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Nastouli A, Moschona A, Bizirtsakis PA, Sweeney J, Angelidaki I, Harasek M, Karabelas AJ, Patsios SI. A Novel Bio-Purification Process Employing an Engineered E. coli Strain for Downstream Processing of Lactic Acid Solutions from the Fermentation of Agro-Industrial by-Products. Bioengineering (Basel) 2024; 11:412. [PMID: 38790280 PMCID: PMC11118208 DOI: 10.3390/bioengineering11050412] [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: 03/16/2024] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
This study aims to integrate a novel bio-purification process employing an engineered E. coli strain in the downstream processing of lactic acid (LA) fermentation broths from low-cost renewable biological feedstocks. Fermentation broth of candy waste and digestate mixture was used as a real biological feedstock. An engineered E. coli strain that selectively catabolize impurities without catabolizing LA was initially adapted on the biological feedstock, followed by shake flask experiments to prove the bio-purification concept. Scale-up and validation in a bench-scale bioreactor followed, before developing a semi-continuous membrane bioreactor (MBR) bio-purification process. The MBR bio-purification was assessed with biological feedstocks which simulated ultrafiltration or nanofiltration permeates. Incomplete removal of impurities and increased fouling was observed in the case of the ultrafiltration permeate. Contrarily, the nanofiltration permeate was successfully treated with MBR bio-purification, since low membrane fouling, 100% maltose and acetic acid removal, and no LA catabolism was achieved. MBR bio-purification as a post-treatment step in the downstream processing of LA was demonstrated as a promising technology for increasing the purity of LA solutions.
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Affiliation(s)
- Alexandra Nastouli
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, AT 1060 Vienna, Austria;
| | - Alexandra Moschona
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
| | - Panagiotis A. Bizirtsakis
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
| | - Joseph Sweeney
- School of Biosystems and Food Engineering, University College Dublin (UCD), D04 V1W8 Dublin, Ireland;
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark;
| | - Michael Harasek
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, AT 1060 Vienna, Austria;
| | - Anastasios J. Karabelas
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
| | - Sotiris I. Patsios
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
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2
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Jaroensuk J, Sutthaphirom C, Phonbuppha J, Chinantuya W, Kesornpun C, Akeratchatapan N, Kittipanukul N, Phatinuwat K, Atichartpongkul S, Fuangthong M, Pongtharangkul T, Hollmann F, Chaiyen P. A versatile in situ cofactor enhancing system for meeting cellular demands for engineered metabolic pathways. J Biol Chem 2024; 300:105598. [PMID: 38159859 PMCID: PMC10850783 DOI: 10.1016/j.jbc.2023.105598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/02/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
Cofactor imbalance obstructs the productivities of metabolically engineered cells. Herein, we employed a minimally perturbing system, xylose reductase and lactose (XR/lactose), to increase the levels of a pool of sugar phosphates which are connected to the biosynthesis of NAD(P)H, FAD, FMN, and ATP in Escherichia coli. The XR/lactose system could increase the amounts of the precursors of these cofactors and was tested with three different metabolically engineered cell systems (fatty alcohol biosynthesis, bioluminescence light generation, and alkane biosynthesis) with different cofactor demands. Productivities of these cells were increased 2-4-fold by the XR/lactose system. Untargeted metabolomic analysis revealed different metabolite patterns among these cells, demonstrating that only metabolites involved in relevant cofactor biosynthesis were altered. The results were also confirmed by transcriptomic analysis. Another sugar reducing system (glucose dehydrogenase) could also be used to increase fatty alcohol production but resulted in less yield enhancement than XR. This work demonstrates that the approach of increasing cellular sugar phosphates can be a generic tool to increase in vivo cofactor generation upon cellular demand for synthetic biology.
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Affiliation(s)
- Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chalermroj Sutthaphirom
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Jittima Phonbuppha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wachirawit Chinantuya
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Faculty of Science, Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Mahidol University, Bangkok, Thailand
| | - Chatchai Kesornpun
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Nattanon Akeratchatapan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Narongyot Kittipanukul
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Kamonwan Phatinuwat
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | | | - Mayuree Fuangthong
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand; Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | | | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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3
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Shin J, Liao S, Kuanyshev N, Xin Y, Kim C, Lu T, Jin YS. Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium. Nat Commun 2024; 15:781. [PMID: 38278783 PMCID: PMC10817915 DOI: 10.1038/s41467-024-45011-w] [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: 08/31/2022] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.
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Affiliation(s)
- Jonghyeok Shin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Siqi Liao
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nurzhan Kuanyshev
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yongping Xin
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chanwoo Kim
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ting Lu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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4
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Seo H, Castro G, Trinh CT. Engineering a Synthetic Escherichia coli Coculture for Compartmentalized de novo Biosynthesis of Isobutyl Butyrate from Mixed Sugars. ACS Synth Biol 2024; 13:259-268. [PMID: 38091519 PMCID: PMC10804408 DOI: 10.1021/acssynbio.3c00493] [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: 08/11/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/23/2024]
Abstract
Short-chain esters are versatile chemicals that can be used as flavors, fragrances, solvents, and fuels. The de novo ester biosynthesis consists of diverging and converging pathway submodules, which is challenging to engineer to achieve optimal metabolic fluxes and selective product synthesis. Compartmentalizing the pathway submodules into specialist cells that facilitate pathway modularization and labor division is a promising solution. Here, we engineered a synthetic Escherichia coli coculture with the compartmentalized sugar utilization and ester biosynthesis pathways to produce isobutyl butyrate from a mixture of glucose and xylose. To compartmentalize the sugar-utilizing pathway submodules, we engineered a xylose-utilizing E. coli specialist that selectively consumes xylose over glucose and bypasses carbon catabolite repression (CCR) while leveraging the native CCR machinery to activate a glucose-utilizing E. coli specialist. We found that the compartmentalization of sugar catabolism enabled simultaneous co-utilization of glucose and xylose by a coculture of the two E. coli specialists, improving the stability of the coculture population. Next, we modularized the isobutyl butyrate pathway into the isobutanol, butyl-CoA, and ester condensation submodules, where we distributed the isobutanol submodule to the glucose-utilizing specialist and the other submodules to the xylose-utilizing specialist. Upon compartmentalization of the isobutyl butyrate pathway submodules into these sugar-utilizing specialist cells, a robust synthetic coculture was engineered to selectively produce isobutyl butyrate, reduce the biosynthesis of unwanted ester byproducts, and improve the production titer as compared to the monoculture.
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Affiliation(s)
- Hyeongmin Seo
- Department
of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center
of Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Gillian Castro
- Department
of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Cong T. Trinh
- Department
of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center
of Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
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5
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Qiu Y, Qiu Z, Xia J, Liu X, Zhang H, Yang Y, Hou W, Li X, He J. Co-expression of Xylose Transporter and Fructose-Bisphosphate Aldolase Enhances the Utilization of Xylose by Lactococcus lactis IO-1. Appl Biochem Biotechnol 2023; 195:816-831. [PMID: 36205844 DOI: 10.1007/s12010-022-04168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
The raw material cost of lactic acid fermentation accounts for the main part of the production cost, and this necessitates the exploration of the efficient use of cheap raw materials in lactic acid production. We compared the outcomes of the homologous expressions of xylose transporters (xylFGH, xylE, araE, and xylT), 6-phosphofructokinase (pfkA), fructose-bisphosphate aldolase (fbaA), and their co-expression in Lactococcus lactis IO-1 on lactic acid production using xylose as the raw material. We found that the production rate of lactic acid on xylose fermentation by L. lactis IO-1 overexpressing fbaA was the highest (14.42%). Among the xylose transporters investigated, XylT had the strongest xylose transport capacity in L. lactis IO-1, with an increase in the lactic acid production rate by 10.38%. The genes near the overexpression of fbaA or xylT in the metabolic pathway were more upregulated than the distant genes. The co-expression of fbaA and xylT increased the production rate of lactic acid by 27.84% on xylose fermentation by L. lactis IO-1. This work presents a novel strategy for the simultaneous enhancement of the expression of important genes at the beginning and midway of the xylose metabolic pathway of L. lactis IO-1, which could greatly improve the target production.
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Affiliation(s)
- Yejuan Qiu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Zhongyang Qiu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Jun Xia
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Xiaoyan Liu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Hanwen Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Yuxiang Yang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Wenyi Hou
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Xiangqian Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China.
| | - Jianlong He
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China.
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6
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Zhang J, Wu D, Zhao Y, Liu D, Guo X, Chen Y, Zhang C, Sun X, Guo J, Yuan D, Xiao D, Li F, Song H. Engineering Shewanella oneidensis to efficiently harvest electricity power by co-utilizing glucose and lactate in thin stillage of liquor industry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158696. [PMID: 36108833 DOI: 10.1016/j.scitotenv.2022.158696] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Thin stillage, rich in glucose and lactate, can seriously pollute water resources when directly discharged into the natural environment. Microbial fuel cells (MFC), as a green and sustainable technology, could utilize exoelectrogens to break down organics in wastewater and harvest electricity. Nevertheless, Shewanella oneidensis MR-1, cannot utilize thin stillage for efficient power generation. Here, to enable S. oneidensis to co-utilize glucose and lactate from thin stillage, an engineered S. oneidensis G7∆RSL1 was first created by constructing glucose metabolism pathway, promoting glucose and lactate co-utilization, and enhancing biofilm formation. Then, to enhance biofilm conductivity, we constructed a 3D self-assembled G7∆RSL1-rGO/CNT biohybrid with maximum power density of 560.4 mW m-2 and 373.7 mW m-2 in artificial and actual thin stillage, respectively, the highest among the reported genetically engineered S. oneidensis with thin stillage as carbon source. This study provides a new strategy to facilitate practical applications of MFC in wastewater remediation and efficient power recovery.
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Affiliation(s)
- Junqi Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, PR China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China; Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Yakun Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Qingdao Institute of Ocean Engineering, Tianjin University, Qingdao 266200, Shandong, China
| | - Dingyuan Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, PR China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Cuiying Zhang
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Xi Sun
- College of Biological Engineering, Tianjin Agricultural University, Tianjin, PR China
| | - Ju Guo
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Dezhi Yuan
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Feng Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, PR China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Qingdao Institute of Ocean Engineering, Tianjin University, Qingdao 266200, Shandong, China.
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7
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Fu J, Li C, Ju X, Bai J, Zhou Y, Zhang Y, Wang Y, Sun Z, Hu C, Li L, Ji L. Efficient production of ε-poly-l-lysine from cassava bagasse hydrolysate used as carbon source by Streptomyces albulus US3-18. Bioprocess Biosyst Eng 2022; 45:1407-1419. [DOI: 10.1007/s00449-022-02755-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
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8
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Dahle ML, Papoutsakis ET, Antoniewicz MR. 13C-metabolic flux analysis of Clostridium ljungdahlii illuminates its core metabolism under mixotrophic culture conditions. Metab Eng 2022; 72:161-170. [DOI: 10.1016/j.ymben.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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Wang K, Wang X, Luo H, Wang Y, Wang Y, Tu T, Qin X, Bai Y, Huang H, Yao B, Su X, Zhang J. Synergetic Fermentation of Glucose and Glycerol for High-Yield N-Acetylglucosamine Production in Escherichia coli. Int J Mol Sci 2022; 23:ijms23020773. [PMID: 35054959 PMCID: PMC8775389 DOI: 10.3390/ijms23020773] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/28/2021] [Accepted: 01/09/2022] [Indexed: 01/13/2023] Open
Abstract
N-acetylglucosamine (GlcNAc) is an amino sugar that has been widely used in the nutraceutical and pharmaceutical industries. Recently, microbial production of GlcNAc has been developed. One major challenge for efficient biosynthesis of GlcNAc is to achieve appropriate carbon flux distribution between growth and production. Here, a synergistic substrate co-utilization strategy was used to address this challenge. Specifically, glycerol was utilized to support cell growth and generate glutamine and acetyl-CoA, which are amino and acetyl donors, respectively, for GlcNAc biosynthesis, while glucose was retained for GlcNAc production. Thanks to deletion of the 6-phosphofructokinase (PfkA and PfkB) and glucose-6-phosphate dehydrogenase (ZWF) genes, the main glucose catabolism pathways of Escherichia coli were blocked. The resultant mutant showed a severe defect in glucose consumption. Then, the GlcNAc production module containing glucosamine-6-phosphate synthase (GlmS*), glucosamine-6-phosphate N-acetyltransferase (GNA1*) and GlcNAc-6-phosphate phosphatase (YqaB) expression cassettes was introduced into the mutant, to drive the carbon flux from glucose to GlcNAc. Furthermore, co-utilization of glucose and glycerol was achieved by overexpression of glycerol kinase (GlpK) gene. Using the optimized fermentation medium, the final strain produced GlcNAc with a high stoichiometric yield of 0.64 mol/mol glucose. This study offers a promising strategy to address the challenge of distributing carbon flux in GlcNAc production.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Xiaoyun Su
- Correspondence: (X.S.); (J.Z.); Tel.: +86-10-62599910 (X.S. & J.Z.)
| | - Jie Zhang
- Correspondence: (X.S.); (J.Z.); Tel.: +86-10-62599910 (X.S. & J.Z.)
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10
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Yin W, Cao Y, Jin M, Xian M, Liu W. Metabolic Engineering of E. coli for Xylose Production from Glucose as the Sole Carbon Source. ACS Synth Biol 2021; 10:2266-2275. [PMID: 34412469 DOI: 10.1021/acssynbio.1c00184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Xylose is the raw material for the synthesis of many important platform compounds. At present, xylose is commercially produced by chemical extraction. However, there are still some bottlenecks in the extraction of xylose, including complicated operation processes and the chemical substances introduced, leading to the high cost of xylose and of synthesizing the downstream compounds of xylose. The current market price of xylose is 8× that of glucose, so using low-cost glucose as the substrate to produce the downstream compounds of xylose can theoretically reduce the cost by 70%. Here, we designed a pathway for the biosynthesis of xylose from glucose in Escherichia coli. This biosynthetic pathway was achieved by overexpressing five genes, namely, zwf, pgl, gnd, rpe, and xylA, while replacing the native xylulose kinase gene xylB with araL from B. subtilis, which displays phosphatase activity toward d-xylulose 5-phosphate. The yield of xylose was increased to 3.3 g/L by optimizing the metabolic pathway. Furthermore, xylitol was successfully synthesized by introducing the xyl1 gene, which suggested that the biosynthetic pathway of xylose from glucose is universally applicable for the synthesis of xylose downstream compounds. This is the first study to synthesize xylose and its downstream compounds by using glucose as a substrate, which not only reduces the cost of raw materials, but also alleviates carbon catabolite repression (CCR), providing a new idea for the synthesis of downstream compounds of xylose.
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Affiliation(s)
- Wencheng Yin
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yujin Cao
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Miaomiao Jin
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Mo Xian
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Wei Liu
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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11
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Wu Y, Jameel A, Xing XH, Zhang C. Advanced strategies and tools to facilitate and streamline microbial adaptive laboratory evolution. Trends Biotechnol 2021; 40:38-59. [PMID: 33958227 DOI: 10.1016/j.tibtech.2021.04.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/17/2021] [Accepted: 04/01/2021] [Indexed: 12/18/2022]
Abstract
Adaptive laboratory evolution (ALE) has served as a historic microbial engineering method that mimics natural selection to obtain desired microbes. The past decade has witnessed improvements in all aspects of ALE workflow, in terms of growth coupling, genotypic diversification, phenotypic selection, and genotype-phenotype mapping. The developing growth-coupling strategies facilitate ALE to a wider range of appealing traits. In vivo mutagenesis methods and multiplexed automated culture platforms open new gates to streamline its execution. Meanwhile, the application of multi-omics analyses and multiplexed genetic engineering promote efficient knowledge mining. This article provides a comprehensive and updated review of these advances, highlights newest significant applications, and discusses future improvements, aiming to provide a practical guide for implementation of novel, effective, and efficient ALE experiments.
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Affiliation(s)
- Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Aysha Jameel
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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12
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Adaptive laboratory evolution of methylotrophic Escherichia coli enables synthesis of all amino acids from methanol-derived carbon. Appl Microbiol Biotechnol 2021; 105:869-876. [PMID: 33404828 DOI: 10.1007/s00253-020-11058-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/21/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
Abstract
Recent attempts to create synthetic Escherichia coli methylotrophs identified that de novo biosynthesis of amino acids, in the presence of methanol, presents significant challenges in achieving autonomous methylotrophic growth. Previously engineered methanol-dependent strains required co-utilization of stoichiometric amounts of co-substrates and methanol. As such, these strains could not be evolved to grow on methanol alone. In this work, we have explored an alternative approach to enable biosynthesis of all amino acids from methanol-derived carbon in minimal media without stoichiometric coupling. First, we identified that biosynthesis of threonine was limiting the growth of our methylotrophic E. coli. To address this, we performed adaptive laboratory evolution to generate a strain that grew efficiently in minimal medium with methanol and threonine. Methanol assimilation and growth of the evolved strain were analyzed, and, interestingly, we found that the evolved strain synthesized all amino acids, including threonine, from methanol-derived carbon. The evolved strain was then further engineered through overexpression of an optimized threonine biosynthetic pathway. We show that the resulting methylotrophic E. coli strain has a methanol-dependent growth phenotype with homoserine as co-substrate. In contrast to previous methanol-dependent strains, co-utilization of homoserine is not stoichiometrically linked to methanol assimilation. As such, future engineering of this strain and successive adaptive evolution could enable autonomous growth on methanol as the sole carbon source. KEY POINTS: • Adaptive evolution of E. coli enables biosynthesis of all amino acids from methanol. • Overexpression of threonine biosynthesis pathway improves methanol assimilation. • Methanol-dependent growth is seen in minimal media with homoserine as co-substrate.
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13
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Wu M, Zhao X, Shen Y, Shi Z, Li G, Ma T. Efficient simultaneous utilization of glucose and xylose from corn straw by Sphingomonas sanxanigenens NX02 to produce microbial exopolysaccharide. BIORESOURCE TECHNOLOGY 2021; 319:124126. [PMID: 32971336 DOI: 10.1016/j.biortech.2020.124126] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
Lignocellulosic biomass is a cheap and abundant carbon source in the microbial manufacturing industry. The native co-utilization of glucose and xylose from corn straw total hydrolysate (CSTH) by Sphingomonas sanxanigenens NX02 to produce exopolysaccharide Sanxan was investigated. Batch fermentation demonstrated that, compared to single sugar fermentation, co-substrate of glucose and xylose accelerated cell growth and Sanxan production in the initial 24 h with the same consumption rate. Additionally, NX02 converted CSTH into Sanxan with a yield of 13.10 ± 0.35 g/Kg, which is slightly higher than that of glucose fermentation. Coexistence of three xylose metabolic pathways (Xylose isomerase, Weimberg, and Dahms pathway), incomplete phosphoenolpyruvate-dependent phosphotransferase system, and reinforced fructose metabolism were recognized as the co-utilization mechanism through comparative transcriptome analysis. Therefore, strain NX02 has a prospect of becoming an attractive platform organism to produce polysaccharides and other bio-based products derived from agricultural waste hydrolysate rich in both glucose and xylose.
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Affiliation(s)
- Mengmeng Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xin Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yaqi Shen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhuangzhuang Shi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
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14
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Opening a Novel Biosynthetic Pathway to Dihydroxyacetone and Glycerol in Escherichia coli Mutants through Expression of a Gene Variant ( fsaAA129S) for Fructose 6-Phosphate Aldolase. Int J Mol Sci 2020; 21:ijms21249625. [PMID: 33348713 PMCID: PMC7767278 DOI: 10.3390/ijms21249625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/05/2020] [Accepted: 12/15/2020] [Indexed: 01/19/2023] Open
Abstract
Phosphofructokinase (PFK) plays a pivotal role in glycolysis. By deletion of the genes pfkA, pfkB (encoding the two PFK isoenzymes), and zwf (glucose 6-phosphate dehydrogenase) in Escherichia coli K-12, a mutant strain (GL3) with a complete block in glucose catabolism was created. Introduction of plasmid-borne copies of the fsaA wild type gene (encoding E. coli fructose 6-phosphate aldolase, FSAA) did not allow a bypass by splitting fructose 6-phosphate (F6P) into dihydroxyacetone (DHA) and glyceraldehyde 3-phosphate (G3P). Although FSAA enzyme activity was detected, growth on glucose was not reestablished. A mutant allele encoding for FSAA with an amino acid exchange (Ala129Ser) which showed increased catalytic efficiency for F6P, allowed growth on glucose with a µ of about 0.12 h−1. A GL3 derivative with a chromosomally integrated copy of fsaAA129S (GL4) grew with 0.05 h−1 on glucose. A mutant strain from GL4 where dhaKLM genes were deleted (GL5) excreted DHA. By deletion of the gene glpK (glycerol kinase) and overexpression of gldA (of glycerol dehydrogenase), a strain (GL7) was created which showed glycerol formation (21.8 mM; yield approximately 70% of the theoretically maximal value) as main end product when grown on glucose. A new-to-nature pathway from glucose to glycerol was created.
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15
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Satanowski A, Dronsella B, Noor E, Vögeli B, He H, Wichmann P, Erb TJ, Lindner SN, Bar-Even A. Awakening a latent carbon fixation cycle in Escherichia coli. Nat Commun 2020; 11:5812. [PMID: 33199707 PMCID: PMC7669889 DOI: 10.1038/s41467-020-19564-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
Carbon fixation is one of the most important biochemical processes. Most natural carbon fixation pathways are thought to have emerged from enzymes that originally performed other metabolic tasks. Can we recreate the emergence of a carbon fixation pathway in a heterotrophic host by recruiting only endogenous enzymes? In this study, we address this question by systematically analyzing possible carbon fixation pathways composed only of Escherichia coli native enzymes. We identify the GED (Gnd-Entner-Doudoroff) cycle as the simplest pathway that can operate with high thermodynamic driving force. This autocatalytic route is based on reductive carboxylation of ribulose 5-phosphate (Ru5P) by 6-phosphogluconate dehydrogenase (Gnd), followed by reactions of the Entner-Doudoroff pathway, gluconeogenesis, and the pentose phosphate pathway. We demonstrate the in vivo feasibility of this new-to-nature pathway by constructing E. coli gene deletion strains whose growth on pentose sugars depends on the GED shunt, a linear variant of the GED cycle which does not require the regeneration of Ru5P. Several metabolic adaptations, most importantly the increased production of NADPH, assist in establishing sufficiently high flux to sustain this growth. Our study exemplifies a trajectory for the emergence of carbon fixation in a heterotrophic organism and demonstrates a synthetic pathway of biotechnological interest.
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Affiliation(s)
- Ari Satanowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Beau Dronsella
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland
| | - Bastian Vögeli
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Hai He
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Philipp Wichmann
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), 35043, Marburg, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany.
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
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16
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Antoniewicz MR. A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications. Metab Eng 2020; 63:2-12. [PMID: 33157225 DOI: 10.1016/j.ymben.2020.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
The field of metabolic engineering is primarily concerned with improving the biological production of value-added chemicals, fuels and pharmaceuticals through the design, construction and optimization of metabolic pathways, redirection of intracellular fluxes, and refinement of cellular properties relevant for industrial bioprocess implementation. Metabolic network models and metabolic fluxes are central concepts in metabolic engineering, as was emphasized in the first paper published in this journal, "Metabolic fluxes and metabolic engineering" (Metabolic Engineering, 1: 1-11, 1999). In the past two decades, a wide range of computational, analytical and experimental approaches have been developed to interrogate the capabilities of biological systems through analysis of metabolic network models using techniques such as flux balance analysis (FBA), and quantify metabolic fluxes using constrained-based modeling approaches such as metabolic flux analysis (MFA) and more advanced experimental techniques based on the use of stable-isotope tracers, i.e. 13C-metabolic flux analysis (13C-MFA). In this review, we describe the basic principles of metabolic flux analysis, discuss current best practices in flux quantification, highlight potential pitfalls and alternative approaches in the application of these tools, and give a broad overview of pragmatic applications of flux analysis in metabolic engineering practice.
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Affiliation(s)
- Maciek R Antoniewicz
- Department of Chemical Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Michigan, Ann Arbor, MI, 48109, USA.
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17
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Li N, Zeng W, Xu S, Zhou J. Toward fine-tuned metabolic networks in industrial microorganisms. Synth Syst Biotechnol 2020; 5:81-91. [PMID: 32542205 PMCID: PMC7283098 DOI: 10.1016/j.synbio.2020.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/30/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
There are numerous microorganisms in nature capable of synthesizing diverse useful compounds; however, these natural microorganisms are generally inefficient in the production of target products on an industrial scale, relative to either chemical synthesis or extraction methods. To achieve industrial production of useful compounds, these natural microorganisms must undergo a certain degree of mutation or effective fine-tuning strategies. This review describes how to achieve an ideal metabolic fine-tuned process, including static control strategies and dynamic control strategies. The static control strategies mainly focus on various matabolic engineering strategies, including protein engineering, upregulation/downregulation, and combinatrorial control of these metabolic engineering strategies, to enhance the flexibility of their application in fine-tuned metabolic metworks. Then, we focus on the dynamic control strategies for fine-tuned metabolic metworks. The design principles derived would guide us to construct microbial cell factories for various useful compounds.
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Affiliation(s)
- Ning Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
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18
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Bennett RK, Dillon M, Gerald Har JR, Agee A, von Hagel B, Rohlhill J, Antoniewicz MR, Papoutsakis ET. Engineering Escherichia coli for methanol-dependent growth on glucose for metabolite production. Metab Eng 2020; 60:45-55. [PMID: 32179162 DOI: 10.1016/j.ymben.2020.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/25/2020] [Accepted: 03/08/2020] [Indexed: 02/05/2023]
Abstract
Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methanol auxotrophs have proved successful, these studies focused on scarce and expensive co-substrates. Here, we engineered E. coli for methanol-dependent growth on glucose, an abundant and inexpensive co-substrate, via deletion of glucose 6-phosphate isomerase (pgi), phosphogluconate dehydratase (edd), and ribose 5-phosphate isomerases (rpiAB). Since the parental strain did not exhibit methanol-dependent growth on glucose in minimal medium, we first achieved methanol-dependent growth via amino acid supplementation and used this medium to evolve the strain for methanol-dependent growth in glucose minimal medium. The evolved strain exhibited a maximum growth rate of 0.15 h-1 in glucose minimal medium with methanol, which is comparable to that of other synthetic methanol auxotrophs. Whole genome sequencing and 13C-metabolic flux analysis revealed the causative mutations in the evolved strain. A mutation in the phosphotransferase system enzyme I gene (ptsI) resulted in a reduced glucose uptake rate to maintain a one-to-one molar ratio of substrate utilization. Deletion of the e14 prophage DNA region resulted in two non-synonymous mutations in the isocitrate dehydrogenase (icd) gene, which reduced TCA cycle carbon flux to maintain the internal redox state. In high cell density glucose fed-batch fermentation, methanol-dependent acetone production resulted in 22% average carbon labeling of acetone from 13C-methanol, which far surpasses that of the previous best (2.4%) found with methylotrophic E. coli Δpgi. This study addresses the need to identify appropriate co-substrates for engineering synthetic methanol auxotrophs and provides a basis for the next steps toward industrial one-carbon bioprocessing.
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Affiliation(s)
- R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Michael Dillon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Jie Ren Gerald Har
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
| | - Alec Agee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Bryan von Hagel
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Julia Rohlhill
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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19
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Alva A, Sabido-Ramos A, Escalante A, Bolívar F. New insights into transport capability of sugars and its impact on growth from novel mutants of Escherichia coli. Appl Microbiol Biotechnol 2020; 104:1463-1479. [PMID: 31900563 DOI: 10.1007/s00253-019-10335-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/12/2019] [Accepted: 12/27/2019] [Indexed: 12/27/2022]
Abstract
The fast-growing capability of Escherichia coli strains used to produce industrially relevant metabolites relies on their capability to transport efficiently glucose or potential industrial feedstocks such as sucrose or xylose as carbon sources. E. coli imports extracellular glucose into the periplasmic space across the outer membrane porins: OmpC, OmpF, and LamB. As the internal membrane is an impermeable barrier for sugars, the cell employs several primary and secondary active transport systems, and the phosphoenolpyruvate (PEP)-sugar phosphotransferase (PTS) system for glucose transport. PTS:glucose is the preferred system by E. coli to transport and phosphorylate the periplasmic glucose; nevertheless, PTS imposes a strict metabolic control mechanism on the preferential consumption of glucose over other carbon sources in sugar mixtures such as glucose and xylose resulting from the hydrolysis of lignocellulosic biomass, by the carbon catabolite repression. In this contribution, we summarize the major sugar transport systems for glucose and disaccharide transport, the exhibited substrate plasticity, and their impact on the growth of E. coli, highlighting the relevance of PTS in the control of the expression of genes for the transport and catabolism of other sugars as xylose. We discuss the strategies developed by evolved mutants of E. coli during adaptive laboratory evolution experiments to overcome the nutritional stress condition imposed by inactivation of PTS as a strategy for the selection of fast-growing derivatives in glucose, xylose, or mixtures of glucose:xylose. This approach results in the recruitment of other primary and secondary active transporters, demonstrating relevant sugar plasticity in derivative-evolved mutants. Elucidation of the molecular and biochemical basis of sugar-transport substrate plasticity represents a consistent approach for sugar-transport system engineering for the design of efficient E. coli derivative strains with improved substrate assimilation for biotechnological purposes.
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Affiliation(s)
- Alma Alva
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Andrea Sabido-Ramos
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Unidad Cuajimalpa, Ciudad de México, México
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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20
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Long CP, Antoniewicz MR. Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism. Metab Eng 2019; 55:249-257. [DOI: 10.1016/j.ymben.2019.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/03/2019] [Accepted: 08/03/2019] [Indexed: 02/08/2023]
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21
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Antoniewicz MR. Synthetic methylotrophy: Strategies to assimilate methanol for growth and chemicals production. Curr Opin Biotechnol 2019; 59:165-174. [PMID: 31437746 DOI: 10.1016/j.copbio.2019.07.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/12/2019] [Accepted: 07/17/2019] [Indexed: 11/29/2022]
Abstract
Methanol is an attractive and broadly available substrate for large-scale bioproduction of fuels and chemicals. It contains more energy and electrons per carbon than carbohydrates and can be cheaply produced from natural gas. Synthetic methylotrophy refers to the development of non-native methylotrophs such as Escherichia coli and Corynebacterium glutamicum to utilize methanol as a carbon source. Here, we discuss recent advances in engineering these industrial hosts to assimilate methanol for growth and chemicals production through the introduction of the ribulose monophosphate (RuMP) cycle. In addition, we present novel strategies based on flux coupling and adaptive laboratory evolution to engineer new strains that can grow exclusively on methanol.
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Affiliation(s)
- Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark DE 19716, USA.
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