Cell-free synthetic biology for in vitro prototype engineering

Cell-free transcription–translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells.

[1]  C. You,et al.  Annexation of a high-activity enzyme in a synthetic three-enzyme complex greatly decreases the degree of substrate channeling. , 2014, ACS synthetic biology.

[2]  Takuya Ueda,et al.  Cell-free translation reconstituted with purified components , 2001, Nature Biotechnology.

[3]  M. Chamberlin,et al.  New RNA Polymerase from Escherichia coli infected with Bacteriophage T7 , 1970, Nature.

[4]  Richard M. Murray,et al.  Synthetic circuit for exact adaptation and fold-change detection , 2014, Nucleic acids research.

[5]  P. Booth,et al.  In vitro synthesis of a Major Facilitator Transporter for specific active transport across Droplet Interface Bilayers , 2016, Scientific Reports.

[6]  R. Murray,et al.  Gene circuit performance characterization and resource usage in a cell-free "breadboard". , 2014, ACS synthetic biology.

[7]  Michele Forlin,et al.  Cell-Free Translation Is More Variable than Transcription. , 2017, ACS synthetic biology.

[8]  Guillaume Lambert,et al.  Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components , 2016, Cell.

[9]  R. Ellis,et al.  Macromolecular crowding: an important but neglected aspect of the intracellular environment. , 2001, Current opinion in structural biology.

[10]  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.

[11]  Zachary Z. Sun,et al.  Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems , 2014, bioRxiv.

[12]  Richard M. Murray,et al.  An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system , 2013, 52nd IEEE Conference on Decision and Control.

[13]  Aaron K. Sato,et al.  A simplified and robust protocol for immunoglobulin expression in E scherichia coli cell‐free protein synthesis systems , 2015, Biotechnology progress.

[14]  Michael C. Jewett,et al.  Establishing a high yielding streptomyces‐based cell‐free protein synthesis system , 2017, Biotechnology and bioengineering.

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

[16]  M. Tuite,et al.  Preparation and use of yeast cell-free translation lysate. , 1996, Methods in molecular biology.

[17]  Christopher A. Voigt,et al.  Genetic circuit design automation , 2016, Science.

[18]  J. Swartz,et al.  Efficient and scalable method for scaling up cell free protein synthesis in batch mode. , 2005, Biotechnology and bioengineering.

[19]  Paul S Freemont,et al.  Streptomyces venezuelae TX-TL - a next generation cell-free synthetic biology tool. , 2017, Biotechnology journal.

[20]  Paul S. Freemont,et al.  Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology , 2013, Nucleic acids research.

[21]  Henrike Niederholtmeyer,et al.  Rapid cell-free forward engineering of novel genetic ring oscillators , 2015, eLife.

[22]  P. Freemont,et al.  Development of a Bacillus subtilis cell-free transcription-translation system for prototyping regulatory elements. , 2016, Metabolic engineering.

[23]  Charles C. Richardson,et al.  Impact of macromolecular crowding on DNA replication , 2012, Nature Communications.

[24]  Michael Eisenstein,et al.  Living factories of the future , 2016, Nature.

[25]  Michael C Jewett,et al.  Synthetic in vitro circuits. , 2012, Current opinion in chemical biology.

[26]  Richard M. Murray,et al.  Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription–Translation (TX-TL) Systems , 2014, ACS synthetic biology.

[27]  Marcel Geertz,et al.  Massively parallel measurements of molecular interaction kinetics on a microfluidic platform , 2012, Proceedings of the National Academy of Sciences.

[28]  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.

[29]  S. Maerkl,et al.  GreA and GreB Enhance Expression of Escherichia coli RNA Polymerase Promoters in a Reconstituted Transcription-Translation System. , 2016, ACS synthetic biology.

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

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

[32]  Steven P Gygi,et al.  Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. , 2012, ACS synthetic biology.

[33]  Matthias Heinemann,et al.  Exploiting cell‐free systems: Implementation and debugging of a system of biotransformations , 2010, Biotechnology and bioengineering.

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

[35]  Roger G. Linington,et al.  Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters , 2014, Cell.

[36]  J. Swartz,et al.  Streamlining Escherichia Coli S30 Extract Preparation for Economical Cell‐Free Protein Synthesis , 2008, Biotechnology progress.

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

[38]  Richard M. Murray,et al.  Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology , 2013, Journal of visualized experiments : JoVE.

[39]  T. Ueda,et al.  The PURE system for the cell-free synthesis of membrane proteins , 2015, Nature Protocols.

[40]  George M Church,et al.  Towards synthesis of a minimal cell , 2006, Molecular systems biology.

[41]  Vincent Noireaux,et al.  Integration of biological parts toward the synthesis of a minimal cell. , 2014, Current opinion in chemical biology.

[42]  Henrike Niederholtmeyer,et al.  Real-time mRNA measurement during an in vitro transcription and translation reaction using binary probes. , 2013, ACS synthetic biology.

[43]  Vincent Noireaux,et al.  Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. , 2012, ACS synthetic biology.

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

[45]  Jill K Thompson,et al.  Coupled transcription — translation in extracts of Streptomyces lividans , 2004, Molecular and General Genetics MGG.

[46]  Kedar G. Patel,et al.  Simplifying and streamlining Escherichia coli‐based cell‐free protein synthesis , 2012, Biotechnology progress.

[47]  Takanori Kigawa,et al.  Preparation of Escherichia coli cell extract for highly productive cell-free protein expression , 2004, Journal of Structural and Functional Genomics.

[48]  F. Arnold,et al.  Optimizing non-natural protein function with directed evolution. , 2011, Current opinion in chemical biology.

[49]  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.

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

[51]  W. Martin,et al.  Hydrothermal vents and the origin of life , 2008, Nature Reviews Microbiology.

[52]  Henrike Niederholtmeyer,et al.  Implementation of cell-free biological networks at steady state , 2013, Proceedings of the National Academy of Sciences.

[53]  J. H. Matthaei,et al.  Characteristics and composition of RNA coding units. , 1962, Proceedings of the National Academy of Sciences of the United States of America.

[54]  David K. Karig,et al.  Expression optimization and synthetic gene networks in cell-free systems , 2011, Nucleic acids research.

[55]  Rui Gan,et al.  A combined cell-free transcription-translation system from Saccharomyces cerevisiae for rapid and robust protein synthe. , 2014, Biotechnology journal.

[56]  Vincent Noireaux,et al.  The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology. , 2016, ACS synthetic biology.

[57]  A. Goldberg,et al.  A soluble ATP-dependent proteolytic system responsible for the degradation of abnormal proteins in reticulocytes. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[58]  R. Bar-Ziv,et al.  Cell-free protein synthesis and assembly on a biochip. , 2012, Nature nanotechnology.

[59]  Paul S. Freemont,et al.  Prototyping of Bacillus megaterium genetic elements through automated cell-free characterization and Bayesian modelling , 2016, bioRxiv.

[60]  Oscar Ces,et al.  Vesicle-based artificial cells as chemical microreactors with spatially segregated reaction pathways , 2014, Nature Communications.

[61]  James J. Collins,et al.  Paper-Based Synthetic Gene Networks , 2014, Cell.

[62]  T. Kigawa,et al.  A highly efficient cell-free protein synthesis system from Escherichia coli. , 1996, European journal of biochemistry.

[63]  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.

[64]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[65]  J. H. Matthaei,et al.  Characteristics and stabilization of DNAase-sensitive protein synthesis in E. coli extracts. , 1961, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Michael C Jewett,et al.  Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry. , 2012, Current opinion in biotechnology.

[67]  T. Kieser.  Practical streptomyces genetics , 2000 .

[68]  G. Jones.  Macromolecular synthesis in Streptomyces antibioticus: in vitro systems for aminoacylation and translation from young and old cells , 1975, Journal of Bacteriology.

[69]  Damien Larivière,et al.  An inventory of the bacterial macromolecular components and their spatial organization. , 2011, FEMS microbiology reviews.

[70]  V. Dötsch,et al.  Preparative scale expression of membrane proteins in Escherichia coli-based continuous exchange cell-free systems , 2007, Nature Protocols.

[71]  George M. Church,et al.  Improved Cell-Free RNA and Protein Synthesis System , 2014, PloS one.

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

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

[74]  Paul Freemont,et al.  EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology. , 2018, Methods in molecular biology.

[75]  J. Swartz,et al.  Energy systems for ATP regeneration in cell-free protein synthesis reactions. , 2007, Methods in molecular biology.