Production of Mevalonate from Glycerol by Escherichia coli Citrate Synthase Variants
Abstract
1. Introduction
2. Materials and Methods
2.1. Shake Flask Studies
2.2. Batch Reactor Studies
2.3. Fed-Batch Reactor Studies
2.4. Analytical Methods
3. Results and Discussion
3.1. Growth of Citrate Synthase Variants on Carbon Sources
3.2. Batch Production of Mevalonate on Glycerol
3.3. Nutrient-Limited Fed-Batch Processes
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Zaroubi, L.; Ozugergin, I.; Mastronardi, K.; Imfeld, A.; Law, C.; Gélina, Y.; Piekny, A.; Findlay, B.L. The ubiquitous soil terpene geosmin acts as a warning chemical. Appl. Environ. Microbiol. 2022, 88, e00093-22. [Google Scholar] [CrossRef] [PubMed]
- Hui, W.; Wang, J.; Ma, L.; Zhao, F.; Jia, L.; Zhong, Y.; Zhang, S.; Gong, W. Identification of key genes in the biosynthesis pathways related to terpenoids, alkaloids and flavonoids in fruits of Zanthoxylum armatum. Sci. Hort. 2021, 290, 110523. [Google Scholar] [CrossRef]
- Guimarães, A.C.; Meireles, L.M.; Lemos, M.F.; Guimarães, M.C.C.; Endringer, D.C.; Fronza, M.; Scherer, R. Antibacterial activity of terpenes and terpenoids present in essential oils. Molecules 2019, 24, 2471. [Google Scholar] [CrossRef] [PubMed]
- Schwab, W.; Fuchs, C.; Huang, F.C. Transformation of terpenes into fine chemicals. Eur. J. Lipid Sci. Technol. 2013, 115, 3–8. [Google Scholar] [CrossRef]
- Kuzuyama, T.; Dairi, T.; Yamashita, H.; Shoji, Y.; Seto, H. Heterologous mevalonate production in Streptomyces lividans TK23. Biosci. Biotechnol. Biochem. 2004, 68, 931–934. [Google Scholar] [CrossRef][Green Version]
- Yogev, Y.; Shorer, Z.; Koifman, A.; Wormser, O.; Drabkin, M.; Halperin, D.; Dolgin, V.; Proskorovski-Ohayon, R.; Hadar, N.; Davidov, G.; et al. Limb girdle muscular disease caused by HMGCR mutation and statin myopathy treatable with mevalonolactone. Proc. Natl. Acad. Sci. USA 2023, 120, e2217831120. [Google Scholar] [CrossRef]
- Lombard, J.; Moreira, D. Origins and early evolution of the mevalonate pathway of isoprenoid biosynthesis in the three domains of life. Mol. Biol. Evol. 2011, 28, 87–99. [Google Scholar] [CrossRef]
- Miziorko, H.M. Enzymes of the mevalonate pathway of isoprenoid biosynthesis. Arch. Biochem. Biophys. 2011, 505, 131–143. [Google Scholar] [CrossRef]
- Kim, J.-H.; Wang, C.; Jang, H.-J.; Cha, M.-S.; Park, J.-E.; Jo, S.-Y.; Choi, E.-S.; Kim, S.-W. Isoprene production by Escherichia coli through the exogenous mevalonate pathway with reduced formation of fermentation byproducts. Microb. Cell Fact. 2016, 15, 214. [Google Scholar] [CrossRef]
- Kamata, K.; Toya, Y.; Shimizu, H. Effect of precise control of flux ratio between the glycolytic pathways on mevalonate production in Escherichia coli. Biotechnol. Bioeng. 2019, 116, 1080–1088. [Google Scholar] [CrossRef]
- Wang, Y.; Zhou, S.; Li, R.; Liu, Q.; Shao, X.; Zhu, L.; Kang, M.-K.; Wei, G.; Kim, S.-W.; Wang, C. Reassessing acetyl-CoA supply and NADPH availability for mevalonate biosynthesis from glycerol in Escherichia coli. Biotechnol. Bioeng. 2022, 119, 2868–2877. [Google Scholar] [CrossRef] [PubMed]
- Rugbjerg, P.; Feist, A.M.; Sommer, M.O.A. Enhanced metabolite productivity of Escherichia coli adapted to glucose M9 minimal medium. Front. Bioeng. Biotechnol. 2018, 6, 166. [Google Scholar] [CrossRef] [PubMed]
- Li, S.; Jendresen, C.B.; Nielsen, A.T. Increasing production yield of tyrosine and mevalonate through inhibition of biomass formation. Process Biochem. 2016, 51, 1992–2000. [Google Scholar] [CrossRef]
- Masuda, A.; Toya, Y.; Shimizu, H. Metabolic impact of nutrient starvation in mevalonate-producing Escherichia coli. Bioresour. Technol. 2017, 245, 1634–1640. [Google Scholar] [CrossRef]
- Xu, X.; Xie, M.; Zhao, Q.; Xian, M.; Liu, H. Microbial production of mevalonate by recombinant Escherichia coli using acetic acid as a carbon source. Bioengineered 2018, 9, 116–123. [Google Scholar] [CrossRef]
- Glycerol Market Size & Share 2024-2034–Market Size by Product Type (Crude, Refined), by Source (Biodiesel, Fatty Acids, Fatty Alcohols, Soap Industry), by Application, Downstream Application & Global Forecast. Global Market Insights. 2025. Available online: https://www.gminsights.com/industry-analysis/glycerol-market-size (accessed on 30 June 2025).
- Chilakamarry, C.R.; Mimi Sakinah, A.M.; Zularisam, A.W.; Pandey, A. Glycerol waste to value added products and its potential applications. Syst. Microbiol. Biomanufact. 2021, 1, 378–396. [Google Scholar] [CrossRef]
- Trinh, C.T.; Srienc, F. Metabolic engineering of Escherichia coli for efficient conversion of glycerol to ethanol. Appl. Environ. Microbiol. 2009, 75, 6696–6705. [Google Scholar] [CrossRef]
- Blankschein, M.D.; Clomberg, J.M.; Gonzalez, R. Metabolic engineering of Escherichia coli for the production of succinate from glycerol. Metabol. Eng. 2010, 12, 409–419. [Google Scholar] [CrossRef]
- Zhu, Y.; Eiteman, M.A.; Lee, S.A.; Altman, E. Conversion of glycerol to pyruvate by Escherichia coli using acetate- and acetate/glucose-limited fed-batch processes. J. Industr. Microbiol. Biotechnol. 2010, 37, 307–312. [Google Scholar] [CrossRef]
- Oh, B.-R.; Heo, S.-Y.; Lee, S.-M.; Hong, W.-K.; Park, J.M.; Jung, Y.R.; Kim, D.-H.; Sohn, J.-H.; Seo, J.-W.; Kim, C.H. Production of 2-butanol from crude glycerol by a genetically-engineered Klebsiella pneumoniae strain. Biotechnol. Lett. 2014, 36, 57–62. [Google Scholar] [CrossRef]
- Wu, X.; Eiteman, M.A. Synthesis of citramalic acid from glycerol by metabolically engineered Escherichia coli. J. Industr. Microbiol. Biotechnol. 2017, 44, 1483–1490. [Google Scholar] [CrossRef]
- Zhang, H.; Li, Z.; Pereira, B.; Stephanopoulos, G. Engineering E. coli–E. coli cocultures for production of muconic acid from glycerol. Microb. Cell Fact. 2015, 14, 134. [Google Scholar] [CrossRef]
- Yang, T.; Rao, Z.; Zhang, X.; Xu, M.; Xu, Z.; Yang, S.-T. Enhanced 2,3-butanediol production from biodiesel-derived glycerol by engineering or cofactor regeneration and manipulating carbon flux in Bacillus amyloliquefaciens. Microb. Cell Fact. 2015, 14, 122. [Google Scholar] [CrossRef]
- Zhao, J.; Baba, T.; Mori, H.; Shimizu, K. Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate. Metabol. Eng. 2004, 6, 164–174. [Google Scholar] [CrossRef] [PubMed]
- Satowa, D.; Fujiwara, R.; Uchio, S.; Nakano, M.; Otomo, C.; Hirata, Y.; Matsumoto, T.; Noda, S.; Tanaka, T.; Kondo, A. Metabolic engineering of E. coli for improving mevalonate production to promote NADPH regeneration and enhance acetyl-CoA supply. Biotechnol. Bioeng. 2020, 117, 2153–2164. [Google Scholar] [CrossRef] [PubMed]
- Vandedrinck, S.; Deschamps, G.; Sablon, E.; Vandamme, E.J. Metabolic engineering of Escherichia coli: Construction and characterization of a gltA (citrate synthase) knockout mutant. Meded. Rijksuniv. Gent. Fak. Landbouwkd. Toegep. Biol. Wet. 2001, 66, 333–336. [Google Scholar] [PubMed]
- Wu, X.; Eiteman, M.A. Production of citramalate by metabolically engineered Escherichia coli. Biotechnol. Bioeng. 2016, 113, 2670–2675. [Google Scholar] [CrossRef]
- Tovilla-Coutiño, D.B.; Momany, C.; Eiteman, M.A. Engineered citrate synthase alters acetate accumulation in Escherichia coli. Metabol. Eng. 2020, 61, 171–180. [Google Scholar] [CrossRef]
- Heo, M.-J.; Jung, H.-M.; Um, J.; Lee, S.-W.; Oh, M.-K. Controlling Citrate Synthase Expression by CRISPR/Cas9 Genome Editing for n-Butanol production in Escherichia coli. ACS Synth. Biol. 2017, 6, 182–189. [Google Scholar] [CrossRef]
- Moxley, W.C.; Eiteman, M.A. Pyruvate production by Escherichia coli using pyruvate dehydrogenase variants. Appl. Environ. Microbiol. 2021, 87, e00487-21. [Google Scholar] [CrossRef]
- Rajpurohit, H.; Eiteman, M.A. Citrate synthase variants improve yield of acetyl-CoA derived 3-hydroxybutyrate in Escherichia coli. Microb. Cell Fact. 2024, 23, 173. [Google Scholar] [CrossRef] [PubMed]
- Wu, X.; Tovilla-Coutiño, D.B.; Eiteman, M.A. Engineered citrate synthase improves citramalic acid generation in Escherichia coli. Biotechnol. Bioeng. 2020, 117, 2781–2790. [Google Scholar] [CrossRef] [PubMed]
- Dodelin, J.K.; Rose, A.E.; Rajpurohit, H.; Eiteman, M.A. Increased mevalonate production using engineered citrate synthase and phosphofructokinase variants of Escherichia coli. Biotechnol. Bioeng. 2024, 122, 548–560. [Google Scholar] [CrossRef] [PubMed]
- Van Ooyen, J.; Noack, S.; Bott, M.; Reth, A.; Eggeling, L. Improved L-lysine production with Corynebacterium glutamicum and systemic insight into citrate synthase flux and activity. Biotechnol. Bioeng. 2012, 109, 2070–2081. [Google Scholar] [CrossRef]
- Soma, Y.; Tsuruno, K.; Wada, M.; Yokota, A.; Hanai, T. Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch. Metabol. Eng. 2014, 23, 175–184. [Google Scholar] [CrossRef]
- Zhou, H.; Zhang, Y.; Long, C.P.; Xia, X.; Xue, Y.; Ma, Y.; Antoniewicz, M.R.; Tao, Y.; Lin, B. A citric acid cycle-deficient Escherichia coli as an efficient chassis for aerobic fermentations. Nat. Commun. 2024, 15, 2372. [Google Scholar] [CrossRef]
- Gonzalez, J.M.; Aranda, B. Microbial Growth under Limiting Conditions-Future Perspectives. Microorganisms 2023, 11, 1641. [Google Scholar] [CrossRef]
- Rajpurohit, H.; Eiteman, M.A. Nutrient-limited operational strategies for the microbial production of biochemicals. Microorganisms 2022, 10, 2226. [Google Scholar] [CrossRef]
- Perez-Zabaleta, M.; Guevara-Martínez, M.; Gustavsson, M.; Quillaguamán, J.; Larsson, G.; van Maris, A.J.A. Comparison of engineered Escherichia coli AF1000 and BL21 strains for (R)-3-hydroxybutyrate production in fed-batch cultivation. Appl. Microbiol. Biotechnol. 2019, 103, 5627–5639. [Google Scholar] [CrossRef]
- Kim, B.S.; Lee, S.C.; Lee, S.Y.; Chang, H.N.; Chang, Y.K.; Woo, S.I. Production of poly(3-hydroxybutyric-co-3-hydroxyvaleric acid) by fed-batch culture of Alcaligenes eutrophus with substrate control using on-line glucose analyzer. Enzym. Microb. Technol. 1994, 16, 556–561. [Google Scholar] [CrossRef]
- Kim, B.S.; Lee, S.C.; Lee, S.Y.; Chang, H.N.; Chang, Y.K.; Woo, S.I. Production of poly(3-hydroxybutyric acid) by fed-batch culture of Alcaligenes eutrophus with glucose concentration control. Biotechnol. Bioeng. 1994, 43, 892–898. [Google Scholar] [CrossRef]
- Stokell, D.J.; Donald, L.J.; Maurus, R.; Nguyen, N.T.; Sadler, G.; Choudhary, K.; Hultin, P.G.; Brayer, G.D.; Duckworth, H.W. Probing the roles of key residues in the unique regulatory NADH binding site of type II citrate synthase of Escherichia coli. J. Biol. Chem. 2003, 278, 35435–35443. [Google Scholar] [CrossRef] [PubMed]
- Rugbjerg, P.; Myling-Petersen, N.; Porse, A.; Sarup-Lytzen, K.; Sommer, M.O.A. Diverse genetic error modes constrain large-scale bio-based production. Nat. Commun. 2018, 9, 787. [Google Scholar] [CrossRef] [PubMed]
- Eiteman, M.A.; Chastain, M.J. Optimization of the ion exchange analysis of organic acids from fermentation. Anal. Chim. Acta 1997, 338, 69–75. [Google Scholar] [CrossRef]
- United States EPA Method 350.1; Determination of Ammonia Nitrogen by Semi-Automated Colorimetry. United States EPA: Cincinnati, OH, USA, 1993.
- United States EPA Method 200.8; Determination of Trace Elements in Waters and Wastes by Inductively Coupled Plasma–Mass Spectrometry. United States EPA: Cincinnati, OH, USA, 1994.
- Duckworth, H.W.; Nguyen, N.T.; Gao, Y.; Donald, L.J.; Maurus, R.; Ayed, A.; Bruneau, B.; Brayer, G.D. Enzyme-substrate complexes of allosteric citrate synthase: Evidence for a novel intermediate in substrate binding. Biochim. Biophys. Acta Protein Proteonomics 2013, 1834, 2546–2553. [Google Scholar] [CrossRef]
- Pereira, D.S.; Donald, L.J.; Hosfield, D.J.; Duckworth, H.W. Active site mutants of Escherichia coli citrate synthase. J. Biol. Chem. 1994, 269, 412–417. [Google Scholar] [CrossRef]
- Dodelin, J.K. Selection and Characterization of Escherichia coli Citrate Synthase Variants That Improve Biosynthesis of Products Derived from Acetyl-CoA. Doctoral Dissertation, University of Georgia, Athens, GA, USA, 2024. [Google Scholar]
- Quandt, E.M.; Gollihar, J.; Blount, Z.D.; Ellington, A.D.; Georgiou, G.; Barrick, J.E. Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. eLife 2015, 4, e09696. [Google Scholar] [CrossRef]
- Takamura, Y.; Nomura, G. Changes in the intracellular concentration of aetyl-CoA and malonyl-CoA in relation to the carbon and energy metabolism of Escherichia coli K12. J. Gen. Microbiol. 1988, 134, 2249–2253. [Google Scholar] [CrossRef]
- Martínez-Gómez, K.; Flores, N.; Castañeda, H.M.; Martínez-Batallar, G.; Hernández-Chávez, G.; Ramírez, O.T.; Gosset, G.; Encarnación, S.; Bolivar, F. New insights into Escherichia coli metabolism: Carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol. Microb. Cell Fact. 2012, 11, 46. [Google Scholar] [CrossRef]
- Van Bogelen, R.A.; Olson, E.R.; Wanner, B.L.; Neidhardt, F.C. Global analysis of proteins synthesized during phosphorus restriction in Escherichia coli. J. Bacteriol. 1996, 178, 4344. [Google Scholar] [CrossRef]






| Strain Name | Citrate Synthase Substitutions | Reference |
|---|---|---|
| E. coli W | Wild-Type enzyme | ATCC 9637 |
| MEC1484 | Y87N, D101D*, P208L | [34] |
| MEC1501 | K167A | [43] |
| MEC1502 | A267T | [29] |
| MEC1503 | F383M | [29,33] |
| MEC1558 | P313S | [34] |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2026 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.
Share and Cite
Hartner, C.E.; Eiteman, M.A. Production of Mevalonate from Glycerol by Escherichia coli Citrate Synthase Variants. Fermentation 2026, 12, 186. https://doi.org/10.3390/fermentation12040186
Hartner CE, Eiteman MA. Production of Mevalonate from Glycerol by Escherichia coli Citrate Synthase Variants. Fermentation. 2026; 12(4):186. https://doi.org/10.3390/fermentation12040186
Chicago/Turabian StyleHartner, Caroline E., and Mark A. Eiteman. 2026. "Production of Mevalonate from Glycerol by Escherichia coli Citrate Synthase Variants" Fermentation 12, no. 4: 186. https://doi.org/10.3390/fermentation12040186
APA StyleHartner, C. E., & Eiteman, M. A. (2026). Production of Mevalonate from Glycerol by Escherichia coli Citrate Synthase Variants. Fermentation, 12(4), 186. https://doi.org/10.3390/fermentation12040186

