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Metabolic engineering strategies to enable microbial utilization of C1 feedstocks

Abstract

One-carbon (C1) substrates are preferred feedstocks for the biomanufacturing industry and have recently gained attention owing to their natural abundance, low production cost and availability as industrial by-products. However, native pathways to utilize these substrates are absent in most biotechnologically relevant microorganisms. Recent advances in synthetic biology, genome engineering and laboratory evolution are enabling the first steps towards the creation of synthetic C1-utilizing microorganisms. Here, we briefly review the native metabolism of methane, methanol, CO2, CO and formate, and how these C1-utilizing pathways can be engineered into heterologous hosts. In addition, this review analyses the potential, the challenges and the perspectives of C1-based biomanufacturing.

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Fig. 1: C1-based biomanufacturing.
Fig. 2: Examples of successful approaches to enable C1 substrate utilization in E. coli.
Fig. 3: Methanol- and methane-utilization pathways in native organisms.
Fig. 4: Typical metabolic engineering strategy applied to construction of synthetic methylotrophic E. coli.
Fig. 5: Natural CO2 fixation pathways.
Fig. 6: Engineered CO2 utilization in E. coli and P. pastoris.

References

  1. 1.

    Zhou, Y. J., Kerkhoven, E. J. & Nielsen, J. Barriers and opportunities in bio-based production of hydrocarbons. Nat. Energy 3, 925–935 (2018).

    CAS  Google Scholar 

  2. 2.

    Clomburg, J. M., Crumbley, A. M. & Gonzalez, R. Industrial biomanufacturing: the future of chemical production. Science 355, aag0804 (2017).

    PubMed  PubMed Central  Google Scholar 

  3. 3.

    Naik, S. N., Goud, V. V., Rout, P. K. & Dalai, A. K. Production of first and second generation biofuels: a comprehensive review. Renew. Sust. Energ. 14, 578–597 (2010).

    CAS  Google Scholar 

  4. 4.

    Strong, P. J., Xie, S. & Clarke, W. P. Methane as a resource: can the methanotrophs add value? Environ. Sci. Technol. 49, 4001–4018 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Pfeifenschneider, J., Brautaset, T. & Wendisch, V. F. Methanol as carbon substrate in the bio-economy: Metabolic engineering of aerobic methylotrophic bacteria for production of value-added chemicals. Biofuel. Bioprod. Biorefin. 11, 719–731 (2017).

    CAS  Google Scholar 

  6. 6.

    Dürre, P. & Eikmanns, B. J. C1-carbon sources for chemical and fuel production by microbial gas fermentation. Curr. Opin. Biotechnol. 35, 63–72 (2015).

    PubMed  PubMed Central  Google Scholar 

  7. 7.

    Whitaker, W. B., Sandoval, N. R., Bennett, R. K., Fast, A. G. & Papoutsakis, E. T. Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization. Curr. Opin. Biotechnol. 33, 165–175 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Yurimoto, H., Sakai, Y. & Kato, N. Hansenula polymorpha: Biology and Applications Ch. 5. (Wiley-Blackwell, Hoboken, 2002).

    Google Scholar 

  9. 9.

    Wang, Y., Fan, L., Tuyishime, P., Zheng, P. & Sun, J. Synthetic methylotrophy: a practical solution for methanol-based biomanufacturing. Trends Biotechnol. 38, 650–666 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Zhang, W. et al. Current advance in bioconversion of methanol to chemicals. Biotechnol. Biofuels 11, 260 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11.

    Gassler, T. et al. The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2. Nat. Biotechnol. 38, 210–216 (2019). This work created a fully synthetic autotrophic eukaryote (P. pastoris), able to produce all biomass carbon from CO2.

    PubMed  PubMed Central  Google Scholar 

  12. 12.

    Gleizer, S. et al. Conversion of Escherichia coli to generate all biomass carbon from CO2. Cell 179, 1255–1263.e12 (2019). This work created a fully synthetic autotrophic prokaryote (E. coli), able to produce all biomass carbon from CO2.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Chen, F. Y.-H., Jung, H.-W., Tsuei, C.-Y. & Liao, J. C. Converting Escherichia coli to a synthetic methylotroph growing solely on methanol. Cell 182, 933–946. e14 (2020). In this work, E. coli was successfully converted into a fully synthetic methylotroph growing solely on methanol.

    CAS  Google Scholar 

  14. 14.

    Kim, S. et al. Growth of E. coli on formate and methanol via the reductive glycine pathway. Nat. Chem. Biol. 16, 538–545 (2020). This work generated an E. coli strain able to grow solely on formate as a carbon source by constructing a synthetic reductive glycine pathway.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Methanol: 2018 World Market Outlook and Forecast up to 2027 (Merchant Research & Consulting, 2018); https://mcgroup.co.uk/researches/methanol

  16. 16.

    Du, X. L., Jiang, Z., Su, D. S. & Wang, J. Q. Research progress on the indirect hydrogenation of carbon dioxide to methanol. ChemSusChem 9, 322–332 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Bertau, M., Offermanns, H., Plass, L., Schmidt, F. & Wernicke, H.-J. Methanol: The Basic Chemical and Energy Feedstock of the Future (Springer, 2014).

  18. 18.

    Schrader, J. et al. Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria. Trends Biotechnol. 27, 107–115 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Yurimoto, H., Oku, M. & Sakai, Y. Yeast methylotrophy: metabolism, gene regulation and peroxisome homeostasis. Int. J. Microbiol. 2011, 101298 (2011).

    PubMed  PubMed Central  Google Scholar 

  20. 20.

    Houard, S., Heinderyckx, M. & Bollen, A. Engineering of non-conventional yeasts for efficient synthesis of macromolecules: the methylotrophic genera. Biochimie 84, 1089–1093 (2002).

    CAS  Google Scholar 

  21. 21.

    Ledeboer, A. et al. Molecular cloning and characterization of a gene coding for methanol oxidase in Hansenula polymorpha. Nucleic Acids Res. 13, 3063–3082 (1985).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Cregg, J. M., Madden, K., Barringer, K., Thill, G. & Stillman, C. Functional characterization of the two alcohol oxidase genes from the yeast Pichia pastoris. Mol. Cell. Biol. 9, 1316–1323 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Sakai, Y. & Tani, Y. Cloning and sequencing of the alcohol oxidase-encoding gene (AOD1) from the formaldehyde-producing asporogeneous methylotrophic yeast, Candida boidinii S2. Gene 114, 67–73 (1992).

    CAS  Google Scholar 

  24. 24.

    Yurimoto, H., Kato, N. & Sakai, Y. Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism. Chem. Rec. 5, 367–375 (2005).

    CAS  Google Scholar 

  25. 25.

    Rußmayer, H. et al. Systems-level organization of yeast methylotrophic lifestyle. BMC Biol. 13, 1–25 (2015).

    Google Scholar 

  26. 26.

    Keltjens, J. T., Pol, A., Reimann, J. & den Camp, H. J. O. PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference. Appl. Microbiol. Biotechnol. 98, 6163–6183 (2014).

    CAS  Google Scholar 

  27. 27.

    Lee, J.-Y. et al. Discovery and biochemical characterization of a methanol dehydrogenase from Lysinibacillus xylanilyticus. Front. Bioeng. Biotechnol. 8, 67 (2020).

    PubMed  PubMed Central  Google Scholar 

  28. 28.

    Orita, I., Sakamoto, N., Kato, N., Yurimoto, H. & Sakai, Y. Bifunctional enzyme fusion of 3-hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase. Appl. Microbiol. Biotechnol. 76, 439–445 (2007).

    CAS  Google Scholar 

  29. 29.

    Kallen, R. G. & Jencks, W. P. The mechanism of the condensation of formaldehyde with tetrahydrofolic acid. J. Biol. Chem. 241, 5851–5863 (1966).

    CAS  Google Scholar 

  30. 30.

    Lindén, P., Keech, O., Stenlund, H., Gardeström, P. & Moritz, T. Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C labelling. J. Exp. Bot. 67, 3123–3135 (2016).

    PubMed  PubMed Central  Google Scholar 

  31. 31.

    Cotton, C. A., Claassens, N. J., Benito-Vaquerizo, S. & Bar-Even, A. Renewable methanol and formate as microbial feedstocks. Curr. Opin. Biotechnol. 62, 168–180 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Vorholt, J. A. Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Arch. Microbiol. 178, 239–249 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Wang, X. et al. Biological conversion of methanol by evolved Escherichia coli carrying a linear methanol assimilation pathway. Bioresour. Bioprocess. 4, 41 (2017).

    Google Scholar 

  34. 34.

    Whitaker, W. B. et al. Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli. Metab. Eng. 39, 49–59 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35.

    Bennett, R. K., Gonzalez, J. E., Whitaker, W. B., Antoniewicz, M. R. & Papoutsakis, E. T. Expression of heterologous non-oxidative pentose phosphate pathway from Bacillus methanolicus and phosphoglucose isomerase deletion improves methanol assimilation and metabolite production by a synthetic Escherichia coli methylotroph. Metab. Eng. 45, 75–85 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. 36.

    De Simone, A. et al. Mixing and matching methylotrophic enzymes to design a novel methanol utilization pathway in E. coli. Metab. Eng. 61, 315–325 (2020).

    PubMed  PubMed Central  Google Scholar 

  37. 37.

    Müller, J. E. et al. Engineering Escherichia coli for methanol conversion. Metab. Eng. 28, 190–201 (2015). The first report of the transplantation of the methanol assimilation pathway to the industrial host E. coli, which paved the way towards synthetic methylotrophic organisms.

    PubMed  PubMed Central  Google Scholar 

  38. 38.

    Price, J. V., Chen, L., Whitaker, W. B., Papoutsakis, E. & Chen, W. Scaffoldless engineered enzyme assembly for enhanced methanol utilization. Proc. Natl Acad. Sci. USA 113, 12691–12696 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Woolston, B. M., King, J. R., Reiter, M., Van Hove, B. & Stephanopoulos, G. Improving formaldehyde consumption drives methanol assimilation in engineered E. coli. Nat. Commun. 9, 1–12 (2018). The authors of this work revealed that methanol assimilation is kinetically limited by methanol dehydrogenase, which provided the direction for future engineering strategies.

    CAS  Google Scholar 

  40. 40.

    Meyer, F. et al. Methanol-essential growth of Escherichia coli. Nat. Commun. 9, 1508 (2018). In this work, methanol utilization by E. coli was achieved using a synthetic pathway and by coupling co-consumption of methanol to growth, which was a first step to complete synthetic methylotrophic E. coli.

  41. 41.

    Chen, C.-T. et al. Synthetic methanol auxotrophy of Escherichia coli for methanol-dependent growth and production. Metab. Eng. 49, 257–266 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. 42.

    Portnoy, V. A., Bezdan, D. & Zengler, K. Adaptive laboratory evolution—harnessing the power of biology for metabolic engineering. Curr. Opin. Biotechnol. 22, 590–594 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Tuyishime, P. et al. Engineering Corynebacterium glutamicum for methanol-dependent growth and glutamate production. Metab. Eng. 49, 220–231 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Espinosa, M.I. et al. Engineering and evolution of methanol assimilation in Saccharomyces cerevisiae. Preprint at bioRxiv https://doi.org/10.1101/717942v2 (2020).

  45. 45.

    Espinosa, M. I. et al. Adaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae. Nat. Commun. 11, 5564 (2020).

  46. 46.

    Hwang, I. Y. et al. Biocatalytic conversion of methane to methanol as a key step for development of methane-based biorefineries. J. Microbiol. Biotechnol. 24, 1597–1605 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Hanson, R. S. & Hanson, T. E. Methanotrophic bacteria. Microbiol. Mol. Biol. Rev. 60, 439–471 (1996).

    CAS  Google Scholar 

  48. 48.

    Semrau, J. D., DiSpirito, A. A. & Yoon, S. Methanotrophs and copper. FEMS Microbiol. Rev. 34, 496–531 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 49.

    de la Torre, A. et al. Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G (B1). Microb. Cell Fact. 14, 188 (2015).

    PubMed  PubMed Central  Google Scholar 

  50. 50.

    Zilly, F. E. et al. Tuning a P450 enzyme for methane oxidation. Angew. Chem. Int. Ed. 50, 2720–2724 (2011).

    CAS  Google Scholar 

  51. 51.

    Meinhold, P., Peters, M. W., Chen, M. M., Takahashi, K. & Arnold, F. H. Direct conversion of ethane to ethanol by engineered cytochrome P450 BM3. ChemBioChem 6, 1765–1768 (2005).

    CAS  Google Scholar 

  52. 52.

    Balasubramanian, R. et al. Oxidation of methane by a biological dicopper centre. Nature 465, 115–119 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Kim, H. J. et al. Biological conversion of methane to methanol through genetic reassembly of native catalytic domains. Nat. Catal. 2, 342–353 (2019). In this work, the catalytic domains of a methane monooxygenases were assembled on apoferritin, resulting in a stable and soluble enzyme expression in the non- methanotrophic host E. coli.

    CAS  Google Scholar 

  54. 54.

    Liew, F. et al. Gas fermentation—a flexible platform for commercial scale production of low-carbon-fuels and chemicals from waste and renewable feedstocks. Front. Microbiol. 7, 694 (2016).

    PubMed  PubMed Central  Google Scholar 

  55. 55.

    Ernst, A. & Zibrak, J. D. Carbon monoxide poisoning. N. Engl. J. Med. 339, 1603–1608 (1998).

    CAS  Google Scholar 

  56. 56.

    Alonso, J. R., Cardellach, F., López, S., Casademont, J. & Miró, Ò. Carbon monoxide specifically inhibits cytochrome c oxidase of human mitochondrial respiratory chain. Pharmacol. Toxicol. 93, 142–146 (2003).

    CAS  Google Scholar 

  57. 57.

    Meyer, O. & Schlegel, H. G. Biology of aerobic carbon monoxide-oxidizing bacteria. Annu. Rev. Microbiol. 37, 277–310 (1983).

    CAS  Google Scholar 

  58. 58.

    Oelgeschläger, E. & Rother, M. Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea. Arch. Microbiol. 190, 257–269 (2008).

    Google Scholar 

  59. 59.

    King, G. M. & Weber, C. F. Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat. Rev. Microbiol. 5, 107–118 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Diender, M., Stams, A. J. & Sousa, D. Z. Pathways and bioenergetics of anaerobic carbon monoxide fermentation. Front. Microbiol. 6, 1275 (2015).

    PubMed  PubMed Central  Google Scholar 

  61. 61.

    Can, M., Armstrong, F. A. & Ragsdale, S. W. Structure, function, and mechanism of the nickel metalloenzymes, CO dehydrogenase, and acetyl-CoA synthase. Chem. Rev. 114, 4149–4174 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. 62.

    Ragsdale, S. W. & Pierce, E. Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation. Biochim. Biophys. Acta 1784, 1873–1898 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. 63.

    Roberts, D. L. et al. Cloning and expression of the gene cluster encoding key proteins involved in acetyl-CoA synthesis in Clostridium thermoaceticum: CO dehydrogenase, the corrinoid/Fe-S protein, and methyltransferase. Proc. Natl Acad. Sci. USA 86, 32–36 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. 64.

    Fast, A. G. & Papoutsakis, E. T. Functional expression of the Clostridium ljungdahlii acetyl-coenzyme A synthase in Clostridium acetobutylicum as demonstrated by a novel in vivo CO exchange activity en route to heterologous installation of a functional Wood-Ljungdahl pathway. Appl. Environ. Microbiol. 84, 7 (2018).

    Google Scholar 

  65. 65.

    Carlson, E. D. & Papoutsakis, E. T. Heterologous expression of the clostridium carboxidivorans CO dehydrogenase alone or together with the acetyl coenzyme a synthase enables both reduction of CO2 and oxidation of CO by clostridium acetobutylicum. Appl. Environ. Microbiol. 83, 16 (2017).

    Google Scholar 

  66. 66.

    Takors, R. et al. Using gas mixtures of CO, CO2 and H2 as microbial substrates: the do’s and don’ts of successful technology transfer from laboratory to production scale. Microb. Biotechnol. 11, 606–625 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. 67.

    Fuchs, G. Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu. Rev. Microbiol. 65, 631–658 (2011).

    CAS  Google Scholar 

  68. 68.

    Ducat, D. C. & Silver, P. A. Improving carbon fixation pathways. Curr. Opin. Chem. Biol. 16, 337–344 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. 69.

    Sánchez-Andrea, I. et al. The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans. Nat. Commun. 11, 5090 (2020).

    PubMed  PubMed Central  Google Scholar 

  70. 70.

    Schwander, T., von Borzyskowski, L. S., Burgener, S., Cortina, N. S. & Erb, T. J. A synthetic pathway for the fixation of carbon dioxide in vitro. Science 354, 900–904 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. 71.

    Gong, F., Cai, Z. & Li, Y. Synthetic biology for CO2 fixation. Sci. China Life Sci. 59, 1106–1114 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. 72.

    Raines, C. A. The Calvin cycle revisited. Photosynth. Res. 75, 1–10 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. 73.

    Claassens, N. J. A warm welcome for alternative CO2 fixation pathways in microbial biotechnology. Microb. Biotechnol. 10, 31 (2017).

    PubMed  PubMed Central  Google Scholar 

  74. 74.

    Andersson, I. & Backlund, A. Structure and function of Rubisco. Plant Physiol. Biochem. 46, 275–291 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. 75.

    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  PubMed Central  Google Scholar 

  76. 76.

    Erb, T. J. & Zarzycki, J. Biochemical and synthetic biology approaches to improve photosynthetic CO2-fixation. Curr. Opin. Chem. Biol. 34, 72–79 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. 77.

    Davidi, D. et al. Highly active rubiscos discovered by systematic interrogation of natural sequence diversity. EMBO J. 39, e104081 (2020).

  78. 78.

    Gong, F., Zhu, H., Zhang, Y. & Li, Y. Biological carbon fixation: from natural to synthetic. J. CO2 Util. 28, 221–227 (2018).

  79. 79.

    Antonovsky, N. et al. Sugar synthesis from CO2 in Escherichia coli. Cell 166, 115–125 (2016). This work achieved a fully functional carbon fixation cycle in E. coli, capable of synthetizing sugars solely form CO2.

    CAS  PubMed  PubMed Central  Google Scholar 

  80. 80.

    von Borzyskowski, L. S. et al. An engineered Calvin-Benson-Bassham cycle for carbon dioxide fixation in Methylobacterium extorquens AM1. Metab. Eng. 47, 423–433 (2018).

    Google Scholar 

  81. 81.

    Flamholz, A. I. et al. Functional reconstitution of a bacterial CO2 concentrating mechanism in Escherichia coli. eLife 9, e59882 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. 82.

    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 

  83. 83.

    Guo, L. et al. Enhancement of malate production through engineering of the periplasmic rTCA pathway in Escherichia coli. Biotechnol. Bioeng. 115, 1571–1580 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84.

    Keller, M. W. et al. Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide. Proc. Natl Acad. Sci. USA 110, 5840–5845 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. 85.

    Liu, Z. & Liu, T. Production of acrylic acid and propionic acid by constructing a portion of the 3-hydroxypropionate/4-hydroxybutyrate cycle from Metallosphaera sedula in Escherichia coli. J. Ind. Microbiol. 43, 1659–1670 (2016).

    CAS  Google Scholar 

  86. 86.

    d Mattozzi, M., Ziesack, M., Voges, M. J., Silver, P. A. & Way, J. C. Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: toward horizontal transfer of autotrophic growth. Metab. Eng. 16, 130–139 (2013).

    Google Scholar 

  87. 87.

    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  PubMed Central  Google Scholar 

  88. 88.

    Yishai, O., Bouzon, M., Doring, V. & Bar-Even, A. In vivo assimilation of one-carbon via a synthetic reductive glycine pathway in Escherichia coli. ACS Synth. Biol. 7, 2023–2028 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. 89.

    Gonzalez de la Cruz, J., Machens, F., Messerschmidt, K. & Bar-Even, A. Core catalysis of the reductive glycine pathway demonstrated in yeast. ACS Synth. Biol. 8, 911–917 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. 90.

    Claassens, N. J. et al. Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator. Metab. Eng. 62, 30–41 (2020).

    CAS  Google Scholar 

  91. 91.

    Satanowski, A. et al. Awakening a latent carbon fixation cycle in Escherichia coli. Nat. Commun. 11, 5812–5812 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. 92.

    Yishai, O., Lindner, S. N., Gonzalez de la Cruz, J., Tenenboim, H. & Bar-Even, A. The formate bio-economy. Curr. Opin. Chem. Biol. 35, 1–9 (2016).

    CAS  Google Scholar 

  93. 93.

    Mao, W. et al. Recent progress in metabolic engineering of microbial formate assimilation. Appl. Microbiol. Biotechnol. 104, 6905–6917 (2020).

    CAS  Google Scholar 

  94. 94.

    Bar-Even, A. Formate assimilation: the metabolic architecture of natural and synthetic pathways. Biochemistry 55, 3851–3863 (2016).

    CAS  Google Scholar 

  95. 95.

    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  PubMed Central  Google Scholar 

  96. 96.

    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  PubMed Central  Google Scholar 

  97. 97.

    Bang, J., Hwang, C. H., Ahn, J. H., Lee, J. A. & Lee, S. Y. Escherichia coli is engineered to grow on CO2 and formic acid. Nat. Microbiol. 5, 1459–1463 (2020). This work created an E. coli strain able to grow on CO2 and formic acid as sole carbon sources at improved cell densities.

    CAS  Google Scholar 

  98. 98.

    Sandberg, T. E., Salazar, M. J., Weng, L. L., Palsson, B. O. & Feist, A. M. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab. Eng. 56, 1–16 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. 99.

    McCarty, N. S. & Ledesma-Amaro, R. Synthetic biology tools to engineer microbial communities for biotechnology. Trends Biotechnol. 37, 181–197 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. 100.

    Chistoserdova, L. Applications of methylotrophs: can single carbon be harnessed for biotechnology? Curr. Opin. Biotechnol. 50, 189–194 (2018).

    CAS  Google Scholar 

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Acknowledgements

W.J. is supported by Monash University under a Monash Graduate Scholarship (MGS), a Monash International Tuition Scholarship (MITS), and a Graduate Research International Travel Award (GRITA). R.L.-A. and H.P. received funding from the Biotechnology and Biological Sciences Research Council (BBSRC; BB/R01602X/1). R.L.-A. received funding from UK research and Innovation (19-ERACoBioTech- 33 SyCoLim BB/T011408/1), the BBSRC (BB/T013176/1), the British Council 527429894, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (DEUSBIO - 949080). D.H-V. is supported by Erasmus+ (E MADRID03 – UK LONDON015). R.L.-A.: Newton Advanced Fellowship (NAF\R1\201187). In addition, the authors thank A. Graham for improving the figures.

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Jiang, W., Hernández Villamor, D., Peng, H. et al. Metabolic engineering strategies to enable microbial utilization of C1 feedstocks. Nat Chem Biol 17, 845–855 (2021). https://doi.org/10.1038/s41589-021-00836-0

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