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Biosynthesis of poly(ester amide)s in engineered Escherichia coli

Nature Chemical Biology (2025)Cite this article

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Abstract

The development of biobased polymers to substitute their current petroleum-based counterparts is crucial for fostering a sustainable plastic industry. Here we report the biosynthesis and characterization of a group of biopolymers, poly(ester amide)s (PEAs), in Escherichia coli. PEAs are biosynthesized by constructing a new-to-nature amino acid polymerization pathway, comprising amino acid activation by β-alanine CoA transferase and subsequent polymerization of amino acyl-CoA by polyhydroxyalkanoate synthase. The engineered E. coli strains harboring this pathway are capable of biosynthesizing various PEAs, each incorporating different amino acid monomers in varying fractions. Examination of the physical, thermal and mechanical properties reveals a dependence of molecular weight on the type of polyhydroxyalkanoate synthase, a decrease in melting temperature and crystallinity as the 3-aminopropionate monomer fraction increases and enhanced elongation at break compared to its polyester analog. The engineered bacterial system will prove beneficial for the biobased production of various PEAs using renewable resources.

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Fig. 1: New-to-nature metabolic pathways for the production of PEAs.
Fig. 2: Biosynthesis of multiple PEAs by metabolically engineered E. coli.
Fig. 3: Promiscuous activities of Act on various substrates.
Fig. 4: Renewable biosynthesis of two PEAs from glucose as a sole carbon source.
Fig. 5: Protein engineering of PhaC1437Ps6-19 for the enhanced 3AP monomer fraction.
Fig. 6: Characterization of biosynthesized poly(3HB-ran-3AP)s.

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Data availability

All the data generated in this study are available within the main text and the Supplementary Information. Data are also available from the corresponding author upon request. The crystal structure of Chromobacterium sp. USM2 PhaC bound to CoA is available from the PDB under accession code 6K3C. The engineered strains developed and the PEAs biosynthesized in this study can only be provided for noncommercial purposes as they are of commercial interest, filed under a patent (Korean Patent Application No. 10-2025-0009527). Source data are provided with this paper.

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Acknowledgements

This work is supported by the following projects from the National Research Foundation supported by the Korean Ministry of Science and Information and Communications Technology: ‘Development of next-generation biorefinery platform technologies for leading biobased chemicals industry project’ (2022M3J5A1056072) and ‘Development of platform technologies of microbial cell factories for the next-generation biorefineries’ (2022M3J5A1056117). We acknowledge the Korea Advanced Institute of Science and Technology Analysis Center for Research Advancement for their help with FTIR analysis.

Author information

Authors and Affiliations

  1. Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea

    Tong Un Chae, So Young Choi, Da-Hee Ahn, Woo Dae Jang & Sang Yup Lee

  2. Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, Republic of Korea

    Tong Un Chae, So Young Choi, Da-Hee Ahn, Woo Dae Jang & Sang Yup Lee

  3. Center for Environmental & Sustainable Resources, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea

    Haemin Jeong & Jihoon Shin

  4. Department of Advanced Materials & Chemical Engineering, University of Science & Technology (UST), Daejeon, Republic of Korea

    Haemin Jeong & Jihoon Shin

  5. KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon, Republic of Korea

    Sang Yup Lee

  6. BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, Republic of Korea

    Sang Yup Lee

  7. Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea

    Sang Yup Lee

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  1. Tong Un Chae
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Contributions

S.Y.L. conceptualized the project. T.U.C. and S.Y.L. designed the concept of the study. T.U.C., S.Y.C., D.-H.A., W.D.J., H.J. and J.S. conducted the experiments. W.D.J. performed the computational analyses. T.U.C., S.Y.C., D.-H.A., W.D.J., H.J., J.S. and S.Y.L. analyzed the data and wrote the paper.

Corresponding author

Correspondence to Sang Yup Lee.

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Competing interests

T.U.C., S.Y.C., D.-H.A. and S.Y.L. declare competing financial interests because the strains, PEAs and strategies described in this paper are of commercial interest and are covered by but not limited to a pending patent (Korean Patent Application No. 10-2025-0009527). This patent covers the methods for producing PEAs using engineered strains in this study. The patent was filed by the Korea Advanced Institute of Science and Technology and S.Y.L., T.U.C., S.Y.C. and D.-H.A. are listed as inventors. The other authors declare no competing interests.

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Extended data

Extended Data Fig. 1 Proposed catalytic mechanism of PhaC for the biosynthesis of PEAs.

a, b, c, Schematic representations showing the addition of an amino acid monomer to PEA with a terminal hydroxy group (a), a hydroxy acid monomer to PEA with a terminal amine group (b), and an amino acid monomer to PEA with a terminal amine group (c). While these schematics are based on a non-processive ping-pong mechanism, other proposed mechanisms of PhaC can also be used to demonstrate the potential for biosynthesizing PEAs. 3HB and 3AP are shown as representative hydroxy acid and amino acid monomers, respectively. Amine and amide functional groups are marked with pink. Hydroxy and ester functional groups are marked with blue. Abbreviations shown are: 3AP, 3-aminopropionate; 3HB, 3-hydroxybutyrate; PEA, poly(ester amide).

Extended Data Fig. 2 Concentrations of amino acids in medium after flask cultivation.

Flask cultures for the biosynthesis of PEAs were conducted in MR medium supplemented with 2 g l−1 of sodium (RS)-3HB and 2 g l−1 of the corresponding amino acids. Abbreviations shown are: 3AP, 3-aminopropionate; 3AB, 3-aminobutyrate; 3AIB, 3-aminoisobutyrate; 3AV, 3-aminovalerate; 4AB, 4-aminobutyrate; 5AV, 5-aminovalerate; 6AC, 6-aminocaproate; 7AH, 7-aminoheptanoate. All the experiments were conducted in triplicates. Data are presented as mean values ± s.d.

Source data

Extended Data Fig. 3 Biosynthesis of poly(3HB-ran-LA-ran-5AV).

Schematic representation of in vivo cultivation of the PEA03 strain in MR medium supplemented with (RS)-3HB and (S)-lysine. Multiple metabolic reactions are presented with black dashed arrows. The presented genes encode the following enzymes: act, β-alanine CoA transferase; davA, δ-aminovaleramidase; davB, (S)-lysine 2-monooxygenase; ldhA, (R)-lactate dehydrogenase; pct540, engineered propionate CoA transferase; phaC1437Ps6-19, engineered Pseudomonas sp. MBEL 6–19 polyhydroxyalkanoate synthase. Abbreviations shown are: 3HB, 3-hydroxybutyrate; 5AV, 5-aminovalerate; LA, lactate.

Extended Data Fig. 4 Stereo-specificities of Act and PhaC1437Ps6-19.

a, SDS-PAGE analysis of the purified His6-tagged Act. The lanes are: L, molecular weight markers; T, total proteins; U, unbound proteins; W, washed proteins with 3 mM of imidazole; and E, eluted proteins with 150 mM of imidazole. Red arrow indicate the expected molecular weight of His6-tagged Act (44.68 kDa). b, Schematic representation of the in vitro assay of purified Act using an amino acid with stereo-isomers as a substrate. c, Specific activities of Act on amino acids with stereo-isomers. d, Schematic representation of the in vivo cultivation of the PEA01 strain in MR medium supplemented with (RS)-3HB and an amino acid with stereo-isomers. Multiple metabolic reactions are presented with black dashed arrows. e, Amino acid monomer fractions of the polymers produced in the PEA01 strain when cultured according to the scheme shown in (d). The presented genes encode the following enzymes: act, β-alanine CoA transferase; ldhA, (R)-lactate dehydrogenase; pct540, engineered propionate CoA transferase; phaC1437Ps6-19, engineered Pseudomonas sp. MBEL 6–19 polyhydroxyalkanoate synthase. Abbreviations shown are: 3AB, 3-aminobutyrate; 3AV, 3-aminovalerate; 3HB, 3-hydroxybutyrate; LA, lactate. All the experiments were conducted in triplicates. The representative SDS-PAGE image is shown. Data are presented as mean values ± s.d.

Source data

Extended Data Fig. 5 Biosynthesis of PEAs with multiple amino acid monomers.

3AP, (R)-3AB and (R)-3AV monomer fractions of the produced polymer in the PEA01 strain when cultured in MR medium supplemented with (RS)-3HB and one of 3AP, 3AP/(RS)-3AV or 3AP/(RS)-3AV/(RS)-3AV. The fractions of 3AP, (R)-3AB and (R)-3AV monomers are presented with pink, yellow and orange. Abbreviations shown are: 3AB, 3-aminobutyrate; 3AP, 3-aminopropionate; 3AV, 3-aminovalerate. All the experiments were conducted in triplicates. Data are presented as mean values ± s.d.

Source data

Extended Data Fig. 6 Biosynthesis of poly(3HB-ran-3AP).

a, Schematic representation of the in vivo cultivation of the PEA04 strain in MR medium supplemented with (RS)-3HB and 3AP. Multiple metabolic reactions are presented with black dashed arrows. Inactivated reactions are presented with red “X” marks. b, (R)-LA and 3AP monomer fractions of the produced polymers in the PEA01 and PEA04 strains when cultured according to the scheme shown in (a). The fractions of (R)-LA and 3AP monomers are presented with gray and pink bars, respectively. c, Fed-batch fermentation profile of the PEA06 strain using glucose as a carbon source. Cell density, polymer content, glucose concentration and PEA concentration are presented with gray, orange, white and red circles, respectively. The presented genes encode the following enzymes: act, β-alanine CoA transferase; ldhA, (R)-lactate dehydrogenase; pct540, engineered propionate CoA transferase; phaC1437Ps6-19, engineered Pseudomonas sp. MBEL 6–19 polyhydroxyalkanoate synthase. Abbreviations shown are: 3AP, 3-aminopropionate; 3HB, 3-hydroxybutyrate; LA, lactate. All flask-cultivation experiments were conducted in triplicates and their data are presented as mean values ± s.d. Fed-batch fermentation experiments were conducted in duplicates and another fed-batch fermentation profile of the PEA06 strain is available in Fig. 4e.

Source data

Extended Data Fig. 7 Optimization of culture conditions for the enhanced 3AP monomer fraction.

a, 3AP monomer fractions of the poly(3HB-ran-3AP)s produced in the PEA04 strain cultured in one of the six different media supplemented with 2 g l−1 of sodium (RS)-3HB and 2 g l−1 of 3AP. b, 3AP monomer fractions of the poly(3HB-ran-3AP)s produced in the PEA04 strain cultured in LB medium supplemented with 2 g l−1 of sodium (RS)-3HB and varying concentrations of 3AP. c, 3AP monomer fractions of the poly(3HB-ran-3AP)s produced in the PEA04 strain cultured in LB medium supplemented with varying concentrations of sodium (RS)-3HB and 50 g l−1 of 3AP. Abbreviations shown are: 3AP, 3-aminopropionate; 3HB, 3-hydroxybutyrate. All the experiments were conducted in triplicates. Data are presented as mean values ± s.d.

Source data

Extended Data Fig. 8 13C NMR spectra and DSC cooling cycle of biosynthesized poly(3HB-ran-3AP)s.

a, 13C NMR spectra of poly(3HB-ran-4.45% 3AP). The enlarged version is shown in Supplementary Fig. 2. b, DSC curves of first cooling cycles of poly(3HB-ran-3AP)s with varied 3AP fractions. The first cooling cycles of poly(3HB-ran-3AP)s with 3AP monomer fractions of 1.59%, 2.58%, 3.38% and 4.45% are marked with green, blue, orange and red, respectively. The results indicate that only poly(3HB-ran-1.59% 3AP) exhibits a melting crystallization peak at 59.91 °C, while the others do not show this characteristic. All the experiments were conducted in triplicates. The representative DSC curves are shown.

Source data

Extended Data Fig. 9 Optimization of culture conditions for the appropriate 3HP monomer fraction.

3HP monomer fractions of the poly(3HB-ran-3HP)s produced in the XL1-Blue ΔldhA strain harboring the plasmids pCneCPct540 and pTac15k cultured in LB medium supplemented with varying concentrations of sodium (RS)-3HB and 3HP. Abbreviations shown are: 3HB, 3-hydroxybutyrate; 3HP, 3-hydroxypropionate. All the experiments were conducted in triplicates. Data are presented as mean values ± s.d.

Source data

Extended Data Fig. 10 Tensile testing of poly(3HB-ran-3AP) and poly(3HB-ran-3HP).

a, Stress-strain curves of poly(3HB-ran-1.74% 3AP). b, Stress-strain curves of poly(3HB-ran-1.77% 3HP). The representative stress-strain curves shown in Fig. 5 are marked with pink and blue. Abbreviations shown are: 3AP, 3-aminopropionate; 3HB, 3-hydroxybutyrate; 3HP, 3-hydroxypropionate. All the experiments were conducted in quadruplicate.

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Supplementary Figs. 1 and 2, Tables 1–8 and Notes 1–4.

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Chae, T.U., Choi, S.Y., Ahn, DH. et al. Biosynthesis of poly(ester amide)s in engineered Escherichia coli. Nat Chem Biol (2025). https://doi.org/10.1038/s41589-025-01842-2

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