Legras, J. L. et al. Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication. Mol. Biol. Evol. 35, 1712–1727 (2018).
Google Scholar
Nielsen, J. & Keasling, J. D. Engineering cellular metabolism. Cell 164, 1185–1197 (2016).
Google Scholar
Ekas, H., Deaner, M. & Alper, H. S. Recent advancements in fungal-derived fuel and chemical production and commercialization. Curr. Opin. Biotechnol. 57, 1–9 (2019).
Google Scholar
Ostergaard, S., Olsson, L. & Nielsen, J. Metabolic engineering of Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 64, 34–50 (2000).
Google Scholar
Nevoigt, E. Progress in metabolic engineering of Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 72, 379–412 (2008).
Google Scholar
Hong, K. K. & Nielsen, J. Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries. Cell Mol. Life Sci. 69, 2671–2690 (2012).
Google Scholar
Nielsen, J. & Jewett, M. C. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res. 8, 122–131 (2008).
Google Scholar
Lian, J., Mishra, S. & Zhao, H. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metab. Eng. 50, 85–108 (2018).
Google Scholar
Schadeweg, V. & Boles, E. Increasing n-butanol production with Saccharomyces cerevisiae by optimizing acetyl-CoA synthesis, NADH levels and trans-2-enoyl-CoA reductase expression. Biotechnol. Biofuels 9, 257 (2016).
Google Scholar
Li, M., Schneider, K., Kristensen, M., Borodina, I. & Nielsen, J. Engineering yeast for high-level production of stilbenoid antioxidants. Sci. Rep. 6, 36827 (2016).
Google Scholar
Ji, R. Y. et al. Metabolic engineering of yeast for the production of 3-Hydroxypropionic acid. Front. Microbiol. 9, 2185 (2018).
Google Scholar
Paddon, C. J. & Keasling, J. D. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat. Rev. Microbiol. 12, 355–367 (2014).
Google Scholar
Galanie, S., Thodey, K., Trenchard, I. J., Interrante, M. F. & Smolke, C. D. Complete biosynthesis of opioids in yeast. Science 349, 1095–1100 (2015).
Google Scholar
Milne, N. et al. Metabolic engineering of Saccharomyces cerevisiae for the de novo production of psilocybin and related tryptamine derivatives. Metab. Eng. 60, 25–36 (2020).
Google Scholar
Pyne, M. E. et al. A yeast platform for high-level synthesis of tetrahydroisoquinoline alkaloids. Nat. Commun. 11, 3337 (2020).
Google Scholar
Srinivasan, P. & Smolke, C. D. Biosynthesis of medicinal tropane alkaloids in yeast. Nature 585, 614–619 (2020).
Google Scholar
Tyo, K. E., Alper, H. S. & Stephanopoulos, G. N. Expanding the metabolic engineering toolbox: more options to engineer cells. Trends Biotechnol. 25, 132–137 (2007).
Google Scholar
Wu, G. et al. Metabolic burden: cornerstones in synthetic biology and metabolic engineering applications. Trends Biotechnol. 34, 652–664 (2016).
Google Scholar
Nirenberg, M. & Matthaei, J. The dependence of cell-free protein synthesis in E. Coli upon naturally ocurring or synthetic polyribonucleotides. PNAS 47, 1588–1602 (1961).
Google Scholar
Iizuka, N., Najita, L., Franzusoff, A. & Sarnow, P. Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae. Mol. Cell. Biol. 14, 7322–7330 (1994).
Google Scholar
Gasior, E., Herrera, S. F., Sadnik, I., McLaughlin, C. S. & Moldave, K. The preparation and characterization of a cell-free system from saccharomyces cerevisiae that translates natural messenger ribonucleic acid. J. Biol. Chem. 254, 3965–3969 (1979).
Google Scholar
Buchner, E. Alkoholische gährung ohne hefezellen. Ber. der Dtsch. chemischen Ges. 30, 117–124 (1897).
Google Scholar
Kohler, R. Reception of eduard buchner’s discovery of cell-free fermentation. J. Hist. Biol. 5, 327–353 (1972).
Google Scholar
Silverman, A. D., Karim, A. S. & Jewett, M. C. Cell-free gene expression: an expanded repertoire of applications. Nat. Rev. Genet. 21, 151–170 (2020).
Google Scholar
Hodgman, C. E. & Jewett, M. C. Cell-free synthetic biology: thinking outside the cell. Metab. Eng. 14, 261–269 (2012).
Google Scholar
Hershewe, J., Kightlinger, W. & Jewett, M. C. Cell-free systems for accelerating glycoprotein expression and biomanufacturing. J. Ind. Microbiol. Biotechnol. 47, 977–991 (2020).
Google Scholar
Swartz, J. R. Expanding biological applications using cell-free metabolic engineering: an overview. Metab. Eng. 50, 156–172 (2018).
Google Scholar
Dudley, Q. M., Karim, A. S. & Jewett, M. C. Cell-free metabolic engineering: biomanufacturing beyond the cell. Biotechnol. J. 10, 69–82 (2015).
Google Scholar
Lim, H. J. & Kim, D. M. Cell-free metabolic engineering: recent developments and future prospects. Methods Protoc. https://doi.org/10.3390/mps2020033 (2019).
Bogart, J. W. et al. Cell-free exploration of the natural product chemical space. Chembiochem. https://doi.org/10.1002/cbic.202000452 (2020).
Rasor, B. J. et al. Toward sustainable, cell-free biomanufacturing. Current Opin Biotechnol. 69, 136-144 (2021).
Bowie, J. U. et al. Synthetic biochemistry: the bio-inspired cell-free approach to commodity chemical production. Trends Biotechnol. https://doi.org/10.1016/j.tibtech.2019.12.024 (2020).
Karim, A. S. et al. In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design. Nat. Chem. Biol. 16, 912–919 (2020).
Google Scholar
Dudley, Q. M., Nash, C. J. & Jewett, M. C. Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates. Synth. Biol. 4, ysz003 (2019).
Google Scholar
Kay, J. E. & Jewett, M. C. A cell-free system for production of 2,3-butanediol is robust to growth-toxic compounds. Metab. Eng. Commun. https://doi.org/10.1016/j.mec.2019.e00114 (2020).
Kay, J. E. & Jewett, M. C. Lysate of engineered Escherichia coli supports high-level conversion of glucose to 2,3-butanediol. Metab. Eng. 32, 133–142 (2015).
Google Scholar
Sherkhanov, S. et al. Isobutanol production freed from biological limits using synthetic biochemistry. Nat. Commun. 11, 4292 (2020).
Google Scholar
Kelwick, R. et al. Cell-free prototyping strategies for enhancing the sustainable production of polyhydroxyalkanoates bioplastics. Synthetic Biol. https://doi.org/10.1093/synbio/ysy016 (2018).
Grubbe, W. S., Rasor, B. J., Krüger, A., Jewett, M. C. & Karim, A. S. Cell-free biosynthesis of styrene at high titers. Metab. Eng. 61, 89–95 (2020).
Google Scholar
Korman, T. P., Opgenorth, P. H. & Bowie, J. U. A synthetic biochemistry platform for cell free production of monoterpenes from glucose. Nat. Commun. 8, 15526 (2017).
Google Scholar
Valliere, M. A. et al. A cell-free platform for the prenylation of natural products and application to cannabinoid production. Nat. Commun. 10, 565 (2019).
Google Scholar
Karim, A. S., Rasor, B. J. & Jewett, M. C. Enhancing control of cell-free metabolism through pH modulation. Synthetic Biol. https://doi.org/10.1093/synbio/ysz027 (2019).
Rollin, J. A., Tam, T. K. & Zhang, Y. H. P. New biotechnology paradigm: cell-free biosystems for biomanufacturing. Green Chem. https://doi.org/10.1039/c3gc40625c (2013).
Li, X. et al. Overproduction of fatty acids in engineered Saccharomyces cerevisiae. Biotechnol. Bioeng. 111, 1841–1852 (2014).
Google Scholar
Cameron, D. C., Altaras, N. E., Hoffman, M. L. & Shaw, A. J. Metabolic engineering of propanediol pathways. Biotechnol. Prog. 14, 116–125 (1998).
Google Scholar
Khattak, W. A. et al. Yeast cell-free enzyme system for bio-ethanol production at elevated temperatures. Process Biochem. 49, 357–364 (2014).
Google Scholar
Karim, A. S. & Jewett, M. C. A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery. Metab. Eng. 36, 116–126 (2016).
Google Scholar
Claassens, N. J., Burgener, S., Vogeli, B., Erb, T. J. & Bar-Even, A. A critical comparison of cellular and cell-free bioproduction systems. Curr. Opin. Biotechnol. 60, 221–229 (2019).
Google Scholar
Kim, S. J., Kim, J. W., Lee, Y. G., Park, Y. C. & Seo, J. H. Metabolic engineering of Saccharomyces cerevisiae for 2,3-butanediol production. Appl Microbiol. Biotechnol. 101, 2241–2250 (2017).
Google Scholar
Hakizimana, O., Matabaro, E. & Lee, B. H. The current strategies and parameters for the enhanced microbial production of 2,3-butanediol. Biotechnol. Rep. 25, e00397 (2020).
Google Scholar
Kim, S. & Hahn, J. S. Efficient production of 2,3-butanediol in Saccharomyces cerevisiae by eliminating ethanol and glycerol production and redox rebalancing. Metab. Eng. 31, 94–101 (2015).
Google Scholar
Deaner, M., Holzman, A. & Alper, H. S. Modular Ligation extension of guide RNA Operons (LEGO) for multiplexed dCas9 regulation of metabolic pathways in saccharomyces cerevisiae. Biotechnol J. https://doi.org/10.1002/biot.201700582 (2018).
Zhang, L. et al. An artificial synthetic pathway for acetoin, 2,3-butanediol, and 2-butanol production from ethanol using cell free multi-enzyme catalysis. Green. Chem. 20, 230–242 (2018).
Google Scholar
Choudhury, A., Hodgman, C. E., Anderson, M. J. & Jewett, M. C. Evaluating fermentation effects on cell growth and crude extract metabolic activity for improved yeast cell-free protein synthesis. Biochem. Eng. J. 91, 140–148 (2014).
Google Scholar
Hodgman, C. E. & Jewett, M. C. Optimized extract preparation methods and reaction conditions for improved yeast cell-free protein synthesis. Biotechnol. Bioeng. 110, 2643–2654 (2013).
Google Scholar
Anderson, M. J., Stark, J. C., Hodgman, C. E. & Jewett, M. C. Energizing eukaryotic cell-free protein synthesis with glucose metabolism. FEBS Lett. 589, 1723–1727 (2015).
Google Scholar
Contreras-Llano, L. E. et al. Holistic engineering of cell-free systems through proteome-reprogramming synthetic circuits. Nat. Commun. 11, 3138 (2020).
Google Scholar
Schoborg, J. A., Clark, L. G., Choudhury, A., Hodgman, C. E. & Jewett, M. C. Yeast knockout library allows for efficient testing of genomic mutations for cell-free protein synthesis. Synth. Syst. Biotechnol. 1, 2–6 (2016).
Google Scholar
Cole, S. D., Miklos, A. E., Chiao, A. C., Sun, Z. Z. & Lux, M. W. Methodologies for preparation of prokaryotic extracts for cell-free expression systems. Synth. Syst. Biotechnol. 5, 252–267 (2020).
Google Scholar
Dopp, J. L. & Reuel, N. F. Simple, functional, inexpensive cell extract for in vitro prototyping of proteins with disulfide bonds. Biochem. Eng. J. https://doi.org/10.1016/j.bej.2020.107790 (2020).
Martin, R. W. et al. Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids. Nat. Commun. 9, 1203 (2018).
Google Scholar
Adachi, J. et al. Cell-free protein synthesis using S30 extracts from Escherichia coli RFzero strains for efficient incorporation of non-natural amino acids into proteins. Int. J. Mol. Sci. https://doi.org/10.3390/ijms20030492 (2019).
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
Garcia, D. C. et al. A lysate proteome engineering strategy for enhancing cell-free metabolite production. Metab. Eng. Commun. 12, e00162 (2021).
Google Scholar
Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).
Google Scholar
Kwon, Y. C. & Jewett, M. C. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci. Rep. 5, 8663 (2015).
Google Scholar
Eriksson, P., Andre, L., Ansell, R., Blomberg, A. & Adler, L. Cloning and characterization of GPD2, a second gene encoding sn-glycerol 3-phosphate dehydrogenase (NAD +) in Saccharomyces cerevisiae, and its comparison with GPD1. Mol. Microbiol. 17, 95–107 (1995).
Google Scholar
Ng, C. Y., Jung, M. Y., Lee, J. & Oh, M. K. Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering. Microb Cell Fact https://doi.org/10.1186/1475-2859-11-68 (2012).
Hubmann, G., Guillouet, S. & Nevoigt, E. Gpd1 and Gpd2 fine-tuning for sustainable reduction of glycerol formation in Saccharomyces cerevisiae. Appl Environ. Microbiol. 77, 5857–5867 (2011).
Google Scholar
Vemuri, G. N., Eiteman, M. A., McEwen, J. E., Olsson, L. & Nielsen, J. Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae. PNAS 104, 2402–2407 (2007).
Google Scholar
Steiger, M. G., Blumhoff, M. L., Mattanovich, D. & Sauer, M. Biochemistry of microbial itaconic acid production. Front. Microbiol. 4, 23 (2013).
Google Scholar
Blazeck, J. et al. Metabolic engineering of Saccharomyces cerevisiae for itaconic acid production. Appl Microbiol. Biotechnol. 98, 8155–8164 (2014).
Google Scholar
Tan, H. W., Abdul Aziz, A. R. & Aroua, M. K. Glycerol production and its applications as a raw material: a review. Renew. Sustain. Energy Rev. 27, 118–127 (2013).
Google Scholar
Deaner, M. & Alper, H. S. Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae. Metab. Eng. 40, 14–22 (2017).
Google Scholar
Gregorio, N. E., Levine, M. Z. & Oza, J. P. A user’s Guide to cell-free protein synthesis. Methods Protocols https://doi.org/10.3390/mps2010024 (2019).
Liu, Z., Dong, H., Cui, Y., Cong, L. & Zhang, D. Application of different types of CRISPR/Cas-based systems in bacteria. Micro. Cell Fact. 19, 172 (2020).
Google Scholar
Raschmanova, H., Weninger, A., Glieder, A., Kovar, K. & Vogl, T. Implementing CRISPR-Cas technologies in conventional and non-conventional yeasts: current state and future prospects. Biotechnol. Adv. 36, 641–665 (2018).
Google Scholar
Yim, S. S. et al. Multiplex transcriptional characterizations across diverse bacterial species using cell-free systems. Mol. Syst. Biol. 15, e8875 (2019).
Google Scholar
Dudley, Q. M., Karim, A. S., Nash, C. J. & Jewett, M. C. In vitro prototyping of limonene biosynthesis using cell-free protein synthesis. Metab. Eng. 61, 251–260 (2020).
Google Scholar
Li, J., Zhang, L. & Liu, W. Cell-free synthetic biology for in vitro biosynthesis of pharmaceutical natural products. Synth. Syst. Biotechnol. 3, 83–89 (2018).
Google Scholar
Kelwick, R. J. R., Webb, A. J. & Freemont, P. S. Biological materials: the next frontier for cell-free synthetic biology. Front. Bioeng. Biotechnol. 8, 399 (2020).
Google Scholar
Bundy, B. C. et al. Cell-free biomanufacturing. Curr. Opin. Chem. Eng. 22, 177–183 (2018).
Google Scholar
Ma, J., Gu, Y., Marsafari, M. & Xu, P. Synthetic biology, systems biology, and metabolic engineering of Yarrowia lipolytica toward a sustainable biorefinery platform. J. Ind. Microbiol. Biotechnol. 47, 845–862 (2020).
Google Scholar
Aw, R. & Polizzi, K. M. Biosensor-assisted engineering of a high-yield Pichia pastoris cell-free protein synthesis platform. Biotechnol. Bioeng. 116, 656–666 (2019).
Google Scholar
Zhang, L., Liu, W. Q. & Li, J. Establishing a Eukaryotic Pichia pastoris cell-free protein synthesis system. Front. Bioeng. Biotechnol. 8, 536 (2020).
Google Scholar
Moore, S. J., Lai, H. E., Needham, H., Polizzi, K. M. & Freemont, P. S. Streptomyces venezuelae TX-TL – a next generation cell-free synthetic biology tool. Biotechnol. J. https://doi.org/10.1002/biot.201600678 (2017).
Zhuang, L. et al. Total in vitro biosynthesis of the nonribosomal macrolactone peptide valinomycin. Metab. Eng. 60, 37–44 (2020).
Google Scholar
Moore, S. J. et al. A streptomyces venezuelae cell-free toolkit for synthetic biology. ACS Synth. Biol. 10, 402–411 (2021).
Google Scholar
Li, J., Wang, H., Kwon, Y. C. & Jewett, M. C. Establishing a high yielding streptomyces-based cell-free protein synthesis system. Biotechnol. Bioeng. 114, 1343–1353 (2017).
Google Scholar
Xu, H., Liu, W. Q. & Li, J. Translation related factors improve the productivity of a streptomyces-based cell-free protein synthesis system. ACS Synth. Biol. 9, 1221–1224 (2020).
Google Scholar
Ye, J. et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinforma. 13, 134 (2012).
Google Scholar

