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Mutz M, Brüning V, Brüsseler C, Müller M, Noack S, Marienhagen J. Metabolic engineering of Corynebacterium glutamicum for the production of anthranilate from glucose and xylose. Microb Biotechnol 2024; 17:e14388. [PMID: 38206123 PMCID: PMC10832554 DOI: 10.1111/1751-7915.14388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/28/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
Anthranilate and its derivatives are important basic chemicals for the synthesis of polyurethanes as well as various dyes and food additives. Today, anthranilate is mainly chemically produced from petroleum-derived xylene, but this shikimate pathway intermediate could be also obtained biotechnologically. In this study, Corynebacterium glutamicum was engineered for the microbial production of anthranilate from a carbon source mixture of glucose and xylose. First, a feedback-resistant 3-deoxy-arabinoheptulosonate-7-phosphate synthase from Escherichia coli, catalysing the first step of the shikimate pathway, was functionally introduced into C. glutamicum to enable anthranilate production. Modulation of the translation efficiency of the genes for the shikimate kinase (aroK) and the anthranilate phosphoribosyltransferase (trpD) improved product formation. Deletion of two genes, one for a putative phosphatase (nagD) and one for a quinate/shikimate dehydrogenase (qsuD), abolished by-product formation of glycerol and quinate. However, the introduction of an engineered anthranilate synthase (TrpEG) unresponsive to feedback inhibition by tryptophan had the most pronounced effect on anthranilate production. Component I of this enzyme (TrpE) was engineered using a biosensor-based in vivo screening strategy for identifying variants with increased feedback resistance in a semi-rational library of TrpE muteins. The final strain accumulated up to 5.9 g/L (43 mM) anthranilate in a defined CGXII medium from a mixture of glucose and xylose in bioreactor cultivations. We believe that the constructed C. glutamicum variants are not only limited to anthranilate production but could also be suitable for the synthesis of other biotechnologically interesting shikimate pathway intermediates or any other aromatic compound derived thereof.
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Affiliation(s)
- Mario Mutz
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum JülichJülichGermany
- Institute of BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Vincent Brüning
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum JülichJülichGermany
| | - Christian Brüsseler
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum JülichJülichGermany
| | - Moritz‐Fabian Müller
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum JülichJülichGermany
| | - Stephan Noack
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum JülichJülichGermany
| | - Jan Marienhagen
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum JülichJülichGermany
- Institute of BiotechnologyRWTH Aachen UniversityAachenGermany
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Kulakowski S, Banerjee D, Scown CD, Mukhopadhyay A. Improving microbial bioproduction under low-oxygen conditions. Curr Opin Biotechnol 2023; 84:103016. [PMID: 37924688 DOI: 10.1016/j.copbio.2023.103016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 10/07/2023] [Indexed: 11/06/2023]
Abstract
Microbial bioconversion provides access to a wide range of sustainably produced chemicals and commodities. However, industrial-scale bioproduction process operations are preferred to be anaerobic due to the cost associated with oxygen transfer. Anaerobic bioconversion generally offers limited substrate utilization profiles, lower product yields, and reduced final product diversity compared with aerobic processes. Bioproduction under conditions of reduced oxygen can overcome the limitations of fully aerobic and anaerobic bioprocesses, but many microbial hosts are not developed for low-oxygen bioproduction. Here, we describe advances in microbial strain engineering involving the use of redox cofactor engineering, genome-scale metabolic modeling, and functional genomics to enable improved bioproduction processes under low oxygen and provide a viable path for scaling these bioproduction systems to industrial scales.
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Affiliation(s)
- Shawn Kulakowski
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corinne D Scown
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Kataoka N, Matsushita K, Yakushi T. Development of a 2-hydroxyglutarate production system by Corynebacterium glutamicum. Appl Microbiol Biotechnol 2023; 107:5987-5997. [PMID: 37555949 DOI: 10.1007/s00253-023-12716-9] [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: 05/17/2023] [Revised: 07/23/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023]
Abstract
2-Oxoglutarate (2-OG) is a tricarboxylate cycle intermediate that can be biologically converted into several industrially important compounds. However, studies on the fermentative production of compounds synthesized from 2-OG, but not via glutamate (defined as 2-OG derivatives), have been limited. Herein, a system that can efficiently produce 2-hydroxyglutarate (2-HG), a 2-OG derivative biosynthesized by the hgdH-encoded NADH-dependent 2-HG dehydrogenase of Acidaminococcus fermentans, was developed as a model using Corynebacterium glutamicum. First, the D3 strain, which lacked the two NADH-consuming enzymes, lactate dehydrogenase and malate dehydrogenase, as well as isocitrate lyase, was constructed as a starting strain. Next, the growth conditions that induced the accumulation of 2-OG were investigated, and it was found that the biotin- and nitrogen-limited (B/N-limited) aerobic growth conditions were suitable for this purpose. Finally, the hgdH gene of A. fermentans became overexpressed in the D3 strain by inserting it into the intergenic regions with the strong constitutive promoter of the tuf gene of C. glutamicum; the engineered strain was cultured under the B/N-limited aerobic growth conditions. The engineered strain produced 80.1 mM 2-HG with a yield of 0.390 mol/mol glucose, which are the highest titer and yield reported thus far, to the best of our knowledge. Furthermore, reverse genetics showed that the produced 2-HG was partially exported via the YggB protein (NCgl1221 protein, a mechanosensitive channel) known as an exporter for glutamate under the conditions used herein. KEY POINTS: • An efficient 2-HG production system was developed with Corynebacterium glutamicum. • Biotin- and nitrogen-limited aerobic growth conditions induced 2-OG production. • Produced 2-HG was partially excreted via the glutamate exporter, YggB.
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Affiliation(s)
- Naoya Kataoka
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan.
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan.
| | - Kazunobu Matsushita
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
| | - Toshiharu Yakushi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
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Liu L, Li J, Gai Y, Tian Z, Wang Y, Wang T, Liu P, Yuan Q, Ma H, Lee SY, Zhang D. Protein engineering and iterative multimodule optimization for vitamin B 6 production in Escherichia coli. Nat Commun 2023; 14:5304. [PMID: 37652926 PMCID: PMC10471632 DOI: 10.1038/s41467-023-40928-0] [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: 03/02/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Vitamin B6 is an essential nutrient with extensive applications in the medicine, food, animal feed, and cosmetics industries. Pyridoxine (PN), the most common commercial form of vitamin B6, is currently chemically synthesized using expensive and toxic chemicals. However, the low catalytic efficiencies of natural enzymes and the tight regulation of the metabolic pathway have hindered PN production by the microbial fermentation process. Here, we report an engineered Escherichia coli strain for PN production. Parallel pathway engineering is performed to decouple PN production and cell growth. Further, protein engineering is rationally designed including the inefficient enzymes PdxA, PdxJ, and the initial enzymes Epd and Dxs. By the iterative multimodule optimization strategy, the final strain produces 1.4 g/L of PN with productivity of 29.16 mg/L/h by fed-batch fermentation. The strategies reported here will be useful for developing microbial strains for the production of vitamins and other bioproducts having inherently low metabolic fluxes.
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Affiliation(s)
- Linxia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jinlong Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanming Gai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhizhong Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yanyan Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tenghe Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qianqian Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 four program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Li K, Li C, Zhao XQ, Liu CG, Bai FW. Engineering Corynebacterium glutamicum for efficient production of succinic acid from corn stover pretreated by concentrated-alkali under steam-assistant conditions. BIORESOURCE TECHNOLOGY 2023; 378:128991. [PMID: 37003455 DOI: 10.1016/j.biortech.2023.128991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Corynebacterium glutamicum was developed for efficient production of succinic acid from corn stover (CS) pretreated by concentrated-alkali under steam-assistant (CASA) conditions. First, C. glutamicum was engineered by 1) blocking the by-products pathways (deletion of ldh, pta-ackA, and cat), 2) enhancing the carbon flux to succinate (overexpression of pyc and ppc), and 3) releasing the end-product inhibition (overexpression of Ncgl0275). The recombinant strain produced 117.8 g/L succinate in fed-batch fermentation. Second, to fully utilize xylose in lignocellulosic hydrolysate, two xylose utilization pathways-the isomerase pathway and the Weimberg pathway-were introduced into the recombinant strain. Third, CS was pretreated by CASA with a higher sugars yield and a lower black liquid. Finally, 64.16 g/L of succinic acid was obtained from 150 g/L CASA-pretreated CS by engineered C. glutamicum. These results showed a succinate high-producing C. glutamicum strain using glucose and xylose simultaneously as well as an effective and environmentally acceptable pretreatment strategy.
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Affiliation(s)
- Kai Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Kuschmierz L, Shen L, Bräsen C, Snoep J, Siebers B. Workflows for optimization of enzyme cascades and whole cell catalysis based on enzyme kinetic characterization and pathway modelling. Curr Opin Biotechnol 2021; 74:55-60. [PMID: 34794111 DOI: 10.1016/j.copbio.2021.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/21/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
To move towards a circular bioeconomy, sustainable strategies for the utilization of renewable, non-food biomass wastes such as lignocellulose, are needed. To this end, an efficient bioconversion of d-xylose - after d-glucose the most abundant sugar in lignocellulose - is highly desirable. Most standard organisms used in biotechnology are limited in metabolising d-xylose, and also in vitro enzymatic strategies for its conversion have not been very successful. We herein discuss that bioconversion of d-xylose is mostly hampered by missing knowledge on the kinetic properties of the enzymes involved in its metabolism. We propose a combination of classical enzyme characterizations and mathematical modelling approaches as a workflow for rational, model-based design to optimize enzyme cascades and/or whole cell biocatalysts for efficient d-xylose metabolism.
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Affiliation(s)
- Laura Kuschmierz
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - Lu Shen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - Jacky Snoep
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa; Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany.
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