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Light-driven CO2 sequestration in Escherichia coli to achieve theoretical yield of chemicals

Abstract

CO2 sequestration engineering is an attractive strategy for achieving carbon- and energy-efficient bioproduction. However, the efficiency of heterotrophic CO2 sequestration is limited by bioproduct dependence and energy deficiency. Here, modular CO2 sequestration engineering was developed to produce target chemicals by integrating synthetic CO2 fixation and CO2 mitigation modules. A synthetic CO2 fixation pathway was designed, and then enhanced by light-driven reducing power using self-assembled cadmium sulfide nanoparticles. Next, a CO2 mitigation switch was designed, and then optimized by light-driven energy via proteorhodopsin. Finally, by integrating CO2 fixation and CO2 mitigation modules, the efficiency of CO2 sequestration was notably enhanced in Escherichia coli and the yields of l-malate and butyrate were increased to 1.48 and 0.79 mol/mol glucose, respectively, reaching theoretical yields. This CO2 sequestration system provides an efficient platform for channelling CO2 into value-added chemicals.

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Fig. 1: Rational design of light-driven CO2 sequestration for improving carbon yield in E. coli.
Fig. 2: Design and construction of HWLS pathway.
Fig. 3: Construction and application of light-driven CO2 fixation in E. coli.
Fig. 4: Carbon balance analysis of l-malate production in the anaerobic fermentation stage.
Fig. 5: Design and characterization of basic units for synthetic switch PN2NdhR in E. coli.
Fig. 6: Construction and application of light-driven CO2 mitigation in E. coli.
Fig. 7: Application of light-driven CO2 sequestration for butyrate production in E. coli.

Data availability

Data supporting the findings of this work are available within the paper and its Supplementary Information files. The datasets generated and analysed during the current study are available from the corresponding author upon request. Data were collected using the software Microsoft Excel, Dionex UltiMate 3000 Series, SoftMax pro and iBright FL1000. Source data are provided with this paper.

References

  1. 1.

    Clomburg, J. M., Crumbley, A. M. & Gonzalez, R. Industrial biomanufacturing: the future of chemical production. Science 355, 1–10 (2017).

    Google Scholar 

  2. 2.

    Liu, Z., Wang, K., Chen, Y., Tan, T. & Nielsen, J. Third-generation biorefineries as the means to produce fuels and chemicals from CO2. Nat. Catal. 3, 274–288 (2020).

    CAS  Google Scholar 

  3. 3.

    Hu, G., Li, Y., Ye, C., Liu, L. & Chen, X. Engineering microorganisms for enhanced CO2 sequestration. Trends Biotechnol. 37, 532–547 (2018).

    PubMed  Google Scholar 

  4. 4.

    Matson, M. M. & Atsumi, S. Photomixotrophic chemical production in cyanobacteria. Curr. Opin. Biotechnol. 50, 65–71 (2018).

    CAS  PubMed  Google Scholar 

  5. 5.

    Muller, V. New horizons in acetogenic conversion of one-carbon substrates and biological hydrogen storage. Trends Biotechnol. 37, 1344–1354 (2019).

    PubMed  Google Scholar 

  6. 6.

    Chen, X., Hu, G. & Liu, L. Hacking an algal transcription factor for lipid biosynthesis. Trends Plant Sci. 23, 181–184 (2018).

    PubMed  Google Scholar 

  7. 7.

    Straathof, A. J. J. et al. Grand research challenges for sustainable industrial biotechnology. Trends Biotechnol. 37, 1042–1050 (2019).

    CAS  PubMed  Google Scholar 

  8. 8.

    Chen, X. et al. DCEO biotechnology: tools to design, construct, evaluate, and optimize the metabolic pathway for biosynthesis of chemicals. Chem. Rev. 118, 4–72 (2018).

    CAS  PubMed  Google Scholar 

  9. 9.

    Yu, J. H. et al. Combinatorial optimization of CO2 transport and fixation to improve succinate production by promoter engineering. Biotechnol. Bioeng. 113, 1531–1541 (2016).

    CAS  PubMed  Google Scholar 

  10. 10.

    Hu, G. et al. Engineering synergetic CO2-fixing pathways for malate production. Metab. Eng. 47, 496–504 (2018).

    CAS  PubMed  Google Scholar 

  11. 11.

    Gleizer, S. et al. Conversion of Escherichia coli to generate all biomass carbon from CO2. Cell 179, 1255–1263 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Gassler, T. The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2. Nat. Biotechnol. 38, 210–216 (2019).

    PubMed  PubMed Central  Google Scholar 

  13. 13.

    Wu, J. et al. Co-production of 2,3-BDO and succinic acid using xylose by Enterobacter cloacae. J. Chem. Technol. Biot. 93, 1462–1467 (2018).

    CAS  Google Scholar 

  14. 14.

    Mehrer, C. R., Incha, M. R., Politz, M. C. & Pfleger, B. F. Anaerobic production of medium-chain fatty alcohols via a beta-reduction pathway. Metab. Eng. 48, 63–71 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Lin, P. P. et al. Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism. Proc. Natl Acad. Sci. USA 115, 3538–3546 (2018).

    CAS  PubMed  Google Scholar 

  16. 16.

    Meadows, A. L. et al. Rewriting yeast central carbon metabolism for industrial isoprenoid production. Nature 537, 694–697 (2016).

    CAS  PubMed  Google Scholar 

  17. 17.

    Bogorad, I. W., Lin, T. S. & Liao, J. C. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 502, 693–697 (2013).

    CAS  PubMed  Google Scholar 

  18. 18.

    Dellomonaco, C., Clomburg, J. M., Miller, E. N. & Gonzalez, R. Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals. Nature 476, 355–359 (2011).

    CAS  PubMed  Google Scholar 

  19. 19.

    Luo, N. et al. Visible-light-driven coproduction of diesel precursors and hydrogen from lignocellulose-derived methylfurans. Nat. Energy 4, 575–584 (2019).

    CAS  Google Scholar 

  20. 20.

    Guzman, M. S. et al. Phototrophic extracellular electron uptake is linked to carbon dioxide fixation in the bacterium Rhodopseudomonas palustris. Nat. Commun. 10, 1355 (2019).

    PubMed  PubMed Central  Google Scholar 

  21. 21.

    Liu, X. et al. A genetically encoded photosensitizer protein facilitates the rational design of a miniature photocatalytic CO2-reducing enzyme. Nat. Chem. 10, 1201–1206 (2018).

    CAS  PubMed  Google Scholar 

  22. 22.

    Zhang, X., Wang, X., Shanmugam, K. T. & Ingram, L. O. l-malate production by metabolically engineered Escherichia coli. Appl. Environ. Microbiol. 77, 427–434 (2011).

    CAS  PubMed  Google Scholar 

  23. 23.

    Singh, A., Cher Soh, K., Hatzimanikatis, V. & Gill, R. T. Manipulating redox and ATP balancing for improved production of succinate in E. coli. Metab. Eng. 13, 76–81 (2011).

    CAS  PubMed  Google Scholar 

  24. 24.

    Wang, L. et al. Metabolic engineering of Escherichia coli for the production of butyric acid at high titer and productivity. Biotechnol. Biofuels 12, 62 (2019).

    PubMed  PubMed Central  Google Scholar 

  25. 25.

    Milo, R., Jorgensen, P., Moran, U., Weber, G. & Springer, M. BioNumbers–the database of key numbers in molecular and cell biology. Nucleic Acids Res. 38, D750–D753 (2010).

    CAS  PubMed  Google Scholar 

  26. 26.

    Siegel, J. B. et al. Computational protein design enables a novel one-carbon assimilation pathway. Proc. Natl Acad. Sci. USA 112, 3704–3709 (2015).

    CAS  PubMed  Google Scholar 

  27. 27.

    Bang, J. & Lee, S. Y. Assimilation of formic acid and CO2 by engineered Escherichia coli equipped with reconstructed one-carbon assimilation pathways. Proc. Natl Acad. Sci. USA 115, E9271–E9279 (2018).

    CAS  PubMed  Google Scholar 

  28. 28.

    Tashiro, Y., Hirano, S., Matson, M. M., Atsumi, S. & Kondo, A. Electrical-biological hybrid system for CO2 reduction. Metab. Eng. 47, 211–218 (2018).

    CAS  PubMed  Google Scholar 

  29. 29.

    Roger, M., Brown, F., Gabrielli, W. & Sargent, F. Efficient hydrogen-dependent carbon dioxide reduction by Escherichia coli. Curr. Biol. 28, 140–145 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Wei, W. et al. A surface-display biohybrid approach to light-drivenhydrogen production in air. Sci. Adv. 4, eaap9253 (2018).

    PubMed  PubMed Central  Google Scholar 

  31. 31.

    Liu, Y., Landick, R. & Raman, S. A regulatory NADH/NAD + redox biosensor for bacteria. ACS Synth. Biol. 8, 264–273 (2019).

    PubMed  Google Scholar 

  32. 32.

    Jiang, Y. L. et al. Coordinating carbon and nitrogen metabolic signaling through the cyanobacterial global repressor NdhR. Proc. Natl Acad. Sci. USA 115, 403–408 (2018).

    CAS  PubMed  Google Scholar 

  33. 33.

    Lee, K. Y. et al. Photosynthetic artificial organelles sustain and control ATP-dependent reactions in a protocellular system. Nat. Biotechnol. 36, 530–535 (2018).

    CAS  PubMed  Google Scholar 

  34. 34.

    Fast, A. G. & Papoutsakis, E. T. Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals. Curr. Opin. Chem. Eng. 1, 380–395 (2012).

    Google Scholar 

  35. 35.

    Fast, A. G., Schmidt, E. D., Jones, S. W. & Tracy, B. P. Acetogenic mixotrophy: novel options for yield improvement in biofuels and biochemicals production. Curr. Opin. Biotechnol. 33, 60–72 (2015).

    CAS  PubMed  Google Scholar 

  36. 36.

    Wolf, C. Sustainable Solutions to Global Energy Challenges (US Department of Energy, 2013); https://www.energy.gov/eere/bioenergy/downloads/sustainable-solutions-global-energy-challenges

  37. 37.

    Bar-Even, A., Noor, E., Lewis, N. E. & Milo, R. Design and analysis of synthetic carbon fixation pathways. Proc. Natl Acad. Sci. USA 107, 8889–8894 (2010).

    CAS  PubMed  Google Scholar 

  38. 38.

    Miller, T. E. et al. Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts. Science 368, 649–654 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Gong, F. & Li, Y. Fixing carbon, unnaturally. Science 354, 830–831 (2016).

    CAS  PubMed  Google Scholar 

  40. 40.

    Jones, S. W. et al. CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion. Nat. Commun. 7, 12800 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Liao, J. C., Mi, L., Pontrelli, S. & Luo, S. Fuelling the future: microbial engineering for the production of sustainable biofuels. Nat. Rev. Microbiol. 14, 288–304 (2016).

    CAS  PubMed  Google Scholar 

  42. 42.

    Wang, Q. et al. Engineering an in vivo EP-bifido pathway in Escherichia coli for high-yield acetyl-CoA generation with low CO2 emission. Metab. Eng. 51, 79–87 (2019).

    CAS  PubMed  Google Scholar 

  43. 43.

    Yu, H., Li, X., Duchoud, F., Chuang, D. S. & Liao, J. C. Augmenting the Calvin-Benson-Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway. Nat. Commun. 9, 2008 (2018).

    PubMed  PubMed Central  Google Scholar 

  44. 44.

    Antonovsky, N. et al. Sugar synthesis from CO2 in Escherichia coli. Cell 166, 115–125 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. 45.

    Liu, N., Santala, S. & Stephanopoulos, G. Mixed carbon substrates: a necessary nuisance or a missed opportunity? Curr. Opin. Biotechnol. 62, 15–21 (2019).

    PubMed  Google Scholar 

  46. 46.

    Claassens, N. J., Volpers, M., dos Santos, V. A., van der Oost, J. & de Vos, W. M. Potential of proton-pumping rhodopsins: engineering photosystems into microorganisms. Trends Biotechnol. 31, 633–642 (2013).

    CAS  PubMed  Google Scholar 

  47. 47.

    Zhou, L. et al. Light-driven methane dry reforming with single atomic site antenna-reactor plasmonic photocatalysts. Nat. Energy 5, 61–70 (2020).

    CAS  Google Scholar 

  48. 48.

    Zheng, Y. et al. A pathway for biological methane production using bacterial iron-only nitrogenase. Nat. Microbiol. 3, 281–286 (2018).

    CAS  PubMed  Google Scholar 

  49. 49.

    Ding, Q. et al. Light-powered Escherichia coli cell division for chemical production. Nat. Commun. 11, 2262 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Gao, C. et al. Programmable biomolecular switches for rewiring flux in Escherichia coli. Nat. Commun. 10, 3751 (2019).

    PubMed  PubMed Central  Google Scholar 

  51. 51.

    Ogasawara, K., Nakamura, N. & Matuzawa, S. The determination of formaldehyde in poly(vinylformal) by the chromotropic acid method. Macromol. Chem. Phys. 149, 291–294 (2003).

    Google Scholar 

  52. 52.

    Gong, F. et al. Quantitative analysis of an engineered CO2-fixing Escherichia coli reveals great potential of heterotrophic CO2 fixation. Biotechnol. Biofuels 8, 86 (2015).

    PubMed  PubMed Central  Google Scholar 

  53. 53.

    Yang, C. H., Liu, E. J., Chen, Y. L., Ou-Yang, F. Y. & Li, S. Y. The comprehensive profile of fermentation products during in situ CO2 recycling by Rubisco-based engineered Escherichia coli. Micro. Cell Fact. 15, 133 (2016).

    Google Scholar 

  54. 54.

    Fischer, E. & Sauer, U. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur. J. Biochem. 270, 880–891 (2003).

    CAS  PubMed  Google Scholar 

  55. 55.

    Fischer, E., Zamboni, N. & Sauer, U. High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal. Biochem. 325, 308–316 (2004).

    CAS  PubMed  Google Scholar 

  56. 56.

    Guo, L. et al. Engineering Escherichia coli lifespan for enhancing chemical production. Nat. Catal. 3, 307–318 (2020).

    CAS  Google Scholar 

  57. 57.

    Luo, B., Groenke, K., Takors, R., Wandrey, C. & Oldiges, M. Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J. Chromatogr. A. 1147, 153–164 (2007).

    CAS  PubMed  Google Scholar 

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Acknowledgements

This work is supported by the Key Programme of the National Natural Science Foundation of China (grant no. 22038005 to L.L.), the National Key R&D Program of China (grant nos. 2020YFA0908500 to L.L. and 2019YFA0904900 to X.C.), National Natural Science Foundation of China (grant nos. 21978113 to X.C. and 22008087 to C.G.) and the National First-Class Discipline Program of Light Industry Technology and Engineering (grant no. LITE2018-08 to L.L.). We thank Y. Li for providing the genomic DNA of Synechocystis sp. PCC 6803, X. Xu for the autodock and Y. Qian for protein structure analysis.

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G.H., X.C. and L.L. conceived the project and wrote the paper. G.H., Z.L., D.M. and L.Z. designed and performed all the experiments. G.H., C.Y. and C.G. analysed the results.

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Correspondence to Xiulai Chen.

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Peer review information Nature Catalysis thanks Anne Gompf, Bryan P. Tracy, Han Min Woo and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Hu, G., Li, Z., Ma, D. et al. Light-driven CO2 sequestration in Escherichia coli to achieve theoretical yield of chemicals. Nat Catal 4, 395–406 (2021). https://doi.org/10.1038/s41929-021-00606-0

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