Mini-review: In vitro Metabolic Engineering for Biomanufacturing of High-value Products

With the breakthroughs in biomolecular engineering and synthetic biology, many valuable biologically active compound and commodity chemicals have been successfully manufactured using cell-based approaches in the past decade. However, because of the high complexity of cell metabolism, the identification and optimization of rate-limiting metabolic pathways for improving the product yield is often difficult, which represents a significant and unavoidable barrier of traditional in vivo metabolic engineering. Recently, some in vitro engineering approaches were proposed as alternative strategies to solve this problem. In brief, by reconstituting a biosynthetic pathway in a cell-free environment with the supplement of cofactors and substrates, the performance of each biosynthetic pathway could be evaluated and optimized systematically. Several value-added products, including chemicals, nutraceuticals, and drug precursors, have been biosynthesized as proof-of-concept demonstrations of in vitro metabolic engineering. This mini-review summarizes the recent progresses on the emerging topic of in vitro metabolic engineering and comments on the potential application of cell-free technology to speed up the “design-build-test” cycles of biomanufacturing.

[1]  Christoph Hold,et al.  Forward design of a complex enzyme cascade reaction , 2016, Nature Communications.

[2]  T. Erb,et al.  A synthetic pathway for the fixation of carbon dioxide in vitro , 2016, Science.

[3]  Michael C Jewett,et al.  Cell-Free Mixing of Escherichia coli Crude Extracts to Prototype and Rationally Engineer High-Titer Mevalonate Synthesis. , 2016, ACS synthetic biology.

[4]  Jeffrey D. Varner,et al.  Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models , 2015 .

[5]  Michael C Jewett,et al.  An integrated cell-free metabolic platform for protein production and synthetic biology , 2008, Molecular systems biology.

[6]  Huimin Zhao,et al.  Engineering microbial factories for synthesis of value-added products , 2011, Journal of Industrial Microbiology & Biotechnology.

[7]  Kenji Okano,et al.  In vitro production of n-butanol from glucose. , 2013, Metabolic engineering.

[8]  James C. Liao,et al.  Stability of Ensemble Models Predicts Productivity of Enzymatic Systems , 2016, PLoS Comput. Biol..

[9]  Ahmet Ay,et al.  Mathematical modeling of gene expression: a guide for the perplexed biologist , 2011, Critical reviews in biochemistry and molecular biology.

[10]  A. Piruska,et al.  Enhanced transcription rates in membrane-free protocells formed by coacervation of cell lysate , 2013, Proceedings of the National Academy of Sciences.

[11]  M. Jewett,et al.  Cell-free synthetic biology: thinking outside the cell. , 2012, Metabolic engineering.

[12]  Vincent Noireaux,et al.  A cost-effective polyphosphate-based metabolism fuels an all E. coli cell-free expression system. , 2015, Metabolic engineering.

[13]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[14]  L. Scott,et al.  Pathway engineered enzymatic de novo purine nucleotide synthesis. , 2008, ACS chemical biology.

[15]  Dong-Myung Kim,et al.  Regeneration of adenosine triphosphate from glycolytic intermediates for cell-free protein synthesis. , 2001, Biotechnology and bioengineering.

[16]  R. Iniesta,et al.  Machine learning, statistical learning and the future of biological research in psychiatry , 2016, Psychological Medicine.

[17]  C Giersch Mathematical modelling of metabolism. , 2000, Current opinion in plant biology.

[18]  The phytoalexin camalexin mediates cytotoxicity towards aggressive prostate cancer cells via reactive oxygen species , 2013, Journal of Natural Medicines.

[19]  B. B. Mishra,et al.  Natural products: an evolving role in future drug discovery. , 2011, European journal of medicinal chemistry.

[20]  Fabio Mavelli,et al.  A Simple Protein Synthesis Model for the PURE System Operation , 2015, Bulletin of mathematical biology.

[21]  Michael C. Jewett,et al.  High-throughput preparation methods of crude extract for robust cell-free protein synthesis , 2015, Scientific Reports.

[22]  James C Liao,et al.  Ensemble modeling for strain development of L-lysine-producing Escherichia coli. , 2009, Metabolic engineering.

[23]  C. Wittmann,et al.  Bio-based production of chemicals, materials and fuels -Corynebacterium glutamicum as versatile cell factory. , 2012, Current opinion in biotechnology.

[24]  Y.‐H.P. Zhang Reviving the carbohydrate economy via multi-product lignocellulose biorefineries , 2008, Journal of Industrial Microbiology & Biotechnology.

[25]  Charles E. Wyman,et al.  BIOMASS ETHANOL: Technical Progress, Opportunities, and Commercial Challenges , 1999 .

[26]  John R. Anderson,et al.  MACHINE LEARNING An Artificial Intelligence Approach , 2009 .

[27]  James U Bowie,et al.  A synthetic biochemistry module for production of bio-based chemicals from glucose. , 2016, Nature chemical biology.

[28]  Michael Margaliot,et al.  Ribosome flow model with positive feedback , 2013, Journal of The Royal Society Interface.

[29]  Martin Fussenegger,et al.  Engineering synergy in biotechnology. , 2014, Nature chemical biology.

[30]  James C Liao,et al.  Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways. , 2014, Metabolic engineering.

[31]  A.P.F. Atman,et al.  Hybrid agent-based model for quantitative in-silico cell-free protein synthesis , 2016, Biosyst..

[32]  Andrew Buchanan,et al.  Coping with complexity: Machine learning optimization of cell‐free protein synthesis , 2011, Biotechnology and Bioengineering.

[33]  V. Hatzimanikatis,et al.  A model for protein translation: polysome self-organization leads to maximum protein synthesis rates. , 2007, Biophysical journal.

[34]  Timothy S. Ham,et al.  Production of the antimalarial drug precursor artemisinic acid in engineered yeast , 2006, Nature.

[35]  Joseph A. Rollin,et al.  High-yield hydrogen production from biomass by in vitro metabolic engineering: Mixed sugars coutilization and kinetic modeling , 2015, Proceedings of the National Academy of Sciences.

[36]  Y.‐H.P. Zhang,et al.  Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations: challenges and opportunities. , 2010, Biotechnology and bioengineering.

[37]  J. Liao,et al.  Ensemble Modeling for Aromatic Production in Escherichia coli , 2009, PloS one.

[38]  Cem Albayrak,et al.  Cell-free co-production of an orthogonal transfer RNA activates efficient site-specific non-natural amino acid incorporation , 2013, Nucleic acids research.

[39]  Vincent Noireaux,et al.  Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription-translation system. , 2014, Biochimie.

[40]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[41]  A. Burgard,et al.  Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. , 2011, Nature chemical biology.

[42]  J. Swartz,et al.  Energizing cell-free protein synthesis with glucose metabolism. , 2005, Biotechnology and bioengineering.

[43]  J. Liao,et al.  Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels , 2008, Nature.

[44]  Cheemeng Tan,et al.  Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems , 2014, Front. Bioeng. Biotechnol..

[45]  Ryan A McClure,et al.  In Vitro Reconstruction of Nonribosomal Peptide Biosynthesis Directly from DNA Using Cell-Free Protein Synthesis. , 2017, ACS synthetic biology.

[46]  J. Gershenzon,et al.  Constitutive plant toxins and their role in defense against herbivores and pathogens. , 2002, Current opinion in plant biology.

[47]  Marshall W. Nirenberg,et al.  The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides , 1961, Proceedings of the National Academy of Sciences.

[48]  Dong-Myung Kim,et al.  Prolonging cell-free protein synthesis with a novel ATP regeneration system. , 1999, Biotechnology and bioengineering.

[49]  Tiangang Liu,et al.  In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli , 2011, Proceedings of the National Academy of Sciences.

[50]  Vincent Noireaux,et al.  Coarse-grained dynamics of protein synthesis in a cell-free system. , 2011, Physical review letters.

[51]  Y. Jang,et al.  Metabolic engineering of Clostridium acetobutylicum M 5 for highly selective butanol production , 2009 .

[52]  Tiangang Liu,et al.  In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction in Escherichia coli , 2014, Biotechnology and bioengineering.

[53]  J. Swartz,et al.  An Economical Method for Cell‐Free Protein Synthesis using Glucose and Nucleoside Monophosphates , 2008, Biotechnology progress.

[54]  C. Khosla,et al.  Quantitative analysis and engineering of fatty acid biosynthesis in E. coli. , 2010, Metabolic engineering.

[55]  M. Jewett,et al.  Mimicking the Escherichia coli cytoplasmic environment activates long‐lived and efficient cell‐free protein synthesis , 2004, Biotechnology and bioengineering.

[56]  Bradley C. Bundy,et al.  Escherichia coli‐based cell‐free synthesis of virus‐like particles , 2008, Biotechnology and bioengineering.

[57]  Dong-Myung Kim,et al.  Prolonging Cell‐Free Protein Synthesis by Selective Reagent Additions , 2000, Biotechnology progress.

[58]  J. Liao,et al.  Ensemble modeling of metabolic networks. , 2008, Biophysical journal.

[59]  B. Halkier,et al.  Isolation and Reconstitution of Cytochrome P450ox and in Vitro Reconstitution of the Entire Biosynthetic Pathway of the Cyanogenic Glucoside Dhurrin from Sorghum , 1997, Plant physiology.

[60]  Matthew K. Theisen,et al.  Building carbon–carbon bonds using a biocatalytic methanol condensation cycle , 2014, Proceedings of the National Academy of Sciences.

[61]  R. Kwok Five hard truths for synthetic biology , 2010, Nature.

[62]  James J. Collins,et al.  Portable, On-Demand Biomolecular Manufacturing , 2016, Cell.

[63]  E. Sattely,et al.  Minimum set of cytochromes P450 for reconstituting the biosynthesis of camalexin, a major Arabidopsis antibiotic. , 2013, Angewandte Chemie.

[64]  R. Zimmer,et al.  Experiment and mathematical modeling of gene expression dynamics in a cell-free system. , 2012, Integrative biology : quantitative biosciences from nano to macro.

[65]  T. Wood,et al.  Hydrogen production by recombinant Escherichia coli strains , 2012, Microbial biotechnology.

[66]  V. Wendisch,et al.  Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for biotechnological production of organic acids and amino acids. , 2006, Current opinion in microbiology.

[67]  Jiong Hong,et al.  Fast identification of thermostable beta‐glucosidase mutants on cellobiose by a novel combinatorial selection/screening approach , 2009, Biotechnology and bioengineering.

[68]  P Sarnow,et al.  Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae , 1994, Molecular and cellular biology.

[69]  D. Chowdhury,et al.  Stochastic kinetics of ribosomes: single motor properties and collective behavior. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[70]  Yit-Heng Chooi,et al.  Metabolic engineering for the production of natural products. , 2011, Annual review of chemical and biomolecular engineering.

[71]  Y.-H. Percival Zhang,et al.  A sweet out-of-the-box solution to the hydrogen economy: is the sugar-powered car science fiction? , 2009 .

[72]  Tetsuya Yomo,et al.  Quantifying epistatic interactions among the components constituting the protein translation system , 2009, Molecular systems biology.

[73]  Xueyang Feng,et al.  OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism , 2016, PloS one.

[74]  Vincent Noireaux,et al.  Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system. , 2014, ACS synthetic biology.

[75]  Jian-Jiang Zhong,et al.  Bioreactor Engineering Research and Industrial Applications I: Cell Factories , 2016 .

[76]  Ashty S Karim,et al.  A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery. , 2016, Metabolic engineering.

[77]  C. Walsh,et al.  In Vitro Reconstitution of Metabolic Pathways: Insights into Nature’s Chemical Logic , 2015, Synlett.

[78]  P. Winters,et al.  Perspective on opportunities in industrial biotechnology in renewable chemicals , 2012, Biotechnology journal.

[79]  Ashty S. Karim,et al.  Cell‐free metabolic engineering: Biomanufacturing beyond the cell , 2015, Biotechnology journal.

[80]  Antonios Armaou,et al.  A Computational Procedure for Optimal Engineering Interventions Using Kinetic Models of Metabolism , 2006, Biotechnology progress.

[81]  C. J. Murray,et al.  Microscale to Manufacturing Scale-up of Cell-Free Cytokine Production—A New Approach for Shortening Protein Production Development Timelines , 2011, Biotechnology and bioengineering.

[82]  Y. Zhang,et al.  Production of biofuels and biochemicals by in vitro synthetic biosystems: Opportunities and challenges. , 2015, Biotechnology advances.