Biosci Bioeng 2021; 132:140-147. [PMID: 33896702 DOI: 10.1016/j.jbiosc.2021.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/28/2021] [Accepted: 03/28/2021] [Indexed: 11/23/2022]
Abstract
Recently, a hyphae-dispersed type of filamentous fungus Aspergillus oryzae was constructed via genetic engineering, and industrial applications are expected due to the ease of handling and to the level of protein production properties. In this study, we constructed cellulase-expressing strains using wild-type and hyphae-dispersed strains to investigate the correlation between protein productivity and metabolism. Compared with the original strain, the hyphae-dispersed cellulase-expressing strain showed elevated cellulase activity, rapid glucose consumption, increased mycelial dry weight, an increased expression of cellulase genes, and activated respiration activity. Comparative metabolomic analysis showed fewer metabolites in the glycolysis and TCA cycles in the dispersed strains than in the original strains. These results indicate that the flux of carbohydrate metabolism in the hyphae-dispersed strains is smoother than that in the original strains. Such efficient metabolic flux would contribute to efficient energy conversion and to sufficient energy supply to anabolisms, such as mycelial growth and protein production. Our findings suggest that the hyphae-dispersed strains could be a useful host not only for protein production but also for the biological production of various chemicals such as organic acids.
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19
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20
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Sun Y, Qian Y, Zhang J, Wang Y, Li X, Zhang W, Wang L, Liu H, Zhong Y. Extracellular protease production regulated by nitrogen and carbon sources in Trichoderma reesei. J Basic Microbiol 2021; 61:122-132. [PMID: 33393718 DOI: 10.1002/jobm.202000566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/25/2020] [Accepted: 12/18/2020] [Indexed: 11/07/2022]
Abstract
The filamentous fungus Trichoderma reesei is an important producer of industrial enzymes, and possesses abundant extracellular protease genes based on the genome sequence data. However, the production of extracellular proteases remains poorly understood. Here, protease production was extensively investigated on different carbon (glucose and lactose) and nitrogen sources ((NH4 )2 SO4 , NaNO3 , peptone, and corn steep liquor). It was found that protease production was dominantly regulated by nitrogen sources. Organic nitrogen sources were beneficial for protease production, while the preferred nitrogen source (NH4 )2 SO4 inhibited the expression of proteases. As for carbon sources, lactose was a more effective inducer than glucose for protease production. The protease activity was further examined by protease inhibitors, which suggested that protease activity was predominantly inhibited by phenylmethanesulfonyl fluoride (PMSF) and slightly suppressed by ethylenediaminetetraacetic acid (EDTA). Moreover, proteomic analysis revealed a total of 29 extracellular proteases, including 13 serine proteases, 6 aspartic proteases, and 10 metalloproteases. In addition, seven proteases were found to be present among all conditions. These results showed the regulatory profile of extracellular protease production in Trichoderma reesei grown on various carbon and nitrogen sources, which will facilitate the development of T. reesei to be an effective workhorse for enzyme or high-value protein production in industry.
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Affiliation(s)
- Yu Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Yuanchao Qian
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Jiaxin Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Yifan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Xihai Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Hong Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
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21
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Veerana M, Mitra S, Ki S, Kim S, Choi E, Lee T, Park G. Plasma-mediated enhancement of enzyme secretion in Aspergillus oryzae. Microb Biotechnol 2021; 14:262-276. [PMID: 33151631 PMCID: PMC7888467 DOI: 10.1111/1751-7915.13696] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/08/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
Technical bottlenecks in protein production and secretion often limit the efficient and robust industrial use of microbial enzymes. The potential of non-thermal atmospheric pressure plasma to overcome these technical barriers was examined. Spores of the fermenting fungus Aspergillus oryzae (A. oryzae) were submerged in potato dextrose broth (PDB) (5 × 106 per ml) and treated with micro dielectric barrier discharge plasma at an input voltage of 1.2 kV and current of 50 to 63 mA using nitrogen as the feed gas. The specific activity of α-amylase in the broth was increased by 7.4 to 9.3% after 24 and 48 h of plasma treatment. Long-lived species, such as NO2 - and NO3 - , generated in PDB after plasma treatment may have contributed to the elevated secretion of α-amylase. Observations after 24 h of plasma treatment also included increased accumulation of vesicles at the hyphal tip, hyphal membrane depolarization and higher intracellular Ca2+ levels. These results suggest that long-lived nitrogen species generated in PDB after plasma treatment can enhance the secretion of α-amylase from fungal hyphae by depolarizing the cell membrane and activating Ca2+ influx into hyphal cells, eventually leading to the accumulation of secretory vesicles near the hyphal tips.
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Affiliation(s)
- Mayura Veerana
- Department of Plasma Bioscience and DisplayKwangwoon UniversitySeoul01897Korea
| | - Sarmistha Mitra
- Department of Plasma Bioscience and DisplayKwangwoon UniversitySeoul01897Korea
| | - Se‐Hoon Ki
- Department of Electrical and Biological PhysicsKwangwoon UniversitySeoul01897Korea
| | - Soo‐Min Kim
- Department of Chemical EngineeringKwangwoon UniversitySeoul01897Korea
| | - Eun‐Ha Choi
- Department of Plasma Bioscience and DisplayKwangwoon UniversitySeoul01897Korea
- Department of Electrical and Biological PhysicsKwangwoon UniversitySeoul01897Korea
| | - Taek Lee
- Department of Chemical EngineeringKwangwoon UniversitySeoul01897Korea
| | - Gyungsoon Park
- Department of Plasma Bioscience and DisplayKwangwoon UniversitySeoul01897Korea
- Department of Electrical and Biological PhysicsKwangwoon UniversitySeoul01897Korea
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22
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Afzal I, Sabir A, Sikandar S. Trichoderma: Biodiversity, Abundances, and Biotechnological Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Suhaimi H, Dailin DJ, Malek RA, Hanapi SZ, Ambehabati KK, Keat HC, Prakasham S, Elsayed EA, Misson M, El Enshasy H. Fungal Pectinases: Production and Applications in Food Industries. Fungal Biol 2021. [DOI: 10.1007/978-3-030-64406-2_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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24
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Mass Transfer and Rheological Characteristics in a Stirred Tank Bioreactor for Cultivation of Escherichia coli BL21. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0028-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Monclaro AV, Petrović DM, Alves GSC, Costa MMC, Midorikawa GEO, Miller RNG, Filho EXF, Eijsink VGH, Várnai A. Characterization of two family AA9 LPMOs from Aspergillus tamarii with distinct activities on xyloglucan reveals structural differences linked to cleavage specificity. PLoS One 2020; 15:e0235642. [PMID: 32640001 PMCID: PMC7343150 DOI: 10.1371/journal.pone.0235642] [Citation(s) in RCA: 20] [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: 03/28/2020] [Accepted: 06/19/2020] [Indexed: 11/23/2022] Open
Abstract
Aspergillus tamarii grows abundantly in naturally composting waste fibers of the textile industry and has a great potential in biomass decomposition. Amongst the key (hemi)cellulose-active enzymes in the secretomes of biomass-degrading fungi are the lytic polysaccharide monooxygenases (LPMOs). By catalyzing oxidative cleavage of glycoside bonds, LPMOs promote the activity of other lignocellulose-degrading enzymes. Here, we analyzed the catalytic potential of two of the seven AA9-type LPMOs that were detected in recently published transcriptome data for A. tamarii, namely AtAA9A and AtAA9B. Analysis of products generated from cellulose revealed that AtAA9A is a C4-oxidizing enzyme, whereas AtAA9B yielded a mixture of C1- and C4-oxidized products. AtAA9A was also active on cellopentaose and cellohexaose. Both enzymes also cleaved the β-(1→4)-glucan backbone of tamarind xyloglucan, but with different cleavage patterns. AtAA9A cleaved the xyloglucan backbone only next to unsubstituted glucosyl units, whereas AtAA9B yielded product profiles indicating that it can cleave the xyloglucan backbone irrespective of substitutions. Building on these new results and on the expanding catalog of xyloglucan- and oligosaccharide-active AA9 LPMOs, we discuss possible structural properties that could underlie the observed functional differences. The results corroborate evidence that filamentous fungi have evolved AA9 LPMOs with distinct substrate specificities and regioselectivities, which likely have complementary functions during biomass degradation.
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Affiliation(s)
- Antonielle V. Monclaro
- Laboratory of Enzymology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Dejan M. Petrović
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gabriel S. C. Alves
- Laboratory of Microbiology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Marcos M. C. Costa
- Brazilian Agricultural Research Corporation, Embrapa CENARGEN, Brasília, Brazil
| | - Glaucia E. O. Midorikawa
- Laboratory of Microbiology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Robert N. G. Miller
- Laboratory of Microbiology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Edivaldo X. F. Filho
- Laboratory of Enzymology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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26
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Liu E, Li M, Abdella A, Wilkins MR. Development of a cost-effective medium for submerged production of fungal aryl alcohol oxidase using a genetically modified Aspergillus nidulans strain. BIORESOURCE TECHNOLOGY 2020; 305:123038. [PMID: 32120232 DOI: 10.1016/j.biortech.2020.123038] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/13/2020] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
Aryl alcohol oxidase (AAO), an extracellular H2O2-providing enzyme, plays a central role in lignin depolymerization. Cost-effective production of AAO has not been achieved, due to the low yield of enzyme-producing microorganisms and the high cost of fermentation media. This study aims to develop a cost-effective medium for high-yield production of AAO in submerged culture using a recombinant Aspergillus nidulans strain. Results demonstrate that corn steep liquor (CSL) was a rich but inexpensive nitrogen source for AAO production, and CSL can provide enough trace metals and vitamins (i.e. pyridoxine) for A. nidulans. A 2-level Plackett-Burman design was utilized to determine the main affecting factors in AAO production. The medium was further optimized by a 3-level Box-Behnken design to obtain the optimum medium component concentrations (61.0 g/L maltose, 26.4 g/L CSL, and 13.8 g/L NaNO3). The greatest AAO activity achieved was 1021 U/L with a protein concentration of 0.75 g/L.
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Affiliation(s)
- Enshi Liu
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Mengxing Li
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Asmaa Abdella
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 22857, Egypt; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Mark R Wilkins
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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27
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Stolarczyk K, Rogalski J, Bilewicz R. NAD(P)-dependent glucose dehydrogenase: Applications for biosensors, bioelectrodes, and biofuel cells. Bioelectrochemistry 2020; 135:107574. [PMID: 32498025 DOI: 10.1016/j.bioelechem.2020.107574] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022]
Abstract
This review discusses the physical and chemical properties of nicotinamide redox cofactor dependent glucose dehydrogenase (NAD(P) dependent GDH) and its extensive application in biosensors and bio-fuel cells. GDHs from different organisms show diverse biochemical properties (e.g., activity and stability) and preferences towards cofactors, such as nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+). The (NAD(P)+) play important roles in biological electron transfer, however, there are some difficulties related to their application in devices that originate from their chemical properties and labile binding to the GDH enzyme. This review discusses the electrode modifications aimed at immobilising NAD+ or NADP+ cofactors and GDH at electrodes. Binding of the enzyme was achieved by appropriate protein engineering techniques, including polymerisation, hydrophobisation or hydrophilisation processes. Various enzyme-modified electrodes applied in biosensors, enzymatic fuel cells, and biobatteries are compared. Importantly, GDH can operate alone or as part of an enzymatic cascade, which often improves the functional parameters of the biofuel cell or simply allows use of cheaper fuels. Overall, this review explores how NAD(P)-dependent GDH has recently demonstrated high potential for use in various systems to generate electricity from biological sources for applications in implantable biomedical devices, wireless sensors, and portable electronic devices.
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Affiliation(s)
- Krzysztof Stolarczyk
- Faculty of Chemistry, University of Warsaw, Pasteura St. 1, 02-093 Warsaw, Poland
| | - Jerzy Rogalski
- Department of Biochemistry and Biotechnology, Maria Curie-Sklodowska University, Akademicka Str. 19, 20-031 Lublin, Poland
| | - Renata Bilewicz
- Faculty of Chemistry, University of Warsaw, Pasteura St. 1, 02-093 Warsaw, Poland.
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28
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Claes A, Deparis Q, Foulquié-Moreno MR, Thevelein JM. Simultaneous secretion of seven lignocellulolytic enzymes by an industrial second-generation yeast strain enables efficient ethanol production from multiple polymeric substrates. Metab Eng 2020; 59:131-141. [DOI: 10.1016/j.ymben.2020.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/01/2020] [Accepted: 02/18/2020] [Indexed: 01/22/2023]
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Wang Q, Zhong C, Xiao H. Genetic Engineering of Filamentous Fungi for Efficient Protein Expression and Secretion. Front Bioeng Biotechnol 2020; 8:293. [PMID: 32322579 PMCID: PMC7156587 DOI: 10.3389/fbioe.2020.00293] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/19/2020] [Indexed: 02/05/2023] Open
Abstract
Filamentous fungi are considered as unique cell factories for protein production due to the high efficiency of protein secretion and superior capability of post-translational modifications. In this review, we firstly introduce the secretory pathway in filamentous fungi. We next summarize the current state-of-the-art works regarding how various genetic engineering strategies are applied for enhancing protein expression and secretion in filamentous fungi. Finally, in a future perspective, we discuss the great potential of genome engineering for further improving protein expression and secretion in filamentous fungi.
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Affiliation(s)
- Qin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and Laboratory of Molecular Biochemical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Zhong
- Materials and Physical Biology Division, School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
- Materials Synthetic Biology Center, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Han Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and Laboratory of Molecular Biochemical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Filkin SY, Lipkin AV, Fedorov AN. Phospholipase Superfamily: Structure, Functions, and Biotechnological Applications. BIOCHEMISTRY (MOSCOW) 2020; 85:S177-S195. [DOI: 10.1134/s0006297920140096] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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CRISPR/Cas9 technology enables the development of the filamentous ascomycete fungus Penicillium subrubescens as a new industrial enzyme producer. Enzyme Microb Technol 2020; 133:109463. [DOI: 10.1016/j.enzmictec.2019.109463] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/08/2019] [Accepted: 11/01/2019] [Indexed: 12/21/2022]
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Ki MR, Pack SP. Fusion tags to enhance heterologous protein expression. Appl Microbiol Biotechnol 2020; 104:2411-2425. [DOI: 10.1007/s00253-020-10402-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022]
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Gopalakrishnan RM, Manavalan T, Ramesh J, Thangavelu KP, Heese K. Improvement of Saccharification and Delignification Efficiency of Trichoderma reesei Rut-C30 by Genetic Bioengineering. Microorganisms 2020; 8:microorganisms8020159. [PMID: 31979278 PMCID: PMC7074786 DOI: 10.3390/microorganisms8020159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 11/16/2022] Open
Abstract
Trichoderma reesei produces various saccharification enzymes required for biomass degradation. However, the lack of an effective lignin-degrading enzyme system reduces the species’ efficiency in producing fermentable sugars and increases the pre-treatment costs for biofuel production. In this study, we heterologously expressed the Ganoderma lucidum RMK1 versatile peroxidase gene (vp1) in the Rut-C30 strain of T. reesei. The expression of purified 6×His-tag–containing recombinant G. lucidum-derived protein (rVP1) was confirmed through western blot, which exhibited a single band with a relative molecular weight of 39 kDa. In saccharification and delignification studies using rice straw, the transformant (tVP7, T. reesei Rut-C30 expressing G. lucidum-derived rVP1) showed significant improvement in the yield of total reducing sugar and delignification, compared with that of the parent T. reesei Rut-C30 strain. Scanning electron microscopy (SEM) of tVP7-treated paddy straw showed extensive degradation of several layers of its surface compared with the parent strain due to the presence of G. lucidum-derived rVP1. Our results suggest that the expression of ligninolytic enzymes in cellulase hyperproducing systems helps to integrate the pre-treatment and saccharification steps that may ultimately reduce the costs of bioethanol production.
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Affiliation(s)
- Raja Mohan Gopalakrishnan
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India; (R.M.G.); (T.M.)
| | - Tamilvendan Manavalan
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India; (R.M.G.); (T.M.)
| | - Janani Ramesh
- Department of Medical Biochemistry, Dr ALM Postgraduate Institute of Biomedical Sciences, University of Madras, Chennai, Tamil Nadu 600 113, India;
| | - Kalaichelvan Puthupalayam Thangavelu
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India; (R.M.G.); (T.M.)
- Correspondence: (K.P.T.); (K.H.)
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea
- Correspondence: (K.P.T.); (K.H.)
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Rathnayake AU, Saravanakumar K, Abuine R, Abeywickrema S, Kathiresan K, MubarakAli D, Gupta VK, Wang MH. Fungal Genes Encoding Enzymes Used in Cheese Production and Fermentation Industries. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Improving expression of thermostable trehalase from Myceliophthora sepedonium in Aspergillus niger mediated by the CRISPR/Cas9 tool and its purification, characterization. Protein Expr Purif 2020; 165:105482. [DOI: 10.1016/j.pep.2019.105482] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/21/2019] [Accepted: 08/21/2019] [Indexed: 12/30/2022]
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Martínez-Espinosa RM. Heterologous and Homologous Expression of Proteins from Haloarchaea: Denitrification as Case of Study. Int J Mol Sci 2019; 21:E82. [PMID: 31877629 PMCID: PMC6981372 DOI: 10.3390/ijms21010082] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/05/2019] [Accepted: 12/18/2019] [Indexed: 12/23/2022] Open
Abstract
Haloarchaea (halophilic microbes belonging to the Archaea domain) are microorganisms requiring mid or even high salt concentrations to be alive. The molecular machinery of these organisms is adapted to such conditions, which are stressful for most life forms. Among their molecular adaptations, halophilic proteins are characterized by their high content of acidic amino acids (Aspartate (Asp) and glumate (Glu)), being only stable in solutions containing high salt concentration (between 1 and 4 M total salt concentration). Recent knowledge about haloarchaeal peptides, proteins, and enzymes have revealed that many haloarchaeal species produce proteins of interest due to their potential applications in biotechnology-based industries. Although proteins of interest are usually overproduced in recombinant prokaryotic or eukaryotic expression systems, these procedures do not accurately work for halophilic proteins, mainly if such proteins contain metallocofactors in their structures. This work summarizes the main challenges of heterologous and homologous expression of enzymes from haloarchaea, paying special attention to the metalloenzymes involved in the pathway of denitrification (anaerobic reduction of nitrate to dinitrogen), a pathway with significant implications in wastewater treatment, climate change, and biosensor design.
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Affiliation(s)
- Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences and Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Ap. 99, E-03080 Alicante, Spain
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Ballmann P, Lightfoot J, Müller M, Dröge S, Prade R. Redesigning the Aspergillus nidulans xylanase regulatory pathway to enhance cellulase production with xylose as the carbon and inducer source. Microb Cell Fact 2019; 18:193. [PMID: 31699093 PMCID: PMC6839167 DOI: 10.1186/s12934-019-1243-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/24/2019] [Indexed: 11/10/2022] Open
Abstract
Background Biomass contains cellulose (C6-sugars), hemicellulose (C5-sugars) and lignin. Biomass ranks amongst the most abundant hydrocarbon resources on earth. However, biomass is recalcitrant to enzymatic digestion by cellulases. Physicochemical pretreatment methods make cellulose accessible but partially destroy hemicellulose, producing a C5-sugar-rich liquor. Typically, digestion of pretreated LCB is performed with commercial cellulase preparations, but C5-sugars could in principle be used for “on site” production of cellulases by genetically engineered microorganism, thereby reducing costs. Results Here we report a succession of genetic interventions in Aspergillus nidulans that redesign the natural regulatory circuitry of cellulase genes in such a way that recombinant strains use C5-sugar liquors (xylose) to grow a vegetative tissue and simultaneously accumulate large amounts of cellulases. Overexpression of XlnR showed that under xylose-induction conditions only xylanase C was produced. XlnR overexpression strains were constructed that use the xynCp promoter to drive the production of cellobiohydrolases, endoglucanases and β-glucosidase. All five cellulases accumulated at high levels when grown on xylose. Production of cellulases in the presence of pretreated-biomass C5-sugar liquors was investigated, and cellulases accumulated to much higher enzyme titers than those obtained for traditional fungal cell factories with cellulase-inducing substrates. Conclusions By replacing expensive substrates with a cheap by-product carbon source, the use of C5-sugar liquors directly derived from LCB pretreatment processes not only reduces enzyme production costs, but also lowers operational costs by eliminating the need for off-site enzyme production, purification, concentration, transport and dilution.
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Affiliation(s)
- Patrick Ballmann
- Prüf- und Forschungsinstitut Pirmasens e.V., Marie-Curie-Strasse 19, 66953, Pirmasens, Germany
| | - Jorge Lightfoot
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Michael Müller
- Prüf- und Forschungsinstitut Pirmasens e.V., Marie-Curie-Strasse 19, 66953, Pirmasens, Germany
| | - Stephan Dröge
- Prüf- und Forschungsinstitut Pirmasens e.V., Marie-Curie-Strasse 19, 66953, Pirmasens, Germany
| | - Rolf Prade
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA.
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Fitz E, Gamauf C, Seiboth B, Wanka F. Deletion of the small GTPase rac1 in Trichoderma reesei provokes hyperbranching and impacts growth and cellulase production. Fungal Biol Biotechnol 2019; 6:16. [PMID: 31641527 PMCID: PMC6798449 DOI: 10.1186/s40694-019-0078-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/03/2019] [Indexed: 11/21/2022] Open
Abstract
Background Trichoderma reesei is widely known for its enormous protein secretion capacity and as an industrially relevant producer of cellulases and hemicellulases. Over the last decades, rational strain engineering was applied to further enhance homologous and heterologous enzyme yields. The introduction of hyperbranching is believed to increase protein secretion, since most exocytosis is located at the hyphal apical tip. There are several genetic modifications which can cause hyperbranching, for example the deletion of the small Rho GTPase rac. Rac plays a crucial role in actin dynamics and is involved in polarisation of the cell during germination and apical extension of the hyphae. Results We deleted rac1 in a T. reesei strain with an ectopically overexpressed endoglucanase, CEL12A, under Pcdna1 control. This deletion provoked a hyperbranching phenotype and strong apolar growth during germination and in mature hyphae. The strains displayed dichotomous branching and shorter total mycelium length with a larger hyphal diameter. Δrac1 strains exhibited a decreased radial growth on solid media. Biomass formation in liquid cultures was carbon source dependent; similar to the reference strain during growth on lactose, increased on d-glucose and slightly enhanced on cellulose. While extracellular cellulase activities remained at parental strain levels on d-glucose and cellulose, the specific activity on lactose cultures was increased up to three times at 72 h accompanied by an upregulation of transcription of the main cellulases. Although the morphology of the Δrac1 strains was considerably altered, the viscosity of the culture broth in fed-batch cultivations were not significantly different in comparison to the parental strain. Conclusions Deletion of the small Rho GTPase rac1 changes the morphology of the hyphae and provokes hyperbranching without affecting viscosity, independent of the carbon source. In contrast, biomass formation and cellulase production are altered in a carbon source dependent manner in the Δrac1 strains.
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Affiliation(s)
- Elisabeth Fitz
- 1Research Division Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering, TU Wien, Vienna, Austria.,2Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Research Division Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Gamauf
- 3Group Biotechnology, Clariant Produkte (Deutschland) GmbH, Planegg, Germany
| | - Bernhard Seiboth
- 1Research Division Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering, TU Wien, Vienna, Austria.,2Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Research Division Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering, TU Wien, Vienna, Austria
| | - Franziska Wanka
- 2Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Research Division Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering, TU Wien, Vienna, Austria
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Tesche S, Rösemeier-Scheumann R, Lohr J, Hanke R, Büchs J, Krull R. Salt-enhanced cultivation as a morphology engineering tool for filamentous actinomycetes: Increased production of labyrinthopeptin A1 in Actinomadura namibiensis. Eng Life Sci 2019; 19:781-794. [PMID: 32624971 DOI: 10.1002/elsc.201900036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/03/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022] Open
Abstract
Salt-enhanced cultivation as a morphology engineering tool for the filamentous actinomycete Actinomadura namibiensis was evaluated in 500-mL shaking flasks (working volume 100 mL) with the aim of increasing the concentration of the pharmaceutically interesting peptide labyrinthopeptin A1. Among the inorganic salts added to a complex production medium, the addition of (NH4)2SO4 led to the highest amount of labyrinthopeptin A1 production. By using 50 mM (NH4)2SO4, the labyrinthopeptin A1 concentration increased up to sevenfold compared to the non-supplemented control, resulting in 325 mg L-1 labyrinthopeptin A1 after 10 days of cultivation. The performance of other ammonium- and sulfate-containing salts (e.g., NH4Cl, K2SO4) was much lower than the performance of (NH4)2SO4. A positive correlation between the uptake of glycerol as one of the main carbon sources and nongrowth-associated labyrinthopeptin productivity was found. The change in the cell morphology of A. namibiensis in conjunction with increased osmolality by the addition of 50 mM (NH4)2SO4, was quantified by image analysis. A. namibiensis always developed a heterogeneous morphology with pellets and loose mycelia present simultaneously. In contrast to the non-supplemented control, the morphology of (NH4)2SO4-supplemented cultures was characterized by smaller and circular pellets that were more stable against disintegration in the stationary production phase.
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Affiliation(s)
- Sebastian Tesche
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
| | - René Rösemeier-Scheumann
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
| | - Jonas Lohr
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
| | - René Hanke
- AVT - Chair of Biochemical Engineering RWTH Aachen University Aachen Germany
| | - Jochen Büchs
- AVT - Chair of Biochemical Engineering RWTH Aachen University Aachen Germany
| | - Rainer Krull
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
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Bonzom C, Hüttner S, Mirgorodskaya E, Chong SL, Uthoff S, Steinbüchel A, Verhaert RMD, Olsson L. Glycosylation influences activity, stability and immobilization of the feruloyl esterase 1a from Myceliophthora thermophila. AMB Express 2019; 9:126. [PMID: 31407106 PMCID: PMC6691016 DOI: 10.1186/s13568-019-0852-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 08/02/2019] [Indexed: 11/26/2022] Open
Abstract
Heterologous protein production is widely used in industrial biotechnology. However, using non-native production hosts can lead to enzymes with altered post-translational modifications, such as glycosylation. We have investigated how production in a non-native host affects the physicochemical properties and enzymatic activity of a feruloyl esterase from Myceliophthora thermophila, MtFae1a. The enzyme was produced in two microorganisms that introduce glycosylation (M. thermophila and Pichia pastoris) and in Escherichia coli (non-glycosylated). Mass spectrometric analysis confirmed the presence of glycosylation and revealed differences in the lengths of glycan chains between the enzymes produced in M. thermophila and P. pastoris. The melting temperature and the optimal temperature for activity of the non-glycosylated enzyme were considerably lower than those of the glycosylated enzymes. The three MtFae1a versions also exhibited differences in specific activity and specificity. The catalytic efficiency of the glycosylated enzymes were more than 10 times higher than that of the non-glycosylated one. In biotechnology, immobilization is often used to allow reusing enzyme and was investigated on mesoporous silica particles. We found the binding kinetics and immobilization yield differed between the enzyme versions. The largest differences were observed when comparing enzymes with and without glycosylation, but significant variations were also observed between the two differently glycosylated enzymes. We conclude that the biotechnological value of an enzyme can be optimized for a specific application by carefully selecting the production host.
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Daranagama ND, Shioya K, Yuki M, Sato H, Ohtaki Y, Suzuki Y, Shida Y, Ogasawara W. Proteolytic analysis of Trichoderma reesei in celluase-inducing condition reveals a role for trichodermapepsin (TrAsP) in cellulase production. ACTA ACUST UNITED AC 2019; 46:831-842. [DOI: 10.1007/s10295-019-02155-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/12/2019] [Indexed: 12/22/2022]
Abstract
Abstract
Filamentous fungi produce a variety of proteases with significant biotechnological potential and show diverse substrate specificities. Proteolytic analysis of the industrial enzyme producer Trichoderma reesei has been sparse. Therefore, we determined the substrate specificity of T. reesei secretome and its main protease Trichodermapepsin (TrAsP) up to P1 position using FRETS-25Xaa-libraries. The role of TrAsP was analyzed using T. reesei QM9414 and the deletant QM∆trasp in Avicel. We observed higher activities of CMCase, Avicelase, and Xylanase in QM∆t rasp compared to that of QM9414. Saccharification rate of cellulosic biomass also increased when using secretome of QM∆trasp but the effect was not significant due to the absence of difference in BGL activity compared to QM9414. Higher TrAsP was produced when monosaccharides were used as a carbon source compared to cellulase inducers such as Avicel and α-sophorose. These results elucidate the relationship between TrAsP and cellulase production in T. reesei and suggest a physiological role for TrAsP.
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Affiliation(s)
- Nayani Dhanushka Daranagama
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology 1603-1, Kamitomioka 940-2188 Nagaoka Japan
| | - Koki Shioya
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology 1603-1, Kamitomioka 940-2188 Nagaoka Japan
| | - Masahiro Yuki
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology 1603-1, Kamitomioka 940-2188 Nagaoka Japan
| | - Haruna Sato
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology 1603-1, Kamitomioka 940-2188 Nagaoka Japan
| | - Yuki Ohtaki
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology 1603-1, Kamitomioka 940-2188 Nagaoka Japan
| | - Yoshiyuki Suzuki
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology 1603-1, Kamitomioka 940-2188 Nagaoka Japan
| | - Yosuke Shida
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology 1603-1, Kamitomioka 940-2188 Nagaoka Japan
| | - Wataru Ogasawara
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology 1603-1, Kamitomioka 940-2188 Nagaoka Japan
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Novel genetic tools that enable highly pure protein production in Trichoderma reesei. Sci Rep 2019; 9:5032. [PMID: 30902998 PMCID: PMC6430808 DOI: 10.1038/s41598-019-41573-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/08/2019] [Indexed: 01/31/2023] Open
Abstract
Trichoderma reesei is an established protein production host with high natural capacity to secrete enzymes. The lack of efficient genome engineering approaches and absence of robust constitutive gene expression systems limits exploitation of this organism in some protein production applications. Here we report engineering of T. reesei for high-level production of highly enriched lipase B of Candida antarctica (calB) using glucose as a carbon source. Multiplexed CRISPR/Cas9 in combination with the use of our recently established synthetic expression system (SES) enabled accelerated construction of strains, which produced high amounts of highly pure calB. Using SES, calB production levels in cellulase-inducing medium were comparable to the levels obtained by using the commonly employed inducible cbh1 promoter, where a wide spectrum of native enzymes were co-produced. Due to highly constitutive expression provided by the SES, it was possible to carry out the production in cellulase-repressing glucose medium leading to around 4 grams per liter of fully functional calB and simultaneous elimination of unwanted background enzymes.
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Wakai S, Nakashima N, Ogino C, Tsutsumi H, Hata Y, Kondo A. Modified expression of multi-cellulases in a filamentous fungus Aspergillus oryzae. BIORESOURCE TECHNOLOGY 2019; 276:146-153. [PMID: 30623869 DOI: 10.1016/j.biortech.2018.12.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/28/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
Aspergillus oryzae, a filamentous fungus, can secrete large amounts of enzymes extracellularly. We constructed a genetically engineered A. oryzae that simultaneously produced cellobiohydrolase, endoglucanase, and β-glucosidase by integrating multiple copies of the genes encoding these cellulases into fungal chromosomes. The resulting strain possessed 5-16 copies of each cellulase gene within the chromosome and showed approximately 10-fold higher activity versus single integration strains. Copy number polymorphisms were attributed to differences in flanking region sequence for the integrated gene fragments. Furthermore, we found that the P-sodM/T-glaB set demonstrated the strongest transcription levels per gene copy number. We therefore modified promoter/terminator set and cellulase gene combinations based on this polymorphism and transcription level data, with the resulting transformant showing 40-fold higher cellulolytic activity versus the single integration strain. This designed expression method could be useful for the overexpression of multiple enzymes and pathway flux control-mediated metabolic engineering in A. oryzae.
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Affiliation(s)
- Satoshi Wakai
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Nanami Nakashima
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hiroko Tsutsumi
- Research Institute, Gekkeikan Sake Co. Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto, Kyoto 612-8385, Japan
| | - Yoji Hata
- Research Institute, Gekkeikan Sake Co. Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto, Kyoto 612-8385, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan.
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Functional characterisation of cellobiohydrolase I (Cbh1) from Trichoderma virens UKM1 expressed in Aspergillus niger. Protein Expr Purif 2019; 154:52-61. [DOI: 10.1016/j.pep.2018.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/12/2018] [Accepted: 09/20/2018] [Indexed: 11/20/2022]
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Lu Y, Ye C, Che J, Xu X, Shao D, Jiang C, Liu Y, Shi J. Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1. Microb Cell Fact 2019; 18:13. [PMID: 30678677 PMCID: PMC6345013 DOI: 10.1186/s12934-019-1063-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/14/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Alternaria sp. MG1, an endophytic fungus isolated from grape, is a native producer of resveratrol, which has important application potential. However, the metabolic characteristics and physiological behavior of MG1 still remains mostly unraveled. In addition, the resveratrol production of the strain is low. Thus, the whole-genome sequencing is highly required for elucidating the resveratrol biosynthesis pathway. Furthermore, the metabolic network model of MG1 was constructed to provide a computational guided approach for improving the yield of resveratrol. RESULTS Firstly, a draft genomic sequence of MG1 was generated with a size of 34.7 Mbp and a GC content of 50.96%. Genome annotation indicated that MG1 possessed complete biosynthesis pathways for stilbenoids, flavonoids, and lignins. Eight secondary metabolites involved in these pathways were detected by GC-MS analysis, confirming the metabolic diversity of MG1. Furthermore, the first genome-scale metabolic network of Alternaria sp. MG1 (named iYL1539) was reconstructed, accounting for 1539 genes, 2231 metabolites, and 2255 reactions. The model was validated qualitatively and quantitatively by comparing the in silico simulation with experimental data, and the results showed a high consistency. In iYL1539, 56 genes were identified as growth essential in rich medium. According to constraint-based analysis, the importance of cofactors for the resveratrol biosynthesis was successfully demonstrated. Ethanol addition was predicted in silico to be an effective method to improve resveratrol production by strengthening acetyl-CoA synthesis and pentose phosphate pathway, and was verified experimentally with a 26.31% increase of resveratrol. Finally, 6 genes were identified as potential targets for resveratrol over-production by the recently developed methodology. The target-genes were validated using salicylic acid as elicitor, leading to an increase of resveratrol yield by 33.32% and the expression of gene 4CL and CHS by 1.8- and 1.6-fold, respectively. CONCLUSIONS This study details the diverse capability and key genes of Alternaria sp. MG1 to produce multiple secondary metabolites. The first model of the species Alternaria was constructed, providing an overall understanding of the physiological behavior and metabolic characteristics of MG1. The model is a highly useful tool for enhancing productivity by rational design of the metabolic pathway for resveratrol and other secondary metabolites.
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Affiliation(s)
- Yao Lu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jinxin Che
- Department of Biological and Food Engineering, College of Chemical Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China
| | - Xiaoguang Xu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China
| | - Dongyan Shao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China
| | - Chunmei Jiang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China
| | - Yanlin Liu
- College of Enology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Junling Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China.
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Nevalainen H, Peterson R, Curach N. Overview of Gene Expression Using Filamentous Fungi. ACTA ACUST UNITED AC 2019; 92:e55. [PMID: 30040195 DOI: 10.1002/cpps.55] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Filamentous fungi are lower eukaryotes increasingly used for expression of foreign proteins ranging from industrial enzymes originating from other fungi and bacteria to proteins of mammalian origin, such as antibodies and growth factors. Their strengths include an excellent capacity for protein secretion and their eukaryotic protein processing machinery. Proteins secreted from filamentous fungi are modified in the secretory pathway, with folding, proteolytic processing, and addition of glycans being the main modifications. Unlike from many other expression systems, however, plasmids and host strains for expression of gene products in filamentous fungi are not readily available commercially, and the expression system must thus be stitched together in the laboratory. In this overview, the key elements of fungal expression systems are discussed from a practical point of view and with a view towards the future. The principles and considerations presented here can be applied to a range of filamentous fungi. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia
| | - Robyn Peterson
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia
| | - Natalie Curach
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
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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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Lin L, Sun Z, Li J, Chen Y, Liu Q, Sun W, Tian C. Disruption of gul-1 decreased the culture viscosity and improved protein secretion in the filamentous fungus Neurospora crassa. Microb Cell Fact 2018; 17:96. [PMID: 29908565 PMCID: PMC6004096 DOI: 10.1186/s12934-018-0944-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/12/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The cellulolytic fungus Neurospora crassa is considered a potential host for enzyme and bioethanol production. However, large scale applications are hindered by its filamentous growth. Although previous investigations have shown that mycelial morphology in submerged culture can be controlled by altering physical factors, there is little knowledge available about the potential for morphology control by genetic modification. RESULTS In this study, we screened morphological mutants in the filamentous fungus N. crassa. Of the 90 morphological mutants screened, 14 mutants exhibited considerably higher viscosity compared with that of the wild type strain, and only two mutants showed low-viscosity morphologies in submerged culture. We observed that disruption of gul-1 (NCU01197), which encodes an mRNA binding protein involved in cell wall remodeling, caused pellet formation as the fermentation progressed, and resulted in the most significant decrease in viscosity of culture broth. Moreover, over-expression of gul-1 caused dramatically increased viscosity, suggesting that the gul-1 had an important function in mycelial morphology during submerged cultivation. Transcriptional profiling showed that expression of genes encoding eight GPI-anchored cell wall proteins was lowered in Δgul-1 while expression of genes associated with two non-anchored cell wall proteins was elevated. Meanwhile, the expression levels of two hydrophobin genes were also significantly altered. These results suggested that GUL-1 affected the transcription of cell wall-related genes, thereby influencing cell wall structure and mycelial morphology. Additionally, the deletion of gul-1 caused increased protein secretion, probably due to a defect in cell wall integrity, suggesting this as an alternative strategy of strain improvement for enzyme production. To confirm practical applications, deletion of gul-1 in the hyper-cellulase producing strain (∆ncw-1∆Ncap3m) significantly reduced the viscosity of culture broth. CONCLUSIONS Using the model filamentous fungus N. crassa, genes that affect mycelial morphology in submerged culture were explored through systematic screening of morphological mutants. Disrupting several candidate genes altered viscosities in submerged culture. This work provides an example for controlling fungal morphology in submerged fermentation by genetic engineering, and will be beneficial for industrial fungal strain improvement.
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Affiliation(s)
- Liangcai Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Zhiyong Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yong Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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Rational design for fungal laccase production in the model host Aspergillus nidulans. SCIENCE CHINA-LIFE SCIENCES 2018; 62:84-94. [DOI: 10.1007/s11427-017-9304-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/12/2018] [Indexed: 12/20/2022]
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Inducible promoters and functional genomic approaches for the genetic engineering of filamentous fungi. Appl Microbiol Biotechnol 2018; 102:6357-6372. [PMID: 29860590 PMCID: PMC6061484 DOI: 10.1007/s00253-018-9115-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Abstract
In industry, filamentous fungi have a prominent position as producers of economically relevant primary or secondary metabolites. Particularly, the advent of genetic engineering of filamentous fungi has led to a growing number of molecular tools to adopt filamentous fungi for biotechnical applications. Here, we summarize recent developments in fungal biology, where fungal host systems were genetically manipulated for optimal industrial applications. Firstly, available inducible promoter systems depending on carbon sources are mentioned together with various adaptations of the Tet-Off and Tet-On systems for use in different industrial fungal host systems. Subsequently, we summarize representative examples, where diverse expression systems were used for the production of heterologous products, including proteins from mammalian systems. In addition, the progressing usage of genomics and functional genomics data for strain improvement strategies are addressed, for the identification of biosynthesis genes and their related metabolic pathways. Functional genomic data are further used to decipher genomic differences between wild-type and high-production strains, in order to optimize endogenous metabolic pathways that lead to the synthesis of pharmaceutically relevant end products. Lastly, we discuss how molecular data sets can be used to modify products for optimized applications.
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