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A microbial process for the production of benzyl acetate

Abstract

Benzyl acetate is a valuable aromatic ester compound with diverse applications in the flavor and fragrance industries. However, its current synthesis primarily relies on inefficient plant extraction methods or chemical/enzymatic processes that depend on non-renewable substrates. Here we report a sustainable approach to benzyl acetate production from d-glucose using metabolically engineered Escherichia coli strains. We explored both benzoic acid-dependent and -independent synthetic pathways by either dividing the pathway between upstream and downstream strain pairs or by introducing the complete pathway into single, integrated strains. In an optimized two-phase extractive fermentation process, a delayed co-culture of an upstream strain that converts d-glucose to benzoic acid and a downstream strain that transforms benzoic acid into benzyl acetate yielded 2,238.3 ± 171.9 mg l−1 of benzyl acetate from d-glucose in 108 h (or 2,204.0 ± 192.2 mg l−1 in 96 h). The economic competitiveness of the microbial process for sustainable benzyl acetate production was also assessed by techno-economic analysis.

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Fig. 1: Schemes of benzoic acid-dependent and -independent pathways for de novo production of benzyl acetate from d-glucose.
Fig. 2: Production of benzyl acetate through co-culture of upstream and downstream strains harboring the benzoic acid-dependent pathway.
Fig. 3: Production of benzyl acetate through co-culture of upstream and downstream strains harboring the benzoic acid-independent pathway.
Fig. 4: Production of benzyl acetate by the BnAc1–BnAc30 strains harboring the complete benzoic acid-independent pathway.
Fig. 5: Delayed co-culture of the Bn1 and Bn-BnAc3 strains for improved production of benzyl acetate through the benzoic acid-independent pathway.
Fig. 6: Techno-economic analysis of the microbial-based benzyl acetate production process.

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Data availability

All source data for figures have been deposited at figshare (https://doi.org/10.6084/m9.figshare.24026634).

Code availability

All codes used for calculating the theoretical maximum flux of benzyl acetate biosynthesis and techno-economic analysis of the microbial-based benzyl acetate production are available at https://github.com/kaistsystemsbiology/BenzylAcetateFluxAnalysis and https://github.com/kaistsystemsbiology/BenzylAcetateTEA.

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Acknowledgements

This work was supported by the ‘Bio & Medical Technology Development Program (2021M3A9I4022740)’ of the National Research Foundation and funded by the Ministry of Science and ICT, Republic of Korea (K.R.C., Z.W.L., G.B.K., H.X. and S.Y.L.). This work was also supported by the ‘Cooperative Research Program for Agriculture Science and Technology Development (Project No. RS-2021-RD009210)’ from the Rural Development Administration, Republic of Korea (K.R.C. and Z.W.L.).

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Authors

Contributions

K.R.C. and S.Y.L. conceptualized the project. K.R.C., Z.W.L. and G.B.K. developed the methodology. K.R.C., Z.W.L., G.B.K. and H.X. conducted experiments. K.R.C., Z.W.L., G.B.K. and H.X. analyzed the data. K.R.C., Z.W.L. and G.B.K. performed visualization. K.R.C., Z.W.L. and G.B.K. wrote the original draft. K.R.C. and S.Y.L. reviewed and edited the paper.

Corresponding author

Correspondence to Sang Yup Lee.

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Extended data

Extended Data Fig. 1 Two-phase extractive fermentation to overcome benzyl acetate toxicity.

a, The growth curve of E. coli W3110 strain in shake-flask culture supplemented with 0-1.0 g L-1 of benzyl acetate. Solid symbols and error bars represent mean values and standard deviations of biological triplicates (n = 3). Smaller open symbols represent raw data points. b, Scheme of aqueous/organic two-phase extractive culture. Toxic products with high hydrophobicity and partition coefficient, such as benzyl acetate, can be effectively sequestered to droplets of organic solvents. As a result, the concentration of the toxic compounds in the aqueous phase and the cytoplasm decreases, leading to reduction of the toxic effects on microorganisms in the aqueous phase.

Extended Data Fig. 2 Non-averaged profiles of two-phase extractive fermentations.

a and b, Non-averaged profiles of the two-phase extractive fermentation for production of benzyl acetate by the co-culture of the Bn1 and Bn-BnAc3 strains. The averaged profile of these duplicated rounds of fermentations is presented in Fig. 2e. c and d, Non-averaged profiles of the two-phase extractive fermentation for production of benzyl acetate by the co-culture of the BnOH7 and BnOH-BnAc2 strains. The averaged profile of these duplicated rounds of fermentation is presented in Fig. 3d. e and f, Non-averaged profiles of the two-phase extractive fermentation for production of benzyl acetate by the BnAc30 strain. The averaged profile of these duplicated rounds of fermentations are presented in Fig. 4e.

Extended Data Fig. 3 Optimization of medium components to improve the cell density and benzyl acetate titre of the BnAc30 strain.

a, Perturbation of component levels in shake-flask culture of the BnAc30 strain supplemented with increased amount of d-glucose (20 g L-1), thiamine (Thi), l-tyrosine (Tyr), l-phenylalanine (Phe), l-aspartic acid (Asp) and yeast extract (YE) than the standard conditions. Bars and solid symbols represent mean values and error bars represent standard deviations of biological triplicates (n = 3). Smaller open symbols represent raw data points. b, Perturbation of component levels in shake-flask culture of the BnAc30 strain supplemented with 20 g L-1 of d-glucose, as well as replacement of yeast extract with l-leucine (Lue) and l-isoleucine (Ile). Bars and solid symbols represent mean values and error bars represent standard deviations of biological triplicates (n = 3). Smaller open symbols represent raw data points. c, Two-phase extractive fermentation of the BnAc30 strain with supplementation of 6 g L-1 of yeast extract and 0.1 g L-1 of l-tyrosine. Symbols represent raw data points (n = 1). d, Two-phase extractive fermentation of the BnAc30 strain with supplementation of 6 g L-1 of yeast extract and 0.2 g L-1 of l-tyrosine. Symbols represent raw data points (n = 1).

Extended Data Fig. 4 Co-culture of the auxotrophic Bn-BnAc5 strain with the auxotrophic Bn1 strain.

a, Population changes in co-culture of an auxotrophic upstream strain (strain 1) and a prototrophic downstream strain (strain 2). b, Population changes in co-culture of an auxotrophic upstream strain (strain 1) and an auxotrophic downstream strain (strain 2). c, Two-phase extractive fermentation profile for benzyl acetate production by co-culture of the auxotrophic Bn1 strain and the auxotrophic Bn-BnAc5 strain. Symbols represent raw data points (n = 1). d, Scheme of promiscuous conversion of trans-cinnamic acid into cinnamyl acetate in co-culture of an upstream strain (strain 1) and a downstream strain (strain 2) harbouring the benzoic acid-dependent pathway for benzyl acetate production.

Extended Data Fig. 5 Optimization of inoculation delay in delayed co-culture of the Bn1 and Bn-BnAc3 strains (part 1).

a, Two-phase extractive fermentation profile of delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1). The Bn-BnAc3 strain inoculum (200 mL; OD600 = 8.5) was added after 36 h of fermentation. b, Apparent average biosynthesis rates of l-phenylalanine (Phe), trans-cinnamic acid (Cin), cinnamyl acetate (CinAc), benzoic acid (Bn), benzaldehyde (BnAl), benzyl alcohol (BnOH) and benzyl acetate (BnAc), calculated based on the changes in titres (panel a) and the molar masses of the compounds. c, Two-phase extractive fermentation profile of delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1). The Bn-BnAc3 strain inoculum (200 mL; OD600 = 11.6) was added after 48 h of fermentation. d, Apparent average biosynthesis rates of benzyl acetate, cinnamyl acetate and intermediates between sampling points were calculated based on the changes in the titres (panel c) and the molar masses of the compounds. Symbols represent raw data points and bars represent apparent average biosynthesis rates.

Extended Data Fig. 6 Optimization of inoculation delay in delayed co-culture of the Bn1 and Bn-BnAc3 strains (part 2).

a, Two-phase extractive fermentation profile of delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1). The Bn-BnAc3 strain inoculum (200 mL; OD600 = 7.8) was added after 72 h of fermentation. b, Apparent average biosynthesis rates of l-phenylalanine (Phe), trans-cinnamic acid (Cin), cinnamyl acetate (CinAc), benzoic acid (Bn), benzaldehyde (BnAl), benzyl alcohol (BnOH) and benzyl acetate (BnAc), calculated based on the changes in titres (panel a) and the molar masses of the compounds. c, Two-phase extractive fermentation profile of delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1). The Bn-BnAc3 strain inoculum (200 mL; OD600 = 9.1) was added after 96 h of fermentation. d, Apparent average biosynthesis rates of benzyl acetate, cinnamyl acetate and intermediates between sampling points were calculated based on the changes in the titres (panel c) and the molar masses of the compounds. Symbols represent raw data points and bars represent apparent average biosynthesis rates.

Extended Data Fig. 7 Non-averaged profiles and average biosynthesis rates for the delayed co-culture of the Bn1 and Bn-BnAc3 strains shown in Fig. 5d.

a, Non-averaged two-phase extractive fermentation profile of delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1). The Bn-BnAc3 strain inoculum (400 mL; OD600 = 13.1) was added after 48 h of fermentation. The profiles of d-glucose and organic acids are summarized in Extended Data Fig. 10a. b, Apparent average biosynthesis rates of l-phenylalanine (Phe), trans-cinnamic acid (Cin), cinnamyl acetate (CinAc), benzoic acid (Bn), benzaldehyde (BnAl), benzyl alcohol (BnOH) and benzyl acetate (BnAc), calculated based on the changes in titres (panel a) and the molar masses of the compounds. c, Non-averaged two-phase extractive fermentation profile of delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1). The Bn-BnAc3 strain inoculum (400 mL; OD600 = 14.4) was added after 48 h of fermentation. The profiles of d-glucose and organic acids are summarized in Extended Data Fig. 10b. d, Apparent average biosynthesis rates of benzyl acetate, cinnamyl acetate and intermediates between sampling points were calculated based on the changes in the titres (panel c) and the molar masses of the compounds. Symbols represent raw data points and bars represent apparent average biosynthesis rates.

Extended Data Fig. 8 Two-phase extractive fermentation profile and average biosynthesis rates for the delayed co-culture of the Bn1 and Bn-BnAc3 strains with the delayed inoculum volume of 400 mL and inoculation delay of 36 h.

a, Two-phase extractive fermentation profile of delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1). The Bn-BnAc3 strain inoculum (400 mL; OD600 = 13.8) was added after 36 h of fermentation. b, Apparent average biosynthesis rates of l-phenylalanine (Phe), trans-cinnamic acid (Cin), cinnamyl acetate (CinAc), benzoic acid (Bn), benzaldehyde (BnAl), benzyl alcohol (BnOH) and benzyl acetate (BnAc), calculated based on the changes in titres (panel a) and the molar masses of the compounds. Symbols represent raw data points and bars represent apparent average biosynthesis rates.

Extended Data Fig. 9 Non-averaged profiles and average biosynthesis rates for the delayed co-culture of the Bn1 and Bn-BnAc3 strains shown in Fig. 5e.

a, Non-averaged two-phase extractive fermentation profile of delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1). The Bn-BnAc3 strain inoculum (400 mL; OD600 = 7.6) was added after 48 h of fermentation. The profiles of d-glucose and organic acids are summarized in Extended Data Fig. 10c. b, Apparent average biosynthesis rates of l-phenylalanine (Phe), trans-cinnamic acid (Cin), cinnamyl acetate (CinAc), benzoic acid (Bn), benzaldehyde (BnAl), benzyl alcohol (BnOH) and benzyl acetate (BnAc), calculated based on the changes in titres (panel a) and the molar masses of the compounds. c, Non-averaged two-phase extractive fermentation profile of delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1). The Bn-BnAc3 strain inoculum (400 mL; OD600 = 8.0) was added after 48 h of fermentation. The profiles of d-glucose and organic acids are summarized in Extended Data Fig. 10d. d, Apparent average biosynthesis rates of benzyl acetate, cinnamyl acetate and intermediates between sampling points were calculated based on the changes in the titres (panel c) and the molar masses of the compounds. Symbols represent raw data points and bars represent apparent average biosynthesis rates.

Extended Data Fig. 10 Non-averaged d-glucose and organic acid profiles for the delayed co-culture of the Bn1 and Bn-BnAc3 strains shown in Extended Data Figs. 7 and 9.

a, Non-averaged d-glucose and organic acid profiles during the delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1) shown in Extended Data Fig. 7a. The Bn-BnAc3 strain inoculum (400 mL; OD600 = 13.1) was added after 48 h of fermentation. b, Non-averaged d-glucose and organic acid profiles for the delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1) shown in Extended Data Fig. 7c. The Bn-BnAc3 strain inoculum (400 mL; OD600 = 14.4) was added after 48 h of fermentation. c, Non-averaged d-glucose and organic acid profiles for the delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1) shown in Extended Data Fig. 9a. The Bn-BnAc3 strain inoculum (400 mL; OD600 = 7.6) was added after 48 h of fermentation. d, Non-averaged d-glucose and organic acid profiles for the delayed co-culture of the Bn1 and Bn-BnAc3 strains (n = 1) shown in Extended Data Fig. 9c. The Bn-BnAc3 strain inoculum (400 mL; OD600 = 8.0) was added after 48 h of fermentation.

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Choi, K.R., Luo, Z.W., Kim, G.B. et al. A microbial process for the production of benzyl acetate. Nat Chem Eng 1, 216–228 (2024). https://doi.org/10.1038/s44286-023-00022-0

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