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Wang L, Yao J, Tu T, Yao B, Zhang J. Heterotrophic and autotrophic production of L-isoleucine and L-valine by engineered Cupriavidus necator H16. Bioresour Technol 2024; 398:130538. [PMID: 38452952 DOI: 10.1016/j.biortech.2024.130538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/14/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Advancement in commodity chemical production from carbon dioxide (CO2) offers a promising path towards sustainable development goal. Cupriavidus necator is an ideal host to convert CO2 into high-value chemicals, thereby achieving this target. Here, C. necator was engineered for heterotrophic and autotrophic production of L-isoleucine and L-valine. Citramalate synthase was introduced to simplify isoleucine synthesis pathway. Blocking poly-hydroxybutyrate biosynthesis resulted in significant accumulation of isoleucine and valine. Besides, strategies like key enzymes screening and overexpressing, reducing power balancing and feedback inhibition removing were applied in strain modification. Finally, the maximum isoleucine and valine titers of the best isoleucine-producing and valine-producing strains reached 857 and 972 mg/L, respectively, in fed-batch fermentation using glucose as substrate, and 105 and 319 mg/L, respectively, in autotrophic fermentation using CO2 as substrate. This study provides a feasible solution for developing C. necator as a microbial factory to produce amino acids from CO2.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Nam SH, Ye DY, Hwang HG, Jung GY. Convergent Synthesis of Two Heterogeneous Fluxes from Glucose and Acetate for High-Yield Citramalate Production. J Agric Food Chem 2024; 72:5797-5804. [PMID: 38465388 DOI: 10.1021/acs.jafc.3c09466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Biological production of citramalate has garnered attention due to its wide application for food additives and pharmaceuticals, although improvement of yield is known to be challenging. When glucose is used as the sole carbon source, carbon loss through decarboxylation steps for providing acetyl-CoA from pyruvate is inevitable. To avoid this, we engineered a strain to co-utilize glucose and cost-effective acetate while preventing carbon loss for enhancing citramalate production. The production pathway diverged to independently supply the precursors required for the synthesis of citramalate from glucose and acetate, respectively. Moreover, the phosphotransferase system was inactivated and the acetate assimilation pathway and the substrate ratio were optimized to enable the simultaneous and efficient utilization of both carbon sources. This yielded results (5.0 g/L, 0.87 mol/mol) surpassing the yield and titer of the control strain utilizing glucose as the sole carbon source in flask cultures, demonstrating an economically efficient strain redesign strategy for synthesizing various products.
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Affiliation(s)
- Sung Hyun Nam
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
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Lee HK, Woo S, Baek D, Min M, Jung GY, Lim HG. Direct and robust citramalate production from brown macroalgae using fast-growing Vibrio sp. dhg. Bioresour Technol 2024; 394:130304. [PMID: 38211713 DOI: 10.1016/j.biortech.2024.130304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/29/2023] [Accepted: 01/06/2024] [Indexed: 01/13/2024]
Abstract
Brown macroalgae is a promising feedstock for biorefinery owing to its high biomass productivity and contents of carbohydrates such as alginate and mannitol. However, the limited availability of microbial platforms efficiently catabolizing the brown macroalgae sugars has restricted its utilization. In this study, the direct production of citramalate, an important industrial compound, was demonstrated from brown macroalgae by utilizing Vibrio sp. dhg, which has a remarkably efficient catabolism of alginate and mannitol. Specifically, citramalate synthase from Methanocaldococcus jannaschii was synthetically expressed, and competing pathways were removed to maximally redirect the carbon flux toward citramalate production. Notably, a resulting strain, VXHC, produced citramalate up to 9.8 g/L from a 20 g/L mixture of alginate and mannitol regardless of their ratios. Citramalate was robustly produced even when diverse brown macroalgae were provided directly. Collectively, this study showcased the high potential of brown macroalgae biorefinery using Vibrio sp. dhg.
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Affiliation(s)
- Hye Kyung Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sunghwa Woo
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Dongyeop Baek
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Myeongwon Min
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea.
| | - Hyun Gyu Lim
- Department of Biological Engineering, Inha University, 100 Inha-Ro, Michuhol-Gu, Incheon 22212, Korea.
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Faulkner M, Hoeven R, Kelly PP, Sun Y, Park H, Liu LN, Toogood HS, Scrutton NS. Chemoautotrophic production of gaseous hydrocarbons, bioplastics and osmolytes by a novel Halomonas species. Biotechnol Biofuels Bioprod 2023; 16:152. [PMID: 37821908 PMCID: PMC10568851 DOI: 10.1186/s13068-023-02404-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Production of relatively low value, bulk commodity chemicals and fuels by microbial species requires a step-change in approach to decrease the capital and operational costs associated with scaled fermentation. The utilisation of the robust and halophilic industrial host organisms of the genus Halomonas could dramatically decrease biomanufacturing costs owing to their ability to grow in seawater, using waste biogenic feedstocks, under non-sterile conditions. RESULTS We describe the isolation of Halomonas rowanensis, a novel facultative chemoautotrophic species of Halomonas from a natural brine spring. We investigated the ability of this species to produce ectoine, a compound of considerable industrial interest, under heterotrophic conditions. Fixation of radiolabelled NaH14CO3 by H. rowanensis was confirmed in mineral medium supplied with thiosulfate as an energy source. Genome sequencing suggested carbon fixation proceeds via a reductive tricarboxylic acid cycle, and not the Calvin-Bensen-Bassham cycle. The mechanism of energy generation to support chemoautotrophy is unknown owing to the absence of an annotated SOX-based thiosulfate-mediated energy conversion system. We investigated further the biotechnological potential of the isolated H. rowanensis by demonstrating production of the gaseous hydrocarbon (bio-propane), bioplastics (poly-3-hydroxybutyrate) and osmolytes (ectoine) under heterotrophic and autotrophic CO2 fixation growth conditions. CONCLUSIONS This proof-of-concept study illustrates the value of recruiting environmental isolates as industrial hosts for chemicals biomanufacturing, where CO2 utilisation could replace, or augment, the use of biogenic feedstocks in non-sterile, industrialised bioreactors.
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Affiliation(s)
- Matthew Faulkner
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Robin Hoeven
- C3 Biotechnologies Ltd, 20 Mannin Way, Caton Road, Lancaster, LA1 35W, Lancashire, UK
- Engineering Building A, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Paul P Kelly
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - Helen Park
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - Helen S Toogood
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- C3 Biotechnologies Ltd, 20 Mannin Way, Caton Road, Lancaster, LA1 35W, Lancashire, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- C3 Biotechnologies Ltd, 20 Mannin Way, Caton Road, Lancaster, LA1 35W, Lancashire, UK.
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Ye DY, Moon JH, Jung GY. Recent Progress in Metabolic Engineering of Escherichia coli for the Production of Various C4 and C5-Dicarboxylic Acids. J Agric Food Chem 2023; 71:10916-10931. [PMID: 37458388 DOI: 10.1021/acs.jafc.3c02156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
As an alternative to petrochemical synthesis, well-established industrial microbes, such as Escherichia coli, are employed to produce a wide range of chemicals, including dicarboxylic acids (DCAs), which have significant potential in diverse areas including biodegradable polymers. The demand for biodegradable polymers has been steadily rising, prompting the development of efficient production pathways on four- (C4) and five-carbon (C5) DCAs derived from central carbon metabolism to meet the increased demand via the biosynthesis. In this context, E. coli is utilized to produce these DCAs through various metabolic engineering strategies, including the design or selection of metabolic pathways, pathway optimization, and enhancement of catalytic activity. This review aims to highlight the recent advancements in metabolic engineering techniques for the production of C4 and C5 DCAs in E. coli.
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Affiliation(s)
- Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
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Apel C, Levasseur M, Lejeune C, Korch SB, Guérard F, David M, Askora A, Litaudon M, Roussi F, Gakière B, Chaput J, Virolle MJ. Metabolic adjustments in response to ATP spilling by the small DX protein in a Streptomyces strain. Front Cell Dev Biol 2023; 11:1129009. [PMID: 36968208 PMCID: PMC10030506 DOI: 10.3389/fcell.2023.1129009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
ATP wasting is recognized as an efficient strategy to enhance metabolic activity and productivity of specific metabolites in several microorganisms. However, such strategy has been rarely implemented in Streptomyces species whereas antibiotic production by members of this genus is known to be triggered in condition of phosphate limitation that is correlated with a low ATP content. In consequence, to assess the effects of ATP spilling on the primary and specialized metabolisms of Streptomyces, the gene encoding the small synthetic protein DX, that has high affinity for ATP and dephosphorylates ATP into ADP, was cloned in the integrative vector pOSV10 under the control of the strong ErmE promoter. This construct and the empty vector were introduced into the species Streptomyces albogriseolus/viridodiastaticus yielding A37 and A36, respectively. A37 yielded higher biomass than A36 indicating that the DX-mediated ATP degradation resulted into a stimulation of A37 metabolism, consistently with what was reported in other microorganisms. The comparative analysis of the metabolomes of A36 and A37 revealed that A37 had a lower content in glycolytic and Tricarboxylic Acid Cycle intermediates as well as in amino acids than A36, these metabolites being consumed for biomass generation in A37. In contrast, the abundance of other molecules indicative either of energetic stress (ADP, AMP, UMP, ornithine and thymine), of activation (NAD and threonic acid) or inhibition (citramalic acid, fatty acids, TAG and L-alanine) of the oxidative metabolism, was higher in A37 than in A36. Furthermore, hydroxyl-pyrimidine derivatives and polycyclic aromatic polyketide antibiotics belonging to the angucycline class and thought to have a negative impact on respiration were also more abundantly produced by A37 than by A36. This comparative analysis thus revealed the occurrence in A37 of antagonistic metabolic strategies, namely, activation or slowing down of oxidative metabolism and respiration, to maintain the cellular energetic balance. This study thus demonstrated that DX constitutes an efficient biotechnological tool to enhance the expression of the specialized metabolic pathways present in the Streptomyces genomes that may include cryptic pathways. Its use thus might lead to the discovery of novel bioactive molecules potentially useful to human health.
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Affiliation(s)
- Cécile Apel
- Département de Chimie des Substances Naturelles et Chimie Médicinale, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Marceau Levasseur
- Département de Chimie des Substances Naturelles et Chimie Médicinale, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Clara Lejeune
- Département de Microbiologie, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Université Paris-Saclay, CEA, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Shaleen B. Korch
- Department of Pharmacology, College of Graduate Studies, Midwestern University, Glendale, AZ, United States
| | - Florence Guérard
- Plateforme SPOmics-Métabolome, Institut des Sciences des Plantes (IPS2), UMR 9213, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Michelle David
- Département de Microbiologie, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Université Paris-Saclay, CEA, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Ahmed Askora
- Département de Microbiologie, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Université Paris-Saclay, CEA, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Marc Litaudon
- Département de Chimie des Substances Naturelles et Chimie Médicinale, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Fanny Roussi
- Département de Chimie des Substances Naturelles et Chimie Médicinale, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - Bertrand Gakière
- Plateforme SPOmics-Métabolome, Institut des Sciences des Plantes (IPS2), UMR 9213, Université Paris-Saclay, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
| | - John Chaput
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Marie-Joelle Virolle
- Département de Microbiologie, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Université Paris-Saclay, CEA, Centre National de le Recherche Scientifique, Gif-sur-Yvette, France
- *Correspondence: Marie-Joelle Virolle,
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Wu ZY, Sun W, Shen Y, Pratas J, Suthers PF, Hsieh PH, Dwaraknath S, Rabinowitz JD, Maranas CD, Shao Z, Yoshikuni Y. Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis, for production of citramalate. Metab Eng Commun 2023; 16:e00220. [PMID: 36860699 PMCID: PMC9969067 DOI: 10.1016/j.mec.2023.e00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Methyl methacrylate (MMA) is an important petrochemical with many applications. However, its manufacture has a large environmental footprint. Combined biological and chemical synthesis (semisynthesis) may be a promising alternative to reduce both cost and environmental impact, but strains that can produce the MMA precursor (citramalate) at low pH are required. A non-conventional yeast, Issatchenkia orientalis, may prove ideal, as it can survive extremely low pH. Here, we demonstrate the engineering of I. orientalis for citramalate production. Using sequence similarity network analysis and subsequent DNA synthesis, we selected a more active citramalate synthase gene (cimA) variant for expression in I. orientalis. We then adapted a piggyBac transposon system for I. orientalis that allowed us to simultaneously explore the effects of different cimA gene copy numbers and integration locations. A batch fermentation showed the genome-integrated-cimA strains produced 2.0 g/L citramalate in 48 h and a yield of up to 7% mol citramalate/mol consumed glucose. These results demonstrate the potential of I. orientalis as a chassis for citramalate production.
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Affiliation(s)
- Zong-Yen Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Wan Sun
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011-1027, USA,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yihui Shen
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Jimmy Pratas
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Patrick F. Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA,Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ping-Hung Hsieh
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sudharsan Dwaraknath
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA,Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Zengyi Shao
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011-1027, USA,Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA,Bioeconomy Institute, Iowa State University, Ames, IA, 50011, USA,The Ames Laboratory, Ames, IA, 50011, USA,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA,Corresponding author. Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011-1027, USA.
| | - Yasuo Yoshikuni
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA,Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA,Global Center for Food, Land, and Water Resources, Hokkaido University, Hokkaido, 060-8589, Japan,Corresponding author. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Umino M, Onozato M, Sakamoto T, Koishi M, Fukushima T. Analyzing Citramalic Acid Enantiomers in Apples and Commercial Fruit Juice by Liquid Chromatography-Tandem Mass Spectrometry with Pre-Column Derivatization. Molecules 2023; 28. [PMID: 36838544 DOI: 10.3390/molecules28041556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Optically active citramalic acid (CMA) is naturally present as an acidic taste component in fruits, such as apples. The absolute configuration of CMA in such fruits was investigated by high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) following pre-column derivatization with a chiral reagent, benzyl 5-(2-aminoethyl)-3-methyl-4-oxoimidazolidine-1-carboxylate. The developed LC-MS/MS method successfully separated the enantiomers of CMA using an octadecylsilica column with a resolution and separation factor of 2.19 and 1.09, respectively. Consequently, the R-form of CMA was detected in the peel and fruit of three kinds of apple at concentrations in the 1.24-37.8 and 0.138-1.033 mg/wet 100 g ranges, respectively. In addition, R- CMA was present in commercial apple juice, whereas no quantity was detected in commercial blueberry, perilla, or Japanese apricot juice.
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Allen JR, Torres-Acosta MA, Mohan N, Lye GJ, Ward JM. Segregationally stabilised plasmids improve production of commodity chemicals in glucose-limited continuous fermentation. Microb Cell Fact 2022; 21:229. [PMID: 36329510 PMCID: PMC9632041 DOI: 10.1186/s12934-022-01958-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/24/2022] [Indexed: 11/05/2022] Open
Abstract
Background The production of chemicals via bio-based routes is held back by limited easy-to-use stabilisation systems. A wide range of plasmid stabilisation mechanisms can be found in the literature, however, how these mechanisms effect genetic stability and how host strains still revert to non-productive variants is poorly understood at the single-cell level. This phenomenon can generate difficulties in production-scale bioreactors as different populations of productive and non-productive cells can arise. To understand how to prevent non-productive strains from arising, it is vital to understand strain behaviour at a single-cell level. The persistence of genes located on plasmid vectors is dependent on numerous factors but can be broadly separated into structural stability and segregational stability. While structural stability refers to the capability of a cell to resist genetic mutations that bring about a loss of gene function in a production pathway, segregational stability refers to the capability of a cell to correctly distribute plasmids into daughter cells to maintain copy number. A lack of segregational stability can rapidly generate plasmid-free variants during replication, which compromises productivity. Results Citramalate synthase expression was linked in an operon to the expression of a fluorescent reporter to enable rapid screening of the retention of a model chemical synthesis pathway in a continuous fermentation of E. coli. Cells without additional plasmid stabilisation started to lose productivity immediately after entering the continuous phase. Inclusion of a multimer resolution site, cer, enabled a steady-state production period of 58 h before a drop in productivity was detected. Single-cell fluorescence measurements showed that plasmid-free variants arose rapidly without cer stabilisation and that this was likely due to unequal distribution of plasmid into daughter cells during cell division. The addition of cer increased total chemical yield by more than 50%. Conclusions This study shows the potential remains high for plasmids to be used as pathway vectors in industrial bio-based chemicals production, providing they are correctly stabilised. We demonstrate the need for accessible bacterial ‘toolkits’ to enable rapid production of known, stabilised bacterial production strains to enable continuous fermentation at scale for the chemicals industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01958-3.
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Hernández-fernández F, de los Ríos A, Licence P, Stephens G. Exploring ionic liquids based on pyrrolidinium and imidazolium cations with low toxicity towards Escherichia coli for designing sustainable bioprocesses. J Biotechnol 2022. [DOI: 10.1016/j.jbiotec.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
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Chen A, Xie Y, Xie S, Liu Y, Liu M, Shi J, Sun J. Production of citramalate in Escherichia coli by mediating colonic acid metabolism and fermentation optimization. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Son J, Joo JC, Baritugo KA, Jeong S, Lee JY, Lim HJ, Lim SH, Yoo JI, Park SJ. Consolidated microbial production of four-, five-, and six-carbon organic acids from crop residues: Current status and perspectives. Bioresour Technol 2022; 351:127001. [PMID: 35292386 DOI: 10.1016/j.biortech.2022.127001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
The production of platform organic acids has been heavily dependent on petroleum-based industries. However, petrochemical-based industries that cannot guarantee a virtuous cycle of carbons released during various processes are now facing obsolescence because of the depletion of finite fossil fuel reserves and associated environmental pollutions. Thus, the transition into a circular economy in terms of the carbon footprint has been evaluated with the development of efficient microbial cell factories using renewable feedstocks. Herein, the recent progress on bio-based production of organic acids with four-, five-, and six-carbon backbones, including butyric acid and 3-hydroxybutyric acid (C4), 5-aminolevulinic acid and citramalic acid (C5), and hexanoic acid (C6), is discussed. Then, the current research on the production of C4-C6 organic acids is illustrated to suggest future directions for developing crop-residue based consolidated bioprocessing of C4-C6 organic acids using host strains with tailor-made capabilities.
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Affiliation(s)
- Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Kei-Anne Baritugo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seona Jeong
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji Yeon Lee
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hye Jin Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seo Hyun Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jee In Yoo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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Lázaro J, Jansen G, Yang Y, Torres-Acosta MA, Lye G, Oliver SG, Júlvez J. Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals. Front Mol Biosci 2022; 9:855735. [PMID: 35573743 PMCID: PMC9091370 DOI: 10.3389/fmolb.2022.855735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/07/2022] [Indexed: 11/15/2022] Open
Abstract
The current production of a number of commodity chemicals relies on the exploitation of fossil fuels and hence has an irreversible impact on the environment. Biotechnological processes offer an attractive alternative by enabling the manufacturing of chemicals by genetically modified microorganisms. However, this alternative approach poses some important technical challenges that must be tackled to make it competitive. On the one hand, the design of biotechnological processes is based on trial-and-error approaches, which are not only costly in terms of time and money, but also result in suboptimal designs. On the other hand, the manufacturing of chemicals by biological processes is almost exclusively carried out by batch or fed-batch cultures. Given that batch cultures are expensive and not easy to scale, technical means must be developed to make continuous cultures feasible and efficient. In order to address these challenges, we have developed a mathematical model able to integrate in a single model both the genome-scale metabolic model for the organism synthesizing the chemical of interest and the dynamics of the bioreactor in which the organism is cultured. Such a model is based on the use of Flexible Nets, a modeling formalism for dynamical systems. The integration of a microscopic (organism) and a macroscopic (bioreactor) model in a single net provides an overall view of the whole system and opens the door to global optimizations. As a case study, the production of citramalate with respect to the substrate consumed by E. coli is modeled, simulated and optimized in order to find the maximum productivity in a steady-state continuous culture. The predicted computational results were consistent with the wet lab experiments.
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Affiliation(s)
- Jorge Lázaro
- Department of Computer Science and Systems Engineering, University of Zaragoza, Zaragoza, Spain
| | - Giorgio Jansen
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Yiheng Yang
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Mario A. Torres-Acosta
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Gary Lye
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jorge Júlvez
- Department of Computer Science and Systems Engineering, University of Zaragoza, Zaragoza, Spain
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14
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Chen J, Yuan Y, Xie F, Zhang Z, Chen J, Zhang R, Zhao J, Hu G, Qin Y. Metabolic Profiling of Organic Acids Reveals the Involvement of HuIPMS2 in Citramalic Acid Synthesis in Pitaya. Horticulturae 2022; 8:167. [DOI: 10.3390/horticulturae8020167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Pitayas are rich in organic acids, especially citramalic acid, which is significantly higher than the plants. However, the mechanism of citramalic acid biosynthesis remains to be fully elucidated. In this study, organic acid compositions and contents, as well as expression patterns of key genes related to organic acid metabolism were analyzed during fruit maturation of four different pitaya cultivars i.e., ‘Guanhuabai’ (GHB), ‘Guanhuahong’ (GHH), ‘Wucihuanglong’ (WCHL), and ‘Youcihuanglong’ (YCHL). The total organic acid contents increased first and then declined during fruit maturation. The main organic acids were citramalic acid during the early stages of GHB, GHH, and WCHL pitayas, and dominated by malic acid as fruit maturation. In comparison, citric acid and malic acid were main organic acid for ‘YCHL’ pitaya. Citramalate synthase (IPMS) was involved in the synthesis of citramalic acid, and three types of HuIPMS i.e., HuIPMS1, HuIPMS2, and HuIPMS3, were obtained in our study. Highest expression levels of HuIPMS1 were detected in sepals, while HuIPMS2 and HuIPMS3 exhibited preferential expression in tender stems and ovaries. The expression levels of HuIPMS2 and HuIPMS3 were positively correlated with the content of citramalic acid in the four pitaya cultivars. HuIPMS2 was a chloroplast-localized protein, while HuIPMS3 presented a cytoplasmic-like and nuclear subcellular localization. These findings provide an important basis for further understanding of the molecular mechanism that leads to citramalic acid metabolism during pitaya fruit maturation.
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15
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Ye Z, Li S, Hennigan JN, Lebeau J, Moreb EA, Wolf J, Lynch MD. Two-stage dynamic deregulation of metabolism improves process robustness & scalability in engineered E. coli. Metab Eng 2021; 68:106-118. [PMID: 34600151 DOI: 10.1016/j.ymben.2021.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 08/12/2021] [Accepted: 09/25/2021] [Indexed: 10/20/2022]
Abstract
We report that two-stage dynamic control improves bioprocess robustness as a result of the dynamic deregulation of central metabolism. Dynamic control is implemented during stationary phase using combinations of CRISPR interference and controlled proteolysis to reduce levels of central metabolic enzymes. Reducing the levels of key enzymes alters metabolite pools resulting in deregulation of the metabolic network. Deregulated networks are less sensitive to environmental conditions improving process robustness. Process robustness in turn leads to predictable scalability, minimizing the need for traditional process optimization. We validate process robustness and scalability of strains and bioprocesses synthesizing the important industrial chemicals alanine, citramalate and xylitol. Predictive high throughput approaches that translate to larger scales are critical for metabolic engineering programs to truly take advantage of the rapidly increasing throughput and decreasing costs of synthetic biology.
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Affiliation(s)
- Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, NC, USA; DMC Biotechnologies, Inc., Durham, NC, USA
| | - Shuai Li
- Department of Chemistry, Duke University, Durham, NC, USA
| | | | - Juliana Lebeau
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Jacob Wolf
- DMC Biotechnologies, Inc., Boulder, CO, USA
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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16
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Song L, Wang R, Che L, Jiang Y, Zhou M, Zhao Y, Pang J, Jiang M, Zhou G, Zheng M, Zhang T. Catalytic Aerobic Oxidation of Lignocellulose-Derived Levulinic Acid in Aqueous Solution: A Novel Route to Synthesize Dicarboxylic Acids for Bio-Based Polymers. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02531] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lei Song
- Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, People’s Republic of China
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Rui Wang
- Division of Energy Materials, Dalian Institute of Chemical Physicals, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Li Che
- Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, People’s Republic of China
| | - Yu Jiang
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Mo Zhou
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Yu Zhao
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Jifeng Pang
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Min Jiang
- Division of Energy Materials, Dalian Institute of Chemical Physicals, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Guangyuan Zhou
- Division of Energy Materials, Dalian Institute of Chemical Physicals, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Mingyuan Zheng
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- Dalian National Laboratory for Clean Energy, Dalian 116023, People’s Republic of China
| | - Tao Zhang
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
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Wu X, Tovilla‐Coutiño DB, Eiteman MA. Engineered citrate synthase improves citramalic acid generation in
Escherichia coli. Biotechnol Bioeng 2020; 117:2781-2790. [DOI: 10.1002/bit.27450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/24/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Xianghao Wu
- School of Chemical, Materials and Biomedical Engineering University of Georgia Athens Georgia
| | | | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering University of Georgia Athens Georgia
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Abstract
Industrial biotechnology can lead to new routes and potentially to more sustainable production of numerous chemicals. We review the potential of biobased routes from sugars to the large volume commodity, methacrylic acid, involving fermentation based bioprocesses. We cover the key progress over the past decade on direct and indirect fermentation based routes to methacrylic acid including both academic as well as patent literature. Finally, we take a critical look at the potential of biobased routes to methacrylic acid in comparison with both incumbent as well as newer greener petrochemical based processes.
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Affiliation(s)
- Juliana Lebeau
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - John P Efromson
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
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Hossain AH, Hendrikx A, Punt PJ. Identification of novel citramalate biosynthesis pathways in Aspergillus niger. Fungal Biol Biotechnol 2019; 6:19. [PMID: 31827810 PMCID: PMC6862759 DOI: 10.1186/s40694-019-0084-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/04/2019] [Indexed: 11/26/2022] Open
Abstract
Background The filamentous fungus Aspergillus niger is frequently used for industrial production of fermentative products such as enzymes, proteins and biochemicals. Notable examples of industrially produced A. niger fermentation products are glucoamylase and citric acid. Most notably, the industrial production of citric acid achieves high titers, yield and productivities, a feat that has prompted researchers to propose A. niger to serve as heterologous production host for the industrial production of itaconic acid (IA), a promising sustainable chemical building-block for the fabrication of various synthetic resins, coatings, and polymers. Heterologous production of IA in A. niger has resulted in unexpected levels of metabolic rewiring that has led us to the identification of IA biodegradation pathway in A. niger. In this study we have attempted to identify the final product of the IA biodegradation pathway and analyzed the effect of metabolic rewiring on the bioproduction of 9 industrially relevant organic acids. Results IA biodegradation manifests in diminishing titers of IA and the occurrence of an unidentified compound in the HPLC profile. Based on published results on the IA biodegradation pathway, we hypothesized that the final product of IA biodegradation in A. niger may be citramalic acid (CM). Based on detailed HPLC analysis, we concluded that the unidentified compound is indeed CM. Furthermore, by transcriptome analysis we explored the effect of metabolic rewiring on the production of 9 industrially relevant organic acids by transcriptome analysis of IA producing and WT A. niger strains. Interestingly, this analysis led to the identification of a previously unknown biosynthetic cluster that is proposed to be involved in the biosynthesis of CM. Upon overexpression of the putative citramalate synthase and a genomically clustered organic acid transporter, we have observed CM bioproduction by A. niger. Conclusion In this study, we have shown that the end product of IA biodegradation pathway in A. niger is CM. Knock-out of the IA biodegradation pathway results in the cessation of CM production. Furthermore, in this study we have identified a citramalate biosynthesis pathway, which upon overexpression drives citramalate bioproduction in A. niger.
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Affiliation(s)
- Abeer H Hossain
- Dutch DNA Biotech B.V., Padualaan 8, 3584 CH Utrecht, The Netherlands.,2Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Aiko Hendrikx
- Dutch DNA Biotech B.V., Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Peter J Punt
- Dutch DNA Biotech B.V., Padualaan 8, 3584 CH Utrecht, The Netherlands
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20
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Webb J, Springthorpe V, Rossoni L, Minde DP, Langer S, Walker H, Alstrom-Moore A, Larson T, Lilley K, Eastham G, Stephens G, Thomas GH, Kelly DJ, Green J. Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate. mSystems 2019; 4:e00187-19. [PMID: 31186337 DOI: 10.1128/mSystems.00187-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Citramalate is an attractive biotechnology target because it is a precursor of methylmethacrylate, which is used to manufacture Perspex and other high-value products. Engineered E. coli strains are able to produce high titers of citramalate, despite having to express a foreign enzyme and tolerate the presence of a nonnative biochemical. A systems analysis of the citramalate fermentation was undertaken to uncover the reasons underpinning its productivity. This showed that E. coli readily adjusts to the redirection of metabolic resources toward recombinant protein and citramalate production and suggests that E. coli is an excellent chassis for manufacturing similar small, polar, foreign molecules. Productivity of bacterial cell factories is frequently compromised by stresses imposed by recombinant protein synthesis and carbon-to-product conversion, but little is known about these bioprocesses at a systems level. Production of the unnatural metabolite citramalate in Escherichia coli requires the expression of a single gene coding for citramalate synthase. Multiomic analyses of a fermentation producing 25 g liter−1 citramalate were undertaken to uncover the reasons for its productivity. Metabolite, transcript, protein, and lipid profiles of high-cell-density, fed-batch fermentations of E. coli expressing either citramalate synthase or an inactivated enzyme were similar. Both fermentations showed downregulation of flagellar genes and upregulation of chaperones IbpA and IbpB, indicating that these responses were due to recombinant protein synthesis and not citramalate production. Citramalate production did not perturb metabolite pools, except for an increased intracellular pyruvate pool. Gene expression changes in response to citramalate were limited; none of the general stress response regulons were activated. Modeling of transcription factor activities suggested that citramalate invoked a GadW-mediated acid response, and changes in GadY and RprA regulatory small RNA (sRNA) expression supported this. Although changes in membrane lipid composition were observed, none were unique to citramalate production. This systems analysis of the citramalate fermentation shows that E. coli has capacity to readily adjust to the redirection of resources toward recombinant protein and citramalate production, suggesting that it is an excellent chassis choice for manufacturing organic acids. IMPORTANCE Citramalate is an attractive biotechnology target because it is a precursor of methylmethacrylate, which is used to manufacture Perspex and other high-value products. Engineered E. coli strains are able to produce high titers of citramalate, despite having to express a foreign enzyme and tolerate the presence of a nonnative biochemical. A systems analysis of the citramalate fermentation was undertaken to uncover the reasons underpinning its productivity. This showed that E. coli readily adjusts to the redirection of metabolic resources toward recombinant protein and citramalate production and suggests that E. coli is an excellent chassis for manufacturing similar small, polar, foreign molecules.
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