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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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Advances and Challenges in CRISPR/Cas-Based Fungal Genome Engineering for Secondary Metabolite Production: A Review. J Fungi (Basel) 2023; 9:jof9030362. [PMID: 36983530 PMCID: PMC10058990 DOI: 10.3390/jof9030362] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Fungi represent an important source of bioactive secondary metabolites (SMs), which have wide applications in many fields, including medicine, agriculture, human health, and many other industries. The genes involved in SM biosynthesis are usually clustered adjacent to each other into a region known as a biosynthetic gene cluster (BGC). The recent advent of a diversity of genetic and genomic technologies has facilitated the identification of many cryptic or uncharacterized BGCs and their associated SMs. However, there are still many challenges that hamper the broader exploration of industrially important secondary metabolites. The recent advanced CRISPR/Cas system has revolutionized fungal genetic engineering and enabled the discovery of novel bioactive compounds. In this review, we firstly introduce fungal BGCs and their relationships with associated SMs, followed by a brief summary of the conventional strategies for fungal genetic engineering. Next, we introduce a range of state-of-the-art CRISPR/Cas-based tools that have been developed and review recent applications of these methods in fungi for research on the biosynthesis of SMs. Finally, the challenges and limitations of these CRISPR/Cas-based systems are discussed and directions for future research are proposed in order to expand their applications and improve efficiency for fungal genetic engineering.
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3
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Gene complementation strategies for filamentous fungi biotechnology. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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4
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Zhang Y, Cheng L, Liu Y, Zhan S, Wu Z, Luo S, Zhang X. Dietary flavonoids: a novel strategy for the amelioration of cognitive impairment through intestinal microbiota. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:488-495. [PMID: 35892267 DOI: 10.1002/jsfa.12151] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/23/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
The chances of people suffering from cognitive impairments increase gradually with age. Diet and lifestyle are closely related to the occurrence and development of cognitive function. Dietary flavonoid supplementation has been shown to be one of the protective factors against cognitive decline. Flavonoids belong to a class of polyphenols that have been proposed for the treatment of cognitive decline. Recent evidence has shown that intestinal flora in the human body can interact with flavonoids. Intestinal microbiota can modify the chemical structure of flavonoids, producing new metabolites, the pharmacological activities of which may be different from those of the parent; meanwhile, flavonoids and their metabolites can, in turn, regulate the composition and structure of intestinal flora. Notably, intestinal flora affect host nervous system activity through the gut-brain axis, ultimately causing changes in cognitive function. This review therefore summarizes the interaction of dietary flavonoids and intestinal flora, and their protective effect against cognitive decline through the gut-brain axis, indicating that dietary flavonoids may ameliorate cognitive impairment through their interaction with intestinal microbiota. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Yuting Zhang
- Department of Food Science and Engineering, Ningbo University, Ningbo, People's Republic of China
| | - Lu Cheng
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Yanan Liu
- Department of Food Science and Engineering, Ningbo University, Ningbo, People's Republic of China
| | - Shengnan Zhan
- Department of Food Science and Engineering, Ningbo University, Ningbo, People's Republic of China
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo, People's Republic of China
| | - Songmei Luo
- Department of Pharmacy, Lishui Central Hospital, Lishui, People's Republic of China
| | - Xin Zhang
- Department of Food Science and Engineering, Ningbo University, Ningbo, People's Republic of China
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Liu X, Luo H, Yu D, Tan J, Yuan J, Li H. Synthetic biology promotes the capture of CO2 to produce fatty acid derivatives in microbial cell factories. BIORESOUR BIOPROCESS 2022; 9:124. [PMID: 38647643 PMCID: PMC10992411 DOI: 10.1186/s40643-022-00615-2] [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: 09/03/2022] [Accepted: 11/27/2022] [Indexed: 12/07/2022] Open
Abstract
Environmental problems such as greenhouse effect, the consumption of fossil energy, and the increase of human demand for energy are becoming more and more serious, which force researcher to turn their attention to the reduction of CO2 and the development of renewable energy. Unsafety, easy to lead to secondary environmental pollution, cost inefficiency, and other problems limit the development of conventional CO2 capture technology. In recent years, many microorganisms have attracted much attention to capture CO2 and synthesize valuable products directly. Fatty acid derivatives (e.g., fatty acid esters, fatty alcohols, and aliphatic hydrocarbons), which can be used as a kind of environmentally friendly and renewable biofuels, are sustainable substitutes for fossil energy. In this review, conventional CO2 capture techniques pathways, microbial CO2 concentration mechanisms and fixation pathways were introduced. Then, the metabolic pathway and progress of direct production of fatty acid derivatives from CO2 in microbial cell factories were discussed. The synthetic biology means used to design engineering microorganisms and optimize their metabolic pathways were depicted, with final discussion on the potential of optoelectronic-microbial integrated capture and production systems.
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Affiliation(s)
- Xiaofang Liu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insects of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, Guizhou, China.
| | - Hangyu Luo
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insects of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, Guizhou, China
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Dayong Yu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insects of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, Guizhou, China
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Jinyu Tan
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Junfa Yuan
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Hu Li
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China.
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6
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Wang Y, Chen H, Ma L, Gong M, Wu Y, Bao D, Zou G. Use of CRISPR-Cas tools to engineer Trichoderma species. Microb Biotechnol 2022; 15:2521-2532. [PMID: 35908288 PMCID: PMC9518982 DOI: 10.1111/1751-7915.14126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022] Open
Abstract
Given their lignocellulose degradability and biocontrol activities, fungi of the ubiquitously distributed genus Trichoderma have multiple industrial and agricultural applications. Genetic manipulation plays a valuable role in tailoring novel engineered strains with enhanced target traits. Nevertheless, as applied to fungi, the classic tools of genetic manipulation tend to be time-consuming and tedious. However, the recent development of the CRISPR-Cas system for gene editing has enabled researchers to achieve genome-wide gene disruptions, gene replacements, and precise editing, and this technology has emerged as a primary focus for novel developments in engineered strains of Trichoderma. Here, we provide a brief overview of the traditional approaches to genetic manipulation, the different strategies employed in establishing CRSIPR-Cas systems, the utilization of these systems to develop engineered strains of Trichoderma for desired applications, and the future trends in biotechnology.
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Affiliation(s)
- Ying Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hongyu Chen
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Liang Ma
- Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an Hangzhou, China
| | - Ming Gong
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yingying Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Dapeng Bao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Gen Zou
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Tsuboi Y, Sakuma T, Yamamoto T, Horiuchi H, Takahashi F, Igarashi K, Hagihara H, Takimura Y. OUP accepted manuscript. FEMS Microbiol Lett 2022; 369:6524178. [PMID: 35137045 PMCID: PMC8863565 DOI: 10.1093/femsle/fnac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/11/2021] [Accepted: 02/04/2022] [Indexed: 12/02/2022] Open
Abstract
The Mucorales fungal genus Rhizopus is used for the industrial production of organic acids, enzymes and fermented foods. The metabolic engineering efficiency of Rhizopus could be improved using gene manipulation; however, exogenous DNA rarely integrates into the host genome. Consequently, a genetic tool for Mucorales fungi needs to be developed. Recently, programmable nucleases that generate DNA double-strand breaks (DSBs) at specific genomic loci have been used for genome editing in various organisms. In this study, we examined gene disruption in Rhizopus oryzae using transcription activator-like effector nucleases (TALENs), with and without exonuclease overexpression. TALENs with an overexpressing exonuclease induced DSBs, followed by target site deletions. Although DSBs are repaired mainly by nonhomologous end joining in most organisms, our results suggested that in R. oryzae microhomology-mediated end joining was the major DSB repair system. Our gene manipulation method using TALENs coupled with exonuclease overexpression contributes to basic scientific knowledge and the metabolic engineering of Rhizopus.
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Affiliation(s)
- Yuichi Tsuboi
- Corresponding author: Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan. Tel: +81-70-3297-1291; Fax: +81-73-426-5027; E-mail:
| | | | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Fumikazu Takahashi
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
| | - Kazuaki Igarashi
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
| | - Hiroshi Hagihara
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
| | - Yasushi Takimura
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
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Abstract
Trichoderma reesei's potential as a rapid and efficient biomass degrader was first recognized in the 1950s when it was isolated from Army textiles during World War II. The microbe secreted cellulases that were degrading cotton-based tents and clothing of service members stationed on the Solomon Islands. In the 1970s, at the time of the first global oil crisis, research interest in T. reesei gained popularity as it was explored as part of the solution to the worlds growing dependence on fossil fuels. Much of this early work focused on classical mutagenesis and selection of hypercellulolytic strains. This early lineage was used as a starting point for both academic research with the goal of understanding secretion and regulation of expression of the complex mixture of enzymes required for cellulosic biomass decay as well as for its development as a host for industrial enzyme production. In 2001, at the onset of the second major oil crisis, the US Department of Energy supported research programs in microbial cellulases to produce ethanol from biomass which led to another surge in the study of T. reesei. This further accelerated the development of molecular biology and recombinant DNA tools in T. reesei. In addition to T. reesei's role in bio-ethanol production, it is used to produce industrial enzymes with a broad range of applications supporting the bio-based economy. To date there are around 243 commercially available enzyme products manufactured by fermentation of microorganisms; 30 of these are made using Trichoderma as a host, 21 of which are recombinant products sold for use in food, feed, and technical applications including textiles and pulp and paper.
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Zhang F, Bunterngsook B, Li JX, Zhao XQ, Champreda V, Liu CG, Bai FW. Regulation and production of lignocellulolytic enzymes from Trichoderma reesei for biofuels production. ADVANCES IN BIOENERGY 2019. [DOI: 10.1016/bs.aibe.2019.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Tian P, Wang J, Shen X, Rey JF, Yuan Q, Yan Y. Fundamental CRISPR-Cas9 tools and current applications in microbial systems. Synth Syst Biotechnol 2017; 2:219-225. [PMID: 29318202 PMCID: PMC5655352 DOI: 10.1016/j.synbio.2017.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/07/2017] [Accepted: 08/25/2017] [Indexed: 01/08/2023] Open
Abstract
Derived from the bacterial adaptive immune system, CRISPR technology has revolutionized conventional genetic engineering methods and unprecedentedly facilitated strain engineering. In this review, we outline the fundamental CRISPR tools that have been employed for strain optimization. These tools include CRISPR editing, CRISPR interference, CRISPR activation and protein imaging. To further characterize the CRISPR technology, we present current applications of these tools in microbial systems, including model- and non-model industrial microorganisms. Specially, we point out the major challenges of the CRISPR tools when utilized for multiplex genome editing and sophisticated expression regulation. To address these challenges, we came up with strategies that place emphasis on the amelioration of DNA repair efficiency through CRISPR-Cas9-assisted recombineering. Lastly, multiple promising research directions were proposed, mainly focusing on CRISPR-based construction of microbial ecosystems toward high production of desired chemicals.
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Affiliation(s)
- Pingfang Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Justin Forrest Rey
- College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Qipeng Yuan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yajun Yan
- College of Engineering, The University of Georgia, Athens, GA 30602, USA
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