Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

A non-carboxylative route for the efficient synthesis of central metabolite malonyl-CoA and its derived products

Nature Catalysis volume 7, pages 361–374 (2024)Cite this article

Subjects

An Author Correction to this article was published on 11 April 2024

This article has been updated

Abstract

Acetyl coenzyme A (CoA) carboxylation is the natural route for endogenous malonyl-CoA formation; however, this pathway presents slow kinetics, carbon and energy inefficiencies, tight regulations and a complicated architecture. These shortcomings limit flux towards malonyl-CoA and become a bottleneck towards the biosynthesis of malonyl-CoA-derived products (MDPs). Here, we design the non-carboxylative malonyl-CoA pathway as a non-natural route for malonyl-CoA biosynthesis, independent from acetyl-CoA. The designed pathway features enzymes such as β-alanine-pyruvate transaminase and malonyl-CoA reductase, exhibits fast kinetics and circumvents tight regulations and the architecture associated with the natural pathway. Furthermore, introducing this pathway into microbes enhances the production of MDPs, including short-chain fatty acids and representative phenol, quinone, alkene, aminoglycoside and macrolide polyketide families, such as spinosad. In summary, this malonyl-CoA formation pathway avoids intrinsic inefficiencies of the natural pathway and can serve as a versatile platform for obtaining MDPs that could be used as fuels, fine chemicals and pharmaceuticals.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Design and implementation of an artificial pathway for malonyl-CoA biosynthesis.
Fig. 2: Metabolic flux after NCM pathway introduction and substituting the artificial NCM pathway for the natural pathway in E. coli cells.
Fig. 3: Introduction of the NCM pathway improves the robustness of cells to inhibitory chemicals and stresses.
Fig. 4: Introduction of the NCM pathway into the model organism E. coli improved MDP production.
Fig. 5: Introduction of the NCM pathway into non-model microorganisms improved MDP production.

Similar content being viewed by others

Data availability

All the data generated in this study are available within the main text and the Supplementary Information file. Source data are provided with this paper. Data are also available from the corresponding author upon request.

Change history

References

  1. Bowman, C. E. & Wolfgang, M. J. Role of the malonyl-CoA synthetase ACSF3 in mitochondrial metabolism. Adv. Biol. Regul. 71, 34–40 (2019).

    Article  CAS  PubMed  Google Scholar 

  2. Wang, Y. et al. Acetyl-CoA carboxylases and diseases. Front. Oncol. 12, 836058 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Folmes, C. D. & Lopaschuk, G. D. Role of malonyl-CoA in heart disease and the hypothalamic control of obesity. Cardiovasc. Res. 73, 278–287 (2007).

    Article  CAS  PubMed  Google Scholar 

  4. Zou, L. et al. Lysine malonylation and its links to metabolism and diseases. Aging Dis. 14, 84–98 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Yang, Y. et al. Regulating malonyl-CoA metabolism via synthetic antisense RNAs for enhanced biosynthesis of natural products. Metab. Eng. 29, 217–226 (2015).

    Article  CAS  PubMed  Google Scholar 

  6. Chan, Y. A. et al. Biosynthesis of polyketide synthase extender units. Nat. Prod. Rep. 26, 90–114 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sajid, M. et al. Synthetic biology towards improved flavonoid pharmacokinetics. Biomolecules 11, 754 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Safe, S. et al. Flavonoids: structure-function and mechanisms of action and opportunities for drug development. Toxicol. Res. 37, 147–162 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Wakil, S. J. A malonic acid derivative as an intermediate in fatty acid synthesis. J. Am. Chem. Soc. 80, 6465–6465 (1958).

    Article  CAS  Google Scholar 

  10. Shi, S. et al. Improving production of malonyl coenzyme A-derived metabolites by abolishing Snf1-dependent regulation of Acc1. mBio 5, e01130–14 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Johnson, A. O. et al. Design and application of genetically-encoded malonyl-CoA biosensors for metabolic engineering of microbial cell factories. Metab. Eng. 44, 253–264 (2017).

    Article  CAS  PubMed  Google Scholar 

  12. Davis, M. S., Solbiati, J. & Cronan, J. E. Overproduction of acetyl-CoA carboxylase activity increases the rate of fatty acid biosynthesis in Escherichia coli. J. Biol. Chem. 275, 28593–28598 (2000).

    Article  CAS  PubMed  Google Scholar 

  13. Kozak, B. U. et al. Engineering acetyl coenzyme A supply: functional expression of a bacterial pyruvate dehydrogenase complex in the cytosol of Saccharomyces cerevisiae. mBio 5, e01696–14 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Skerlova, J. et al. Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. Nat. Commun. 12, 5277 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Atherton, H. J. et al. Role of pyruvate dehydrogenase inhibition in the development of hypertrophy in the hyperthyroid rat heart: a combined magnetic resonance imaging and hyperpolarized magnetic resonance spectroscopy study. Circulation 123, 2552–2561 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Milke, L. & Marienhagen, J. Engineering intracellular malonyl-CoA availability in microbial hosts and its impact on polyketide and fatty acid synthesis. Appl. Microbiol. Biotechnol. 104, 6057–6065 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Leonard, E. et al. Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli. Appl. Environ. Microbiol. 73, 3877–3886 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Wu, J. et al. Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli. Sci. Rep. 5, 13477 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  19. Francois, J. M., Alkim, C. & Morin, N. Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives. Biotechnol. Biofuels 13, 118 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Stinson, R. A. & Spencer, M. S. Beta alanine aminotransferase (s) from a plant source. Biochem. Biophys. Res. Commun. 34, 120–127 (1969).

    Article  CAS  PubMed  Google Scholar 

  21. Wilding, M. et al. A beta-alanine catabolism pathway containing a highly promiscuous omega-transaminase in the 12-aminododecanate-degrading Pseudomonas sp. strain AAC. Appl. Environ. Microbiol. 82, 3846–3856 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Dellomonaco, C. et al. Engineered reversal of the bβ-oxidation cycle for the synthesis of fuels and chemicals. Nature 476, 355–359 (2011).

    Article  CAS  PubMed  Google Scholar 

  23. Liu, C. et al. Dissection of malonyl-coenzyme A reductase of Chloroflexus aurantiacus results in enzyme activity improvement. PLoS ONE 8, e75554 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Liu, C. et al. Functional balance between enzymes in malonyl-CoA pathway for 3-hydroxypropionate biosynthesis. Metab. Eng. 34, 104–111 (2016).

    Article  PubMed  Google Scholar 

  25. Davis, M. S. & Cronan, J. E. Jr Inhibition of Escherichia coli acetyl coenzyme A carboxylase by acyl-acyl carrier protein. J. Bacteriol. 183, 1499–1503 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Alves, J. et al. Cloning, expression, and enzymatic activity of Acinetobacter baumannii and Klebsiella pneumoniae acetyl-coenzyme A carboxylases. Anal. Biochem. 417, 103–111 (2011).

    Article  CAS  PubMed  Google Scholar 

  27. Mishina, M., Roggenkamp, R. & Schweizer, E. Yeast mutants defective in acetyl-coenzyme A carboxylase and biotin: apocarboxylase ligase. Eur. J. Biochem. 111, 79–87 (1980).

    Article  CAS  PubMed  Google Scholar 

  28. Sun, J. D. et al. Biochemical and molecular biological characterization of CAC2, the Arabidopsis thaliana gene coding for the biotin carboxylase subunit of the plastidic acetyl-coenzyme A carboxylase. Plant Physiol. 115, 1371–1383 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Kim, K. W. et al. Expression, purification, and characterization of human acetyl-CoA carboxylase 2. Protein Expr. Purif. 53, 16–23 (2007).

    Article  CAS  PubMed  Google Scholar 

  30. Yeh, L. A., Song, C. S. & Kim, K. H. Coenzyme A activation of acetyl-CoA carboxylase. J. Biol. Chem. 256, 2289–2296 (1981).

    Article  CAS  PubMed  Google Scholar 

  31. Qi, Q. et al. Pyruvate dehydrogenase complex and acetyl-CoA carboxylase in pea root plastids: their characterization and role in modulating glycolytic carbon flow to fatty acid biosynthesis. J. Exp. Bot. 47, 1889–1896 (1996).

    Article  CAS  Google Scholar 

  32. Hansford, R. G. Studies on the effects of coenzyme A-SH:acetyl coenzyme A, nicotinamide adenine dinucleotide:reduced nicotinamide adenine dinucleotide, and adenosine diphosphate:adenosine triphosphate ratios on the interconversion of active and inactive pyruvate dehydrogenase in isolated rat heart mitochondria. J. Biol. Chem. 251, 5483–5489 (1976).

    Article  CAS  PubMed  Google Scholar 

  33. Herzig, S. & Shaw, R. J. AMPK: guardian of metabolism and mitochondrial homeostasis. Nat. Rev. Mol. Cell Biol. 19, 121–135 (2018).

    Article  CAS  PubMed  Google Scholar 

  34. Sumegi, B. et al. Electron microscopic study on the size of pyruvate dehydrogenase complex in situ. Eur. J. Biochem. 169, 223–230 (1987).

    Article  CAS  PubMed  Google Scholar 

  35. Walter, C., Marada, A. & Meisinger, C. Monitoring checkpoints of metabolism and protein biogenesis in mitochondria by Phos-tag technology. J. Proteom. 252, 104430 (2022).

    Article  CAS  Google Scholar 

  36. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 0008 (2006). 2006.

    Article  Google Scholar 

  37. Fang, L. et al. Genome-scale target identification in Escherichia coli for high-titer production of free fatty acids. Nat. Commun. 12, 4976 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Olin-Sandoval, V. et al. Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism. Nature 572, 249–253 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Spaans, S. K. et al. NADPH-generating systems in bacteria and archaea. Front. Microbiol. 6, 742 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Tan, Z. et al. Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production. Biotechnol. Biofuels 11, 87 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Tan, Z. et al. Membrane engineering via trans unsaturated fatty acids production improves Escherichia coli robustness and production of biorenewables. Metab. Eng. 35, 105–113 (2016).

    Article  CAS  PubMed  Google Scholar 

  42. Rizzo, P., Altschmied, L., Ravindran, B. M., Rutten, T. & D’Auria, J. C. The biochemical and genetic basis for the biosynthesis of bioactive compounds in Hypericum perforatum L., one of the largest medicinal crops in Europe. Genes 11, 1210 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Kawasaki, T. et al. Biosynthesis of a natural polyketide-isoprenoid hybrid compound, furaquinocin A: identification and heterologous expression of the gene cluster. J. Bacteriol. 188, 1236–1244 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Tan, Z., Clomburg, J. M. & Gonzalez, R. Synthetic pathway for the production of olivetolic acid in Escherichia coli. ACS Synth. Biol. 7, 1886–1896 (2018).

    Article  CAS  PubMed  Google Scholar 

  45. Yan, D. et al. Repurposing type III polyketide synthase as a malonyl-CoA biosensor for metabolic engineering in bacteria. Proc. Natl Acad. Sci. USA 115, 9835–9844 (2018).

    Article  Google Scholar 

  46. Liu, Q. et al. Engineering an iterative polyketide pathway in Escherichia coli results in single-form alkene and alkane overproduction. Metab. Eng. 28, 82–90 (2015).

    Article  CAS  PubMed  Google Scholar 

  47. Zhang, J. et al. A phosphopantetheinylating polyketide synthase producing a linear polyene to initiate enediyne antitumor antibiotic biosynthesis. Proc. Natl Acad. Sci. USA 105, 1460–1465 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Chen, D., Ruzicka, F. J. & Frey, P. A. A novel lysine 2,3-aminomutase encoded by the yodO gene of bacillus subtilis: characterization and the observation of organic radical intermediates. Biochem. J. 348, 539–549 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Jessen, H. J. et al. Alanine 2, 3 aminomutases. US Patent Application 11/658,795 (2009).

  50. Lacmata, S. T. et al. Enhanced poly(3-hydroxypropionate) production via beta-alanine pathway in recombinant Escherichia coli. PLoS ONE 12, e0173150 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  51. Wang, L. et al. Advances in biotechnological production of beta-alanine. World J. Microbiol. Biotechnol. 37, 79 (2021).

    Article  CAS  PubMed  Google Scholar 

  52. Zong, G. et al. Complete genome sequence of the high-natamycin-producing strain Streptomyces gilvosporeus F607. Genome Announc. 6, e01402–e01417 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Wang, Y. M. et al. Iteratively improving natamycin production in Streptomyces gilvosporeus by a large operon-reporter based strategy. Metab. Eng. 38, 418–426 (2016).

    Article  PubMed  Google Scholar 

  54. Wang, X., Deng, Z. & Liu, T. Marker-free system using ribosomal promoters enhanced xylose/glucose isomerase production in Streptomyces rubiginosus. Biotechnol. J. 14, e1900114 (2019).

    Article  PubMed  Google Scholar 

  55. An, Z. et al. Increasing the heterologous production of spinosad in Streptomyces albus J1074 by regulating biosynthesis of its polyketide skeleton. Synth. Syst. Biotechnol. 6, 292–301 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Choi, J. W. & Da Silva, N. A. Improving polyketide and fatty acid synthesis by engineering of the yeast acetyl-CoA carboxylase. J. Biotechnol. 187, 56–59 (2014).

    Article  CAS  PubMed  Google Scholar 

  57. Tan, Z. et al. Designing artificial pathways for improving chemical production. Biotechnol. Adv. 64, 108119 (2023).

    Article  CAS  PubMed  Google Scholar 

  58. Kang, W. et al. Modular enzyme assembly for enhanced cascade biocatalysis and metabolic flux. Nat. Commun. 10, 4248 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  59. Crawford, J. M. & Townsend, C. A. New insights into the formation of fungal aromatic polyketides. Nat. Rev. Microbiol. 8, 879–889 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Chen, L. et al. Acetyl-CoA carboxylase (ACC) as a therapeutic target for metabolic syndrome and recent developments in ACC1/2 inhibitors. Expert Opin. Inv. Drugs 28, 917–930 (2019).

    Article  CAS  Google Scholar 

  61. Bierman, M. et al. Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. Gene 116, 43–49 (1992).

    Article  CAS  PubMed  Google Scholar 

  62. Liu, Q. et al. Development of Streptomyces sp. FR-008 as an emerging chassis. Synth. Syst. Biotechnol. 1, 207–214 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Yuan, J. et al. Kinetic flux profiling for quantitation of cellular metabolic fluxes. Nat. Protoc. 3, 1328–1340 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Dong, W. et al. Mycobacterial fatty acid catabolism is repressed by FdmR to sustain lipogenesis and virulence. Proc. Natl Acad. Sci. USA 118, e2019305118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Krauser, S., Kiefer, P. & Heinzle, E. Multienzyme whole-cell in situ biocatalysis for the production of flaviolin in permeabilized cells of Escherichia coli. Chem. Cat. Chem. 4, 786–788 (2012).

    CAS  Google Scholar 

Download references

Acknowledgements

This work was funded by the National Key R&D Program of China (grant nos. 2020YFA0907700, 2018YFA0900400 and 2021YFC2104400), the National Natural Science Foundation of China (grant nos. 32071419, 31925001 and 31921006), State Key Laboratory of Microbial Technology Open Projects Fund (grant no. M2021-02). We thank C. Zhu at Shanghai Jiao Tong University for assistance in the gel filtration assay. We thank Y. Cao at Tianjin University for providing the pCF and Sg-0 plasmids. We also thank C. Lou at Shenzhen Institutes of Advanced Technology (SIAT-CAS) for providing the pCum plasmid.

Author information

Author notes

  1. These authors contributed equally: Jian Li, Xin Mu, Wenyue Dong.

Authors and Affiliations

  1. State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China

    Jian Li, Yun Chen, Qianjin Kang, Linquan Bai, Yan Feng, Tiangang Liu & Zaigao Tan

  2. Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China

    Jian Li, Yun Chen, Qianjin Kang, Linquan Bai, Tiangang Liu & Zaigao Tan

  3. Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Centre for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China

    Xin Mu & Tiangang Liu

  4. CAS-Key Laboratory of Synthetic Biology, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China

    Wenyue Dong & Chen Yang

  5. State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China

    Guang Zhao & Jin Hou

  6. Department of Chemical, Biological and Materials Engineering, University of South Florida, Tampa, FL, USA

    Ramon Gonzalez

Authors
  1. Jian Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xin Mu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wenyue Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yun Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qianjin Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Guang Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jin Hou
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ramon Gonzalez
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Linquan Bai
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yan Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Chen Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Tiangang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Zaigao Tan
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Z.T., T.L. and C.Y. designed the research. J.L., X.M. and Y.C. performed the in vitro and in vivo analysis of NCM pathway. W.D. and C.Y. performed the metabolic flux analysis. Q.K., G.Z. and J.H. constructed the plasmids. Z.T., T.L., C.Y., J.L., X.M., W.D., Y.C., Q.K., G.Z., J.H., R.G., L.B. and Y.F. analysed the data. Z.T., T.L., C.Y. and R.G. wrote the paper.

Corresponding authors

Correspondence to Chen Yang, Tiangang Liu or Zaigao Tan.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Catalysis thanks Yaping Xue, Dongsoo Yang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 The intracellular contents of NCM pathway cofactors in E. coli.

a, The intracellular concentration of NADPH in E. coli. b, The intracellular concentration of NADP+ in E. coli. c, The NADPH/NADP+ ratio in E. coli. P = 0.0037. d, The intracellular concentrations of PLP in E. coli at logarithmic growth phase and stationary phase. e, The intracellular concentrations of CoA in E. coli at logarithmic growth phase and stationary phase. All data were represented as mean ± SD (n = 3 independent experiments). Statistical analysis was performed using two-tailed Student’s t-test.

Source data

Extended Data Fig. 2 The intracellular contents of PLP, CoA, NADPH, NADP+ and NADPH/NADP+ ratio in Streptomyces gilvosporeus.

a, The relative content of PLP in Streptomyces gilvosporeus at logarithmic growth phase and stationary phase. b, The relative content of CoA in Streptomyces gilvosporeus at logarithmic growth phase and stationary phase. (The relative content: we set the sample with the smallest peak area to 1, and the remaining samples are converted according to the peak area ratio). c, The content of NADPH per dry cell weight in Streptomyces gilvosporeus at logarithmic growth phase and stationary phase. P value is 0.0007 at logarithmic phase and is 0.0055 at stationary phase. d, The content of NADP+ per dry cell weight in Streptomyces gilvosporeus at logarithmic growth phase and stationary phase. e, The molar ratio of NADPH/NADP+ in Streptomyces gilvosporeus at logarithmic growth phase and stationary phase. P value is 0.0003 at logarithmic phase and is 0.0011 at stationary phase. All data were represented as mean ± SD (n = 3 independent experiments). Statistical analysis was performed using two-tailed Student’s t-test.

Source data

Extended Data Fig. 3 The intracellular contents of PLP, CoA, NADPH, NADP+ and NADPH/NADP+ ratio in Saccharopolyspora spinosa.

a, The relative content of PLP in Saccharopolyspora spinosa at logarithmic growth phase and stationary phase. b, The relative content of CoA in Saccharopolyspora spinosa at logarithmic growth phase and stationary phase. c, The content of NADPH per dry cell weight in Saccharopolyspora spinosa at logarithmic growth phase and stationary phase. P value is 0.0033 at logarithmic phase and is 0.0016 at stationary phase. d, The content per dry cell weight of NADP+ in Saccharopolyspora spinosa at logarithmic growth phase and stationary phase. e, The molar ratio of NADPH/NADP+ in Saccharopolyspora spinosa at logarithmic growth phase and stationary phase. P value is 0.0003 at logarithmic phase and is 5.5 × 10−5 at stationary phase. All data were represented as mean ± SD (n = 3 independent experiments). Statistical analysis was performed using two-tailed Student’s t-test.

Source data

Extended Data Fig. 4 The intracellular contents of malonyl-CoA in Streptomyces gilvosporeus, Saccharopolyspora spinosa and E. coli.

a, The concentration of malonyl-CoA per dry cell weight in Streptomyces gilvosporeus at logarithmic growth phase and stationary phase. P value is 0.0011 at logarithmic phase and is 0.0002 at stationary phase. b, The concentration of malonyl-CoA per dry cell weight in Saccharopolyspora spinosa at logarithmic growth phase and stationary phase. P value is 7.8 × 10−6at logarithmic phase and is 6.5 × 10−6 at stationary phase. c, The concentration of malonyl-CoA per dry cell weight in E. coli at logarithmic growth phase and stationary phase. P value is 1.7 × 10−5 at logarithmic phase and is 3.3 × 10−7 at stationary phase. All data were represented as mean ± SD (n = 3 independent experiments). Statistical analysis was performed using two-tailed Student’s t-test.

Source data

Extended Data Fig. 5 In vivo production of MDPs in the model microorganism E. coli.

a, the biosynthetic pathway of octanoic acid in recombinant E. coli. b, the biosynthetic pathway of phloroglucinol in recombinant E. coli. c, the biosynthetic pathway of flaviolin in recombinant E. coli. d, the biosynthetic pathway of pentadecaheptaene in recombinant E. coli.

Extended Data Fig. 6 The biomass of MDPs (malonyl-CoA-derived products) producing strains.

a, the final biomass (OD550) of short-chain fatty acid (octanoic acid) producing strains. b, the final biomass (OD550) of phloroglucinol producing strains. c, the final biomass (OD550) of phloroglucinol flaviolin strains. d, the final biomass (OD550) of pentadecaheptaene producing strains. e, the final biomass (g/mL) of natamycin producing strains. f, the final biomass (g/mL) of spinosad producing strains. All data were represented as mean ± SD (n = 3 independent experiments).

Source data

Extended Data Fig. 7 The intracellular contents of β-alanine per dry cell weight in Streptomyces gilvosporeus and Saccharopolyspora spinosa.

a, The content of β-alanine per dry cell weight in Streptomyces gilvosporeus at logarithmic growth phase and stationary phase. b, The content of β-alanine per dry cell weight in Saccharopolyspora spinosa at logarithmic growth phase and stationary phase. All data were represented as mean ± SD (n = 3 independent experiments).

Source data

Extended Data Fig. 8 In vivo production of MDPs in non-model microorganisms.

a, the biosynthetic pathway of natamycin in S. gilvosporeus. b, the biosynthetic pathway of Spinosad in S. spinosa.

Extended Data Fig. 9 Assembly of the NCM pathway enzymes for malonyl-CoA derived flaviolin production.

a, the 2 types of assembly optimization. b, the malonyl-CoA dependent synthesis of flaviolin. c, the flaviolin titers of different strains. P = 0.0048. d, the final biomass (OD550) of flaviolin producing strains. All data were represented as mean ± SD (n = 3 independent experiments). Statistical analysis was performed using two-tailed Student’s t-test.

Source data

Supplementary information

Supplementary Information

Supplementary Tables 1–4 and Figs. 1–7.

Reporting Summary

Source data

Source Data Fig. 1

Statistical source data.

Source Data Fig. 2

Statistical source data.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 4

Statistical source data.

Source Data Fig. 5

Statistical source data.

Source Data Extended Data Fig. 1

Statistical source data.

Source Data Extended Data Fig. 2

Statistical source data.

Source Data Extended Data Fig. 3

Statistical source data.

Source Data Extended Data Fig. 4

Statistical source data.

Source Data Extended Data Fig. 6

Statistical source data.

Source Data Extended Data Fig. 7

Statistical source data.

Source Data Extended Data Fig. 9

Statistical source data.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, J., Mu, X., Dong, W. et al. A non-carboxylative route for the efficient synthesis of central metabolite malonyl-CoA and its derived products. Nat Catal 7, 361–374 (2024). https://doi.org/10.1038/s41929-023-01103-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41929-023-01103-2

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research