Nielsen, J. & Keasling, J. D. Engineering cellular metabolism. Cell 164, 1185–1197 (2016).
Google Scholar
Csete, M. & Doyle, J. Bow ties, metabolism and disease. Trends Biotechnol. 22, 446–450 (2004).
Google Scholar
Bar-Even, A., Noor, E. & Milo, R. A survey of carbon fixation pathways through a quantitative lens. J. Exp. Bot. 63, 2325–2342 (2012).
Google Scholar
Kalyuzhnaya, M. G., Puri, A. W. & Lidstrom, M. E. Metabolic engineering in methanotrophic bacteria. Metab. Eng. 29, 142–152 (2015).
Google Scholar
Bogorad, I. W. et al. Building carbon–carbon bonds using a biocatalytic methanol condensation cycle. Proc. Natl Acad. Sci. USA 111, 15928–15933 (2014).
Google Scholar
Siegel, J. B. et al. Computational protein design enables a novel one-carbon assimilation pathway. Proc. Natl Acad. Sci. USA 112, 3704–3709 (2015).
Google Scholar
Schwander, T., Schada von Borzyskowski, L., Burgener, S., Cortina, N. S. & Erb, T. J. A synthetic pathway for the fixation of carbon dioxide in vitro. Science 354, 900–904 (2016).
Google Scholar
Lu, X. et al. Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design. Nat. Commun. 10, 1378 (2019).
Google Scholar
Kim, S. et al. Growth of E. coli on formate and methanol via the reductive glycine pathway. Nat. Chem. Biol. 16, 538–545 (2020).
Google Scholar
Clomburg, J. M., Crumbley, A. M. & Gonzalez, R. Industrial biomanufacturing: the future of chemical production. Science 355, aag0804 (2017).
Liu, C. C., Jewett, M. C., Chin, J. W. & Voigt, C. A. Toward an orthogonal central dogma. Nat. Chem. Biol. 14, 103–106 (2018).
Google Scholar
Pandit, A. V., Srinivasan, S. & Mahadevan, R. Redesigning metabolism based on orthogonality principles. Nat. Commun. 8, 1–11 (2017).
Costello, A. & Badran, A. H. Synthetic biological circuits within an orthogonal central dogma. Trends Biotechnol. https://doi.org/10.1016/j.tibtech.2020.05.013 (2020).
Natarajan, A. et al. Engineering orthogonal human O-linked glycoprotein biosynthesis in bacteria. Nat. Chem. Biol. 16, 1062–1070 (2020).
Google Scholar
Black, W. B. et al. Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis. Nat. Chem. Biol. 16, 87–94 (2020).
Google Scholar
Chou, A., Clomburg, J. M., Qian, S. & Gonzalez, R. 2-Hydroxyacyl-CoA lyase catalyzes acyloin condensation for one-carbon bioconversion. Nat. Chem. Biol. 15, 900–906 (2019).
Google Scholar
Burgener, S., Cortina, N. S. & Erb, T. J. Oxalyl-CoA decarboxylase enables nucleophilic one-carbon extension of aldehydes to chiral α-hydroxy acids. Angew. Chem. Int. Ed. Engl. https://doi.org/10.1002/anie.201915155 (2020).
Müller, J. E. N. et al. Engineering Escherichia coli for methanol conversion. Metab. Eng. 28, 190–201 (2015).
Google Scholar
Wu, T. Y. et al. Characterization and evolution of an activator-independent methanol dehydrogenase from Cupriavidus necator N-1. Appl. Microbiol. Biotechnol. 100, 4969–4983 (2016).
Google Scholar
Whitaker, W. B. et al. Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli. Metab. Eng. 39, 49–59 (2017).
Google Scholar
Jonsson, S., Ricagno, S., Lindqvist, Y. & Richards, N. G. J. Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes. J. Biol. Chem. 279, 36003–36012 (2004).
Google Scholar
Sly, W. W. S. & Stadtman, E. R. Formate metabolism II. Enzymatic synthesis of formyl phosphate and formyl coenzyme a in Clostridium cylindrosporum. J. Biol. Chem. 238, 2639–2647 (1963).
Google Scholar
Singh, R. K. et al. Insights into cell-free conversion of CO2 to chemicals by a multienzyme cascade reaction. ACS Catal. 8, 11085–11093 (2018).
Google Scholar
Schuchmann, K. & Muller, V. Direct and reversible hydrogenation of CO2 to formate by a bacterial carbon dioxide reductase. Science 342, 1382–1385 (2013).
Google Scholar
Roger, M., Brown, F., Gabrielli, W. & Sargent, F. Efficient hydrogen-dependent carbon dioxide reduction by Escherichia coli. Curr. Biol. 28, 140–145 (2018).
Google Scholar
Sirajuddin, S. & Rosenzweig, A. C. Enzymatic oxidation of methane. Biochemistry 54, 2283–2294 (2015).
Google Scholar
Felnagle, E. A., Chaubey, A., Noey, E. L., Houk, K. N. & Liao, J. C. Engineering synthetic recursive pathways to generate non-natural small molecules. Nat. Chem. Biol. 8, 518–526 (2012).
Google Scholar
Kim, J., Hetzel, M., Boiangiu, C. D. & Buckel, W. Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of α-amino acids by anaerobic bacteria. FEMS Microbiol. Rev. 28, 455–468 (2004).
Google Scholar
Kandasamy, V. et al. Engineering Escherichia coli with acrylate pathway genes for propionic acid synthesis and its impact on mixed-acid fermentation. Appl. Microbiol. Biotechnol. 97, 1191–1200 (2013).
Google Scholar
Clomburg, J. M., Vick, J. E., Blankschien, M. D., Rodríguez-Moyá, M. & Gonzalez, R. A synthetic biology approach to engineer a functional reversal of the β-oxidation cycle. ACS Synth. Biol. 1, 541–554 (2012).
Google Scholar
Vick, J. E. et al. Escherichia coli enoyl-acyl carrier protein reductase (FabI) supports efficient operation of a functional reversal of the β-oxidation cycle. Appl. Environ. Microbiol. 81, 1406–1416 (2014).
Cheong, S., Clomburg, J. M. & Gonzalez, R. Energy-and carbon-efficient synthesis of functionalized small molecules in bacteria using non-decarboxylative Claisen condensation reactions. Nat. Biotechnol. 34, 556–561 (2016).
Google Scholar
Buckel, W. et al. Enzyme catalyzed radical dehydrations of hydroxy acids. Biochim. Biophys. Acta 1824, 1278–1290 (2012).
Google Scholar
Obradors, N., Cabiscol, E., Aguilar, J. & Ros, J. Site-directed mutagenesis studies of the metal-binding center of the iron-dependent propanediol oxidoreductase from Escherichia coli. Eur. J. Biochem. 258, 207–213 (1998).
Google Scholar
Tobimatsu, T. et al. Heterologous expression, purification, and properties of diol dehydratase, an adenosylcobalamin-dependent enzyme of Klebsiella oxytoca. Arch. Biochem. Biophys. 347, 132–140 (1997).
Google Scholar
Jain, R., Sun, X., Yuan, Q. & Yan, Y. Systematically engineering Escherichia coli for enhanced production of 1,2-propanediol and 1-propanol. ACS Synth. Biol. 4, 746–756 (2015).
Google Scholar
Wang, J. et al. Rational engineering of diol dehydratase enables 1,4-butanediol biosynthesis from xylose. Metab. Eng. 40, 148–156 (2017).
Google Scholar
Lennen, R. M. & Pfleger, B. F. Engineering Escherichia coli to synthesize free fatty acids. Trends Biotechnol. 30, 659–667 (2012).
Google Scholar
Dellomonaco, C., Clomburg, J. M., Miller, E. N. & Gonzalez, R. Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature 476, 355–359 (2011).
Google Scholar
Kunjapur, A. M. & Prather, K. L. J. Microbial engineering for aldehyde synthesis. Appl. Environ. Microbiol. 81, 1892–1901 (2015).
Google Scholar
Noor, E. et al. Pathway thermodynamics highlights kinetic obstacles in central metabolism. PLoS Comput. Biol. 10, e1003483 (2014).
Google Scholar
Mitsui, R., Omori, M., Kitazawa, H. & Tanaka, M. Formaldehyde-limited cultivation of a newly isolated methylotrophic bacterium, Methylobacterium sp. MF1: enzymatic analysis related to C1 metabolism. J. Biosci. Bioeng. 99, 18–22 (2005).
Google Scholar
Meyer, F. et al. Methanol-essential growth of Escherichia coli. Nat. Commun. 9, 1508 (2018).
Google Scholar
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).
Google Scholar
De Graef, M. R., Alexeeva, S., Snoep, J. L. & Teixeira De Mattos, M. J. The steady-state internal redox state (NADH/NAD) reflects the external redox state and is correlated with catabolic adaptation in Escherichia coli. J. Bacteriol. 181, 2351–2357 (1999).
Google Scholar
Berríos-Rivera, S. J., Bennett, G. N. & San, K. Y. The effect of increasing NADH availability on the redistribution of metabolic fluxes in Escherichia coli chemostat cultures. Metab. Eng. 4, 230–237 (2002).
San, K. Y. et al. Metabolic engineering through cofactor manipulation and its effects on metabolic flux redistribution in Escherichia coli. Metab. Eng. 4, 182–192 (2002).
Google Scholar
Dudley, Q. M., Anderson, K. C. & Jewett, M. C. Cell-free mixing of Escherichia coli crude extracts to prototype and rationally engineer high-titer mevalonate synthesis. ACS Synth. Biol. 5, 1578–1588 (2016).
Google Scholar
Rodriguez, G. M. & Atsumi, S. Toward aldehyde and alkane production by removing aldehyde reductase activity in Escherichia coli. Metab. Eng. 25, 227–237 (2014).
Google Scholar
Caballero, E., Baldomá, L., Ros, J., Boronat, A. & Aguilar, J. Identification of lactaldehyde dehydrogenase and glycolaldehyde dehydrogenase as functions of the same protein in Escherichia coli. J. Biol. Chem. 258, 7788–7792 (1983).
Google Scholar
Nattermann, M. et al. Engineering a highly efficient carboligase for synthetic one-carbon metabolism. ACS Catal. https://doi.org/10.1021/acscatal.1c01237 (2021).
Monk, J. M. et al. iML1515, a knowledgebase that computes Escherichia coli traits. Nat. Biotechnol. 35, 904–908 (2017).
Google Scholar
Mak, W. S. et al. Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat. Commun. 6, 10005 (2015).
Google Scholar
Yishai, O., Bouzon, M., Döring, 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).
Google Scholar
Schada von Borzyskowski, L. et al. Marine proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle. Nature 575, 500–504 (2019).
Google Scholar
Yamane, T. & Hirano, S. Semi-batch culture of microorganisms with constant feed of substrate: a mathematical simulation. J. Ferment. Technol. 55, 156–165 (1977).
Google Scholar
Rudroff, F. Whole-cell based synthetic enzyme cascades—light and shadow of a promising technology. Curr. Opin. Chem. Biol. 49, 84–90 (2019).
Google Scholar
Burg, J. M. et al. Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations. Curr. Opin. Chem. Eng. 14, 121–136 (2016).
Dinh, C. V. & Prather, K. L. Layered and multi-input autonomous dynamic control strategies for metabolic engineering. Curr. Opin. Biotechnol. 65, 156–162 (2020).
Google Scholar
Shen, X., Wang, J., Li, C., Yuan, Q. & Yan, Y. Dynamic gene expression engineering as a tool in pathway engineering. Curr. Opin. Biotechnol. 59, 122–129 (2019).
Google Scholar
Kim, S. & Gonzalez, R. Selective production of decanoic acid from iterative reversal of β-oxidation pathway. Biotechnol. Bioeng. 115, 1311–1320 (2018).
Google Scholar
Hernández Lozada, N. J. et al. Highly active C8-acyl-ACP thioesterase variant isolated by a synthetic selection strategy. ACS Synth. Biol. 7, 2205–2215 (2018).
Google Scholar
Yan, Q. & Pfleger, B. F. Revisiting metabolic engineering strategies for microbial synthesis of oleochemicals. Metab. Eng. 58, 35–46 (2020).
Google Scholar
Rohwerder, T., Rohde, M., Jehmlich, N. & Purswani, J. Actinobacterial degradation of 2-hydroxyisobutyric acid proceeds via acetone and Formyl-CoA by employing a thiamine-dependent lyase reaction. Front. Microbiol 11, 00691 (2020).
Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 42, D459–D471 (2014).
Google Scholar
Hannum, G. et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat. Protoc. 2, 727–738 (2019).
Sambrook, J., Fritsch, E. F., Maniatis, T. & Russell, D. W. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 2001).
Neidhardt, F. C., Bloch, P. L. & Smith, D. F. Culture medium for enterobacteria. J. Bacteriol. 119, 736–747 (1974).
Google Scholar
