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Ikeda S, Tomita K, Nakagawa G, Kouzuma A, Watanabe K. Supplementation with Amino Acid Sources Facilitates Fermentative Growth of Shewanella oneidensis MR-1 in Defined Media. Appl Environ Microbiol 2023; 89:e0086823. [PMID: 37367298 PMCID: PMC10370299 DOI: 10.1128/aem.00868-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/04/2023] [Indexed: 06/28/2023] Open
Abstract
Shewanella oneidensis MR-1 is a facultative anaerobe that grows by respiration using a variety of electron acceptors. This organism serves as a model to study how bacteria thrive in redox-stratified environments. A glucose-utilizing engineered derivative of MR-1 has been reported to be unable to grow in glucose minimal medium (GMM) in the absence of electron acceptors, despite this strain having a complete set of genes for reconstructing glucose to lactate fermentative pathways. To gain insights into why MR-1 is incapable of fermentative growth, this study examined a hypothesis that this strain is programmed to repress the expression of some carbon metabolic genes in the absence of electron acceptors. Comparative transcriptomic analyses of the MR-1 derivative were conducted in the presence and absence of fumarate as an electron acceptor, and these found that the expression of many genes involved in carbon metabolism required for cell growth, including several tricarboxylic acid (TCA) cycle genes, was significantly downregulated in the absence of fumarate. This finding suggests a possibility that MR-1 is unable to grow fermentatively on glucose in minimal media owing to the shortage of nutrients essential for cell growth, such as amino acids. This idea was demonstrated in subsequent experiments that showed that the MR-1 derivative fermentatively grows in GMM containing tryptone or a defined mixture of amino acids. We suggest that gene regulatory circuits in MR-1 are tuned to minimize energy consumption under electron acceptor-depleted conditions, and that this results in defective fermentative growth in minimal media. IMPORTANCE It is an enigma why S. oneidensis MR-1 is incapable of fermentative growth despite having complete sets of genes for reconstructing fermentative pathways. Understanding the molecular mechanisms behind this defect will facilitate the development of novel fermentation technologies for the production of value-added chemicals from biomass feedstocks, such as electro-fermentation. The information provided in this study will also improve our understanding of the ecological strategies of bacteria living in redox-stratified environments.
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Affiliation(s)
- Sota Ikeda
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Keisuke Tomita
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Gen Nakagawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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2
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Laibach N, Bröring S. The Emergence of Genome Editing—Innovation Network Dynamics of Academic Publications, Patents, and Business Activities. Front Bioeng Biotechnol 2022; 10:868736. [PMID: 35497359 PMCID: PMC9049213 DOI: 10.3389/fbioe.2022.868736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Transformative societal change can both be triggered and influenced by both macro-level political means and the emergence of technologies. Key enabling technologies and therein biotechnology hold the power to drive those changes forward, evolving from breakthrough academic discoveries into business activities. Due to its increasing empirical relevance, we picked genome editing as an example for an emerging technology and extracted publication, patent, and company data from the years 2000 to 2020. By drawing upon social network analysis, we identify major networks and clusters that are dominating the respective time and layer. Based on these networks, we draw vertical connections between scientific knowledge, patented technologies, and business activities to visualize the interlevel relationships between actors through technological development. Thereby, we identify network dynamics of the emergence of genome editing, the most important actors and clusters evolving, and its spread into different areas.
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Affiliation(s)
- Natalie Laibach
- Laboratory for Sterol and Terpenoid Metabolism in Plant Development and Stress Responses, Department of Plant Synthetic Biology and Metabolic Engineering, Centre for Research in Agricultural Genomics (CRAG), Barcelona, Spain
- *Correspondence: Natalie Laibach, ; Stefanie Bröring,
| | - Stefanie Bröring
- Chair Entrepreneurship and Innovative Business Models, Center for Entrepreneurship, Innovation and Transformation, Ruhr-University Bochum, Bochum, Germany
- *Correspondence: Natalie Laibach, ; Stefanie Bröring,
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3
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Yamada S, Takamatsu Y, Ikeda S, Kouzuma A, Watanabe K. Towards Application of Electro-Fermentation for the Production of Value-Added Chemicals From Biomass Feedstocks. Front Chem 2022; 9:805597. [PMID: 35127650 PMCID: PMC8807546 DOI: 10.3389/fchem.2021.805597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/24/2021] [Indexed: 12/03/2022] Open
Abstract
According to recent social demands for sustainable developments, the value of biomass as feedstocks for chemical industry is increasing. With the aid of metabolic engineering and genome editing, microbial fermentation has been developed for producing value-added chemicals from biomass feedstocks, while further improvements are desired for producing more diverse chemicals and increasing the production efficiency. The major intrinsic limitation in conventional fermentation technologies is associated with the need for balancing the net redox equivalents between substrates and products, resulting in limited repertories of fermentation products. One solution for this limitation would be “electro-fermentation (EF)” that utilizes bioelectrochemical systems for modifying the intracellular redox state of electrochemically active bacteria, thereby overcoming the redox constraint of fermentation. Recent studies have attempted the production of chemicals based on the concept of EF, while its utility has not been sufficiently demonstrated in terms of low production efficiencies. Here we discuss EF in terms of its concept, current status and future directions, which help us develop its practical applications to sustainable chemical industries.
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Zhou Y, Kumar M, Sarsaiya S, Sirohi R, Awasthi SK, Sindhu R, Binod P, Pandey A, Bolan NS, Zhang Z, Singh L, Kumar S, Awasthi MK. Challenges and opportunities in bioremediation of micro-nano plastics: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149823. [PMID: 34454140 DOI: 10.1016/j.scitotenv.2021.149823] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Rising level of micro-nano plastics (MNPs) in the natural ecosystem adversely impact the health of the environment and living organisms globally. MNPs enter in to the agro-ecosystem, flora and fauna, and human body via trophic transfer, ingestion and inhalation, resulting impediment in blood vessel, infertility, and abnormal behaviors. Therefore, it becomes indispensable to apply a novel approach to remediate MNPs from natural environment. Amongst the several prevailing technologies of MNPs remediation, microbial remediation is considered as greener technology. Microbial degradation of plastics is typically influenced by several biotic as well as abiotic factors, such as enzymatic mechanisms, substrates and co-substrates concentration, temperature, pH, oxidative stress, etc. Therefore, it is pivotal to recognize the key pathways adopted by microbes to utilize plastic fragments as a sole carbon source for the growth and development. In this context, this review critically discussed the role of various microbes and their enzymatic mechanisms involved in biodegradation of MNPs in wastewater (WW) stream, municipal sludge, municipal solid waste (MSW), and composting starting with biological and toxicological impacts of MNPs. Moreover, this review comprehensively discussed the deployment of various MNPs remediation technologies, such as enzymatic, advanced molecular, and bio-membrane technologies in fostering the bioremediation of MNPs from various environmental compartments along with their pros and cons and prospects for future research.
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Affiliation(s)
- Yuwen Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Manish Kumar
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440020, Maharashtra, India
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Ranjna Sirohi
- Department of Chemical and Biological Engineering, Korea University, Seoul, South Korea
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala 695019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala 695019, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226 001, India
| | - Nanthi S Bolan
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; School of Engineering, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440020, Maharashtra, India
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440020, Maharashtra, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China.
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Jang WD, Kim GB, Kim Y, Lee SY. Applications of artificial intelligence to enzyme and pathway design for metabolic engineering. Curr Opin Biotechnol 2021; 73:101-107. [PMID: 34358728 DOI: 10.1016/j.copbio.2021.07.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 01/07/2023]
Abstract
Metabolic engineering for developing industrial strains capable of overproducing bioproducts requires good understanding of cellular metabolism, including metabolic reactions and enzymes. However, metabolic pathways and enzymes involved are still unknown for many products of interest, which presents a key challenge in their biological production. This challenge can be partly overcome by constructing novel biosynthetic pathways through enzyme and pathway design approaches. With the increase in bio-big data, data-driven approaches using artificial intelligence (AI) techniques are allowing more advanced protein and pathway design. In this paper, we review recent studies on AI-aided protein engineering and design, focusing on directed evolution that uses AI approaches to efficiently construct mutant libraries. Also, recent works of AI-aided pathway design strategies, including template-based and template-free approaches, are discussed.
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Affiliation(s)
- Woo Dae Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; KAIST Institute for the BioCentury, KAIST Institute for Artificial Intelligence, BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Gi Bae Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeji Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; KAIST Institute for the BioCentury, KAIST Institute for Artificial Intelligence, BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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6
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Luo ZW, Ahn JH, Chae TU, Choi SY, Park SY, Choi Y, Kim J, Prabowo CPS, Lee JA, Yang D, Han T, Xu H, Lee SY. Metabolic Engineering of
Escherichia
coli. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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7
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Escherichia coli as a platform microbial host for systems metabolic engineering. Essays Biochem 2021; 65:225-246. [PMID: 33956149 DOI: 10.1042/ebc20200172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022]
Abstract
Bio-based production of industrially important chemicals and materials from non-edible and renewable biomass has become increasingly important to resolve the urgent worldwide issues including climate change. Also, bio-based production, instead of chemical synthesis, of food ingredients and natural products has gained ever increasing interest for health benefits. Systems metabolic engineering allows more efficient development of microbial cell factories capable of sustainable, green, and human-friendly production of diverse chemicals and materials. Escherichia coli is unarguably the most widely employed host strain for the bio-based production of chemicals and materials. In the present paper, we review the tools and strategies employed for systems metabolic engineering of E. coli. Next, representative examples and strategies for the production of chemicals including biofuels, bulk and specialty chemicals, and natural products are discussed, followed by discussion on materials including polyhydroxyalkanoates (PHAs), proteins, and nanomaterials. Lastly, future perspectives and challenges remaining for systems metabolic engineering of E. coli are discussed.
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8
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Otero-Muras I, Carbonell P. Automated engineering of synthetic metabolic pathways for efficient biomanufacturing. Metab Eng 2020; 63:61-80. [PMID: 33316374 DOI: 10.1016/j.ymben.2020.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/15/2020] [Accepted: 11/20/2020] [Indexed: 12/19/2022]
Abstract
Metabolic engineering involves the engineering and optimization of processes from single-cell to fermentation in order to increase production of valuable chemicals for health, food, energy, materials and others. A systems approach to metabolic engineering has gained traction in recent years thanks to advances in strain engineering, leading to an accelerated scaling from rapid prototyping to industrial production. Metabolic engineering is nowadays on track towards a truly manufacturing technology, with reduced times from conception to production enabled by automated protocols for DNA assembly of metabolic pathways in engineered producer strains. In this review, we discuss how the success of the metabolic engineering pipeline often relies on retrobiosynthetic protocols able to identify promising production routes and dynamic regulation strategies through automated biodesign algorithms, which are subsequently assembled as embedded integrated genetic circuits in the host strain. Those approaches are orchestrated by an experimental design strategy that provides optimal scheduling planning of the DNA assembly, rapid prototyping and, ultimately, brings forward an accelerated Design-Build-Test-Learn cycle and the overall optimization of the biomanufacturing process. Achieving such a vision will address the increasingly compelling demand in our society for delivering valuable biomolecules in an affordable, inclusive and sustainable bioeconomy.
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Affiliation(s)
- Irene Otero-Muras
- BioProcess Engineering Group, IIM-CSIC, Spanish National Research Council, Vigo, 36208, Spain.
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (ai2), Universitat Politècnica de València, 46022, Spain.
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9
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Machine learning applications in systems metabolic engineering. Curr Opin Biotechnol 2020; 64:1-9. [DOI: 10.1016/j.copbio.2019.08.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/23/2019] [Accepted: 08/25/2019] [Indexed: 12/11/2022]
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10
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Zhou L, Ren J, Li Z, Nie J, Wang C, Zeng AP. Characterization and Engineering of a Clostridium Glycine Riboswitch and Its Use To Control a Novel Metabolic Pathway for 5-Aminolevulinic Acid Production in Escherichia coli. ACS Synth Biol 2019; 8:2327-2335. [PMID: 31550137 DOI: 10.1021/acssynbio.9b00137] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A riboswitch, a regulatory RNA that controls gene expression by specifically binding a ligand, is an attractive genetic element for the control of conditional gene expression and metabolic pathways. In this study, we identified a glycine riboswitch located in the 5'-untranslated regions of a glycine:proton symporter gene in Clostridium pasteurianum. The glycine riboswitch is shown to contain two tandem aptamers and to function as an activator of expression of genes fused to its expression platform. Results of singlet aptamer experiments indicated that aptamer-2 has a much higher impact on regulating gene expression than aptamer-1. Further, we successfully obtained synthetic glycine-OFF riboswitches using a dual selection approach, and one of them repressed gene expression up to 10.2-fold with an improved dynamic range. The specific glycine-OFF riboswitch can function as an independent repressor in the presence of glycine, and its repression mechanism is inferred from predicted secondary structure. The selected glycine-OFF riboswitch was used to dynamically control the biosynthesis of 5-aminolevulinic acid (5-ALA) in Escherichia coli with an unnatural 5-ALA synthetic pathway, in which glycine plays a key role. It is demonstrated that the use of a synthetic Clostridium glycine-OFF riboswitch can lead to a significant increase (11%) of 5-ALA in E. coli harboring an unnatural biosynthetic pathway.
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Affiliation(s)
- Libang Zhou
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
- College of Food Science and Technology , Nanjing Agricultural University , Weigang 1 , Nanjing 210095 , PR China
| | - Jie Ren
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
| | - Zhidong Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
| | - Jinglei Nie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
| | - Chuang Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
| | - An-Ping Zeng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , North Third Ring Road 15 , Chaoyang District, Beijing 100029 , China
- Institute of Bioprocess and Biosystems Engineering , Hamburg University of Technology , Denickestrasse 15 , D-21073 Hamburg , Germany
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11
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Petersen A, Crocoll C, Halkier BA. De novo production of benzyl glucosinolate in Escherichia coli. Metab Eng 2019; 54:24-34. [DOI: 10.1016/j.ymben.2019.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/11/2019] [Accepted: 02/24/2019] [Indexed: 12/30/2022]
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12
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Cho JS, Gu C, Han TH, Ryu JY, Lee SY. Reconstruction of context-specific genome-scale metabolic models using multiomics data to study metabolic rewiring. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.02.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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13
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Taniguchi I, Yoshida S, Hiraga K, Miyamoto K, Kimura Y, Oda K. Biodegradation of PET: Current Status and Application Aspects. ACS Catal 2019. [DOI: 10.1021/acscatal.8b05171] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ikuo Taniguchi
- Department of Polymer Science, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Shosuke Yoshida
- Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kazumi Hiraga
- Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yoshiharu Kimura
- Department of Polymer Science, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kohei Oda
- Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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14
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Lee SY, Kim HU, Chae TU, Cho JS, Kim JW, Shin JH, Kim DI, Ko YS, Jang WD, Jang YS. A comprehensive metabolic map for production of bio-based chemicals. Nat Catal 2019. [DOI: 10.1038/s41929-018-0212-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Choi KR, Kim WJ, Lee SY. Metabolomics for industrial fermentation. Bioprocess Biosyst Eng 2018; 41:1073-1077. [PMID: 29931578 DOI: 10.1007/s00449-018-1967-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 06/06/2018] [Indexed: 11/28/2022]
Abstract
Metabolomics is essential to understand the metabolism and identify engineering targets to improve the performances of strains and bioprocesses. Although numerous metabolomics techniques have been developed and applied to various organisms, the metabolome of Saccharopolyspora erythraea, a native producer of erythromycin, had never been studied. The 2017 best paper of Bioprocess and Biosystems Engineering reports examination of three methods for quenching and extraction to analyze the intracellular metabolome of S. erythraea, and identified the most reliable methods for studying different groups of the metabolites. Subsequent studies on the dynamics of the intracellular metabolome of S. erythraea during the fed-batch fermentation identified a positive correlation between the specific erythromycin production rate and the pool size of intracellular propionyl-CoA and other precursors of erythromycin. A series of follow-up studies, such as demonstrating the applicability of the quenching/extraction methods in other related antibiotic producers, demonstrating the generality of the best matches between the quenching/extraction methods and the metabolite groups, and combining metabolomics approaches with the fluxomics and systems metabolic engineering approaches, will facilitate the metabolomics studies on important antibiotic producers, enable standardization of the quenching/extraction protocols, and improve the performance of the antibiotic production with deeper insight into their metabolism.
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Affiliation(s)
- Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea.,BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea
| | - Won Jun Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea.,BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea. .,Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea. .,BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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Enabling the valorization of guaiacol-based lignin: Integrated chemical and biochemical production of cis,cis-muconic acid using metabolically engineered Amycolatopsis sp ATCC 39116. Metab Eng 2017; 45:200-210. [PMID: 29246517 DOI: 10.1016/j.ymben.2017.12.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/18/2017] [Accepted: 12/01/2017] [Indexed: 01/20/2023]
Abstract
Lignin is nature's second most abundant polymer and displays a largely unexploited renewable resource for value-added bio-production. None of the lignin-based fermentation processes so far managed to use guaiacol (2-methoxy phenol), the predominant aromatic monomer in depolymerized lignin. In this work, we describe metabolic engineering of Amycolatopsis sp. ATCC 39116 to produce cis,cis-muconic acid (MA), a precursor of recognized industrial value for commercial plastics, from guaiacol. The microbe utilized a very broad spectrum of lignin-based aromatics, such as catechol, guaiacol, phenol, toluene, p-coumarate, and benzoate, tolerated them in elevated amounts and even preferred them over sugars. As a next step, we developed a novel approach for genomic engineering of this challenging, GC-rich actinomycete. The successful introduction of conjugation and blue-white screening, using β-glucuronidase, enabled tailored genomic modifications within ten days. Successive deletion of two putative muconate cycloisomerases from the genome provided the mutant Amycolatopsis sp. ATCC 39116 MA-2, which accumulated 3.1gL-1 MA from guaiacol within 24h, achieving a yield of 96%. The mutant was found also capable to produce MA from a guaiacol-rich true lignin hydrolysate, obtained from pine through hydrothermal conversion. This provides an important proof-of-concept to successfully coupling chemical and biochemical process steps into a value chain from the lignin polymer to an industrial chemical. In addition, Amycolatopsis sp. ATCC 39116 MA-2 was able to produce 2-methyl MA from o-cresol (2-methyl phenol), which opens possibilities towards polymers with novel architecture and properties.
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Yang D, Cho JS, Choi KR, Kim HU, Lee SY. Systems metabolic engineering as an enabling technology in accomplishing sustainable development goals. Microb Biotechnol 2017; 10:1254-1258. [PMID: 28696000 PMCID: PMC5609237 DOI: 10.1111/1751-7915.12766] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 11/26/2022] Open
Abstract
With pressing issues arising in recent years, the United Nations proposed 17 Sustainable Development Goals (SDGs) as an agenda urging international cooperations for sustainable development. In this perspective, we examine the roles of systems metabolic engineering (SysME) and its contribution to improving the quality of life and protecting our environment, presenting how this field of study offers resolutions to the SDGs with relevant examples. We conclude with offering our opinion on the current state of SysME and the direction it should move forward in the generations to come, explicitly focusing on addressing the SDGs.
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Affiliation(s)
- Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jae Sung Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.,BioProcess Engineering Research Center, KAIST, Daejeon, 34141, Republic of Korea
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