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.
Subscribe to Journal
Get full journal access for 1 year
only $8.25 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
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.
Clomburg, J. M., Crumbley, A. M. & Gonzalez, R. Industrial biomanufacturing: the future of chemical production. Science 355, 1–10 (2017).
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).
Hu, G., Li, Y., Ye, C., Liu, L. & Chen, X. Engineering microorganisms for enhanced CO2 sequestration. Trends Biotechnol. 37, 532–547 (2018).
Matson, M. M. & Atsumi, S. Photomixotrophic chemical production in cyanobacteria. Curr. Opin. Biotechnol. 50, 65–71 (2018).
Muller, V. New horizons in acetogenic conversion of one-carbon substrates and biological hydrogen storage. Trends Biotechnol. 37, 1344–1354 (2019).
Chen, X., Hu, G. & Liu, L. Hacking an algal transcription factor for lipid biosynthesis. Trends Plant Sci. 23, 181–184 (2018).
Straathof, A. J. J. et al. Grand research challenges for sustainable industrial biotechnology. Trends Biotechnol. 37, 1042–1050 (2019).
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).
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).
Hu, G. et al. Engineering synergetic CO2-fixing pathways for malate production. Metab. Eng. 47, 496–504 (2018).
Gleizer, S. et al. Conversion of Escherichia coli to generate all biomass carbon from CO2. Cell 179, 1255–1263 (2019).
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).
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).
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).
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).
Meadows, A. L. et al. Rewriting yeast central carbon metabolism for industrial isoprenoid production. Nature 537, 694–697 (2016).
Bogorad, I. W., Lin, T. S. & Liao, J. C. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 502, 693–697 (2013).
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).
Luo, N. et al. Visible-light-driven coproduction of diesel precursors and hydrogen from lignocellulose-derived methylfurans. Nat. Energy 4, 575–584 (2019).
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).
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).
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).
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).
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).
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).
Siegel, J. B. et al. Computational protein design enables a novel one-carbon assimilation pathway. Proc. Natl Acad. Sci. USA 112, 3704–3709 (2015).
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).
Tashiro, Y., Hirano, S., Matson, M. M., Atsumi, S. & Kondo, A. Electrical-biological hybrid system for CO2 reduction. Metab. Eng. 47, 211–218 (2018).
Roger, M., Brown, F., Gabrielli, W. & Sargent, F. Efficient hydrogen-dependent carbon dioxide reduction by Escherichia coli. Curr. Biol. 28, 140–145 (2018).
Wei, W. et al. A surface-display biohybrid approach to light-drivenhydrogen production in air. Sci. Adv. 4, eaap9253 (2018).
Liu, Y., Landick, R. & Raman, S. A regulatory NADH/NAD + redox biosensor for bacteria. ACS Synth. Biol. 8, 264–273 (2019).
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).
Lee, K. Y. et al. Photosynthetic artificial organelles sustain and control ATP-dependent reactions in a protocellular system. Nat. Biotechnol. 36, 530–535 (2018).
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).
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).
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
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).
Miller, T. E. et al. Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts. Science 368, 649–654 (2020).
Gong, F. & Li, Y. Fixing carbon, unnaturally. Science 354, 830–831 (2016).
Jones, S. W. et al. CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion. Nat. Commun. 7, 12800 (2016).
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).
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).
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).
Antonovsky, N. et al. Sugar synthesis from CO2 in Escherichia coli. Cell 166, 115–125 (2016).
Liu, N., Santala, S. & Stephanopoulos, G. Mixed carbon substrates: a necessary nuisance or a missed opportunity? Curr. Opin. Biotechnol. 62, 15–21 (2019).
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).
Zhou, L. et al. Light-driven methane dry reforming with single atomic site antenna-reactor plasmonic photocatalysts. Nat. Energy 5, 61–70 (2020).
Zheng, Y. et al. A pathway for biological methane production using bacterial iron-only nitrogenase. Nat. Microbiol. 3, 281–286 (2018).
Ding, Q. et al. Light-powered Escherichia coli cell division for chemical production. Nat. Commun. 11, 2262 (2020).
Gao, C. et al. Programmable biomolecular switches for rewiring flux in Escherichia coli. Nat. Commun. 10, 3751 (2019).
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).
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).
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).
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).
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).
Guo, L. et al. Engineering Escherichia coli lifespan for enhancing chemical production. Nat. Catal. 3, 307–318 (2020).
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).
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.
The authors declare no competing interests.
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.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Statistical source data for Fig. 2.
Unprocessed gels Fig. 2b.
Statistical source data for Fig. 3.
Statistical source data for Fig. 4.
Statistical source data for Fig. 5.
Statistical source data for Fig. 6.
Statistical source data for Fig. 7.
About this article
Cite this article
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