1932

Abstract

The cell-free molecular synthesis of biochemical systems is a rapidly growing field of research. Advances in the Human Genome Project, DNA synthesis, and other technologies have allowed the in vitro construction of biochemical systems, termed cell-free biology, to emerge as an exciting domain of bioengineering. Cell-free biology ranges from the molecular to the cell-population scales, using an ever-expanding variety of experimental platforms and toolboxes. In this review, we discuss the ongoing efforts undertaken in the three major classes of cell-free biology methodologies, namely protein-based, nucleic acids–based, and cell-free transcription–translation systems, and provide our perspectives on the current challenges as well as the major goals in each of the subfields.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-bioeng-092019-111110
2020-06-04
2024-12-05
Loading full text...

Full text loading...

/deliver/fulltext/bioeng/22/1/annurev-bioeng-092019-111110.html?itemId=/content/journals/10.1146/annurev-bioeng-092019-111110&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Schwille P. 2011. Bottom-up synthetic biology: engineering in a tinkerer's world. Science 333:60471252–54
    [Google Scholar]
  2. 2. 
    Jia H, Schwille P. 2019. Bottom-up synthetic biology: reconstitution in space and time. Curr. Opin. Biotechnol. 6:60179–87
    [Google Scholar]
  3. 3. 
    Seelig G, Soloveichik D, Zhang DY, Winfree E 2006. Enzyme-free nucleic acid logic circuits. Science 314:58051585–88
    [Google Scholar]
  4. 4. 
    Qian L, Winfree E. 2011. Scaling up digital circuit computation with DNA strand displacement cascades. Science 332:60341196–201
    [Google Scholar]
  5. 5. 
    Franco E, Friedrichs E, Kim J, Jungmann R, Murray R et al. 2011. Timing molecular motion and production with a synthetic transcriptional clock. PNAS 108:40E784–93
    [Google Scholar]
  6. 6. 
    Green LN, Subramanian HKK, Mardanlou V, Kim J, Hariadi RF, Franco E 2019. Autonomous dynamic control of DNA nanostructure self-assembly. Nat. Chem. 11:6510–20
    [Google Scholar]
  7. 7. 
    Smith MT, Wilding KM, Hunt JM, Bennett AM, Bundy BC 2014. The emerging age of cell-free synthetic biology. FEBS Lett 588:172755–61
    [Google Scholar]
  8. 8. 
    Perez JG, Stark JC, Jewett MC 2016. Cell-free synthetic biology: engineering beyond the cell. Cold Spring Harb. Perspect. Biol. 2:2a023853
    [Google Scholar]
  9. 9. 
    Garenne D, Noireaux V. 2019. Cell-free transcription–translation: engineering biology from the nanometer to the millimeter scale. Curr. Opin. Biotechnol. 58:19–27
    [Google Scholar]
  10. 10. 
    Solé RV. 2009. Evolution and self-assembly of protocells. Int. J. Biochem. Cell Biol. 41:2274–84
    [Google Scholar]
  11. 11. 
    Noireaux V, Maeda YT, Libchaber A 2011. Development of an artificial cell, from self-organization to computation and self-reproduction. PNAS 108:93473–80
    [Google Scholar]
  12. 12. 
    Ding Y, Wu F, Tan C 2014. Synthetic biology: a bridge between artificial and natural cells. Life 4:41092–116
    [Google Scholar]
  13. 13. 
    Tayar AM, Daube SS, Bar-Ziv RH 2017. Progress in programming spatiotemporal patterns and machine-assembly in cell-free protein expression systems. Curr. Opin. Chem. Biol. 40:37–46
    [Google Scholar]
  14. 14. 
    Liu AP, Fletcher DA. 2009. Biology under construction: in vitro reconstitution of cellular function. Nat. Rev. Mol. Cell Biol. 10:644–50
    [Google Scholar]
  15. 15. 
    Bashirzadeh Y, Liu AP. 2019. Encapsulation of the cytoskeleton: towards mimicking the mechanics of a cell. Soft Matter 15:8425–36
    [Google Scholar]
  16. 16. 
    Dumont S, Prakash M. 2014. Emergent mechanics of biological structures. Mol. Biol. Cell 25:223461–65
    [Google Scholar]
  17. 17. 
    Miyata H, Hotani H. 1992. Morphological changes in liposomes caused by polymerization of encapsulated actin and spontaneous formation of actin bundles. PNAS 89:2311547–51
    [Google Scholar]
  18. 18. 
    Loisel TP, Boujemaa R, Pantaloni D, Cartier MF 1999. Reconstitution of actin-based motility of Listeria and Shigella using pure proteins. Nature 401:6753613–16
    [Google Scholar]
  19. 19. 
    Liu AP, Fletcher DA. 2006. Actin polymerization serves as a membrane domain switch in model lipid bilayers. Biophys. J. 91:114064–70
    [Google Scholar]
  20. 20. 
    Liu AP, Richmond DL, Maibaum L, Pronk S, Geissler PL, Fletcher DA 2008. Membrane-induced bundling of actin filaments. Nat. Phys. 4:789–93
    [Google Scholar]
  21. 21. 
    Simon C, Kusters R, Caorsi V, Allard A, Abou-Ghali M et al. 2019. Actin dynamics drive cell-like membrane deformation. Nat. Phys. 15:602–9
    [Google Scholar]
  22. 22. 
    Sonal Ganzinger KA, Vogel SK, Mücksch J, Blumhardt P, Schwille P 2019. Myosin-II activity generates a dynamic steady state with continuous actin turnover in a minimal actin cortex. J. Cell Sci. 132:jcs219899
    [Google Scholar]
  23. 23. 
    Murrell MP, Gardel ML. 2012. F-actin buckling coordinates contractility and severing in a biomimetic actomyosin cortex. PNAS 109:5120820–25
    [Google Scholar]
  24. 24. 
    Köster DV, Husain K, Iljazi E, Bhat A, Bieling P et al. 2016. Actomyosin dynamics drive local membrane component organization in an in vitro active composite layer. PNAS 113:12E1646–54
    [Google Scholar]
  25. 25. 
    Dürre K, Keber FC, Bleicher P, Brauns F, Cyron CJ et al. 2018. Capping protein-controlled actin polymerization shapes lipid membranes. Nat. Commun. 9:1630
    [Google Scholar]
  26. 26. 
    Loiseau E, Schneider JAM, Keber FC, Pelzl C, Massiera G et al. 2016. Shape remodeling and blebbing of active cytoskeletal vesicles. Sci. Adv. 2:4e1500465
    [Google Scholar]
  27. 27. 
    Guevorkian K, Manzi J, Pontani LL, Brochard-Wyart F, Sykes C 2015. Mechanics of biomimetic liposomes encapsulating an actin shell. Biophys. J. 109:122471–79
    [Google Scholar]
  28. 28. 
    Miyazaki M, Chiba M, Eguchi H, Ohki T, Ishiwata S 2015. Cell-sized spherical confinement induces the spontaneous formation of contractile actomyosin rings in vitro. Nat. Cell Biol. 17:480–89
    [Google Scholar]
  29. 29. 
    Tsai FC, Stuhrmann B, Koenderink GH 2011. Encapsulation of active cytoskeletal protein networks in cell-sized liposomes. Langmuir 27:1610061–71
    [Google Scholar]
  30. 30. 
    Carvalho K, Tsai F-C, Lees E, Voituriez R, Koenderink GH, Sykes C 2013. Cell-sized liposomes reveal how actomyosin cortical tension drives shape change. PNAS 110:4116456–61
    [Google Scholar]
  31. 31. 
    Abu Shah E, Keren K 2014. Symmetry breaking in reconstituted actin cortices. eLife 3:e01433
    [Google Scholar]
  32. 32. 
    Tan TH, Malik-Garbi M, Abu-Shah E, Li J, Sharma A et al. 2018. Self-organized stress patterns drive state transitions in actin cortices. Sci. Adv. 4:6eaar2847
    [Google Scholar]
  33. 33. 
    Vogel SK, Woelfer C, Ramirez DA, Flassig RJ, Sundmacher K, Schwille P 2019. Emergence of directional actomyosin flows from active matter vibrations. bioRxiv 394700. https://doi.org/10.1101/394700
    [Crossref]
  34. 34. 
    Weiss M, Frohnmayer JP, Benk LT, Haller B, Janiesch J-W et al. 2018. Sequential bottom-up assembly of mechanically stabilized synthetic cells by microfluidics. Nat. Mater. 17:89–96
    [Google Scholar]
  35. 35. 
    Nédélec FJ, Surrey T, Maggs AC, Leibler S 1997. Self-organization of microtubules and motors. Nature 389:305–8
    [Google Scholar]
  36. 36. 
    Keber FC, Loiseau E, Sanchez T, DeCamp SJ, Giomi L et al. 2014. Topology and dynamics of active nematic vesicles. Science 345:62011135–39
    [Google Scholar]
  37. 37. 
    Kinoshita K, Arnal I, Desai A, Drechsel DN, Hyman AA 2001. Reconstitution of physiological microtubule dynamics using purified components. Science 294:55451340–43
    [Google Scholar]
  38. 38. 
    Roostalu J, Rickman J, Thomas C, Nédélec F, Surrey T 2018. Determinants of polar versus nematic organization in networks of dynamic microtubules and mitotic motors. Cell 175:3796–808
    [Google Scholar]
  39. 39. 
    Volkov VA, Huis In ‘t Veld PJ, Dogterom M, Musacchio A 2018. Mutivalency of NDC80 in the outer kinetochore is essential to track shortening microtubules and generate forces. eLife 7:e36764
    [Google Scholar]
  40. 40. 
    Huis In ‘t Veld PJ, Volkov VA, Stender ID, Musacchio A, Dogterom M 2019. Molecular determinants of the Ska-Ndc80 interaction and their influence on microtubule tracking and force-coupling. eLife 8:e49539
    [Google Scholar]
  41. 41. 
    Good MC, Vahey MD, Skandarajah A, Fletcher DA, Heald R 2013. Cytoplasmic volume modulates spindle size during embryogenesis. Science 342:6160856–60
    [Google Scholar]
  42. 42. 
    Hazel J, Krutkramelis K, Mooney P, Tomschik M, Gerow K et al. 2013. Changes in cytoplasmic volume are sufficient to drive spindle scaling. Science 342:6160853–56
    [Google Scholar]
  43. 43. 
    Suzuki K, Miyazaki M, Takagi J, Itabashi T, Ishiwata S 2017. Spatial confinement of active microtubule networks induces large-scale rotational cytoplasmic flow. PNAS 114:112922–27
    [Google Scholar]
  44. 44. 
    López MP, Huber F, Grigoriev I, Steinmetz MO, Akhmanova A et al. 2014. Actin–microtubule coordination at growing microtubule ends. Nat. Commun. 5:4778
    [Google Scholar]
  45. 45. 
    Garner EC, Campbell CS, Mullins RD 2004. Dynamic instability in a DNA-segregating prokaryotic actin homolog. Science 306:56981021–25
    [Google Scholar]
  46. 46. 
    Hwang LC, Vecchiarelli AG, Han YW, Mizuuchi M, Harada Y et al. 2013. ParA-mediated plasmid partition driven by protein pattern self-organization. EMBO J 32:91238–49
    [Google Scholar]
  47. 47. 
    Hussain S, Wivagg CN, Szwedziak P, Wong F, Schaefer K et al. 2018. MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis. eLife 7:e32471
    [Google Scholar]
  48. 48. 
    Osawa M, Anderson DE, Erickson HP 2008. Reconstitution of contractile FtsZ rings in liposomes. Science 320:5877792–94
    [Google Scholar]
  49. 49. 
    Jiménez M, Martos A, Vicente M, Rivas G 2011. Reconstitution and organization of Escherichia coli proto-ring elements (FtsZ and FtsA) inside giant unilamellar vesicles obtained from bacterial inner membranes. J. Biol. Chem. 286:1311236–41
    [Google Scholar]
  50. 50. 
    Loose M, Mitchison TJ. 2014. The bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns. Nat. Cell Biol. 16:38–46
    [Google Scholar]
  51. 51. 
    Ramirez-Diaz DA, García-Soriano DA, Raso A, Mücksch J, Feingold M et al. 2018. Treadmilling analysis reveals new insights into dynamic FtsZ ring architecture. PLOS Biol 16:5e2004845
    [Google Scholar]
  52. 52. 
    Mizuuchi K, Vecchiarelli AG. 2018. Mechanistic insights of the Min oscillator via cell-free reconstitution and imaging. Phys. Biol. 15:3031001
    [Google Scholar]
  53. 53. 
    Loose M, Fischer-Friedrich E, Ries J, Kruse K, Schwille P 2008. Spatial regulators for bacterial cell division self-organize into surface waves in vitro. Science 320:5877789–92
    [Google Scholar]
  54. 54. 
    Vecchiarelli AG, Li M, Mizuuchi M, Hwang LC, Seol Y et al. 2016. Membrane-bound MinDE complex acts as a toggle switch that drives Min oscillation coupled to cytoplasmic depletion of MinD. PNAS 113:11E1479–88
    [Google Scholar]
  55. 55. 
    Zieske K, Schwille P. 2014. Reconstitution of self-organizing protein gradients as spatial cues in cell-free systems. eLife 3:e04949
    [Google Scholar]
  56. 56. 
    Caspi Y, Dekker C. 2016. Mapping out Min protein patterns in fully confined fluidic chambers. eLife 5:e19271
    [Google Scholar]
  57. 57. 
    Litschel T, Ramm B, Maas R, Heymann M, Schwille P 2018. Beating vesicles: encapsulated protein oscillations cause dynamic membrane deformations. Angew. Chem. 57:5016286–90
    [Google Scholar]
  58. 58. 
    Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y et al. 2005. Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 308:5720414–15
    [Google Scholar]
  59. 59. 
    Leypunskiy E, Lin J, Yoo H, Lee U, Dinner AR, Rust MJ 2017. The cyanobacterial circadian clock follows midday in vivo and in vitro. eLife 6:e23539
    [Google Scholar]
  60. 60. 
    Guan Y, Li Z, Wang S, Barnes PM, Liu X et al. 2018. A robust and tunable mitotic oscillator in artificial cells. eLife 7:e33549
    [Google Scholar]
  61. 61. 
    McMahon HT, Gallop JL. 2005. Membrane curvature and mechanisms of dynamic cell membrane remodelling. Nature 438:7068590–96
    [Google Scholar]
  62. 62. 
    Pucadyil TJ, Schmid SL. 2008. Real-time visualization of dynamin-catalyzed membrane fission and vesicle release. Cell 135:1263–75
    [Google Scholar]
  63. 63. 
    Saleem M, Morlot S, Hohendahl A, Manzi J, Lenz M, Roux A 2015. A balance between membrane elasticity and polymerization energy sets the shape of spherical clathrin coats. Nat. Commun. 6:6249
    [Google Scholar]
  64. 64. 
    Wollert T, Wunder C, Lippincott-Schwartz J, Hurley JH 2009. Membrane scission by the ESCRT-III complex. Nature 458:7235172–77
    [Google Scholar]
  65. 65. 
    Chiaruttini N, Redondo-Morata L, Colom A, Humbert F, Lenz M et al. 2015. Relaxation of loaded ESCRT-III spiral springs drives membrane deformation. Cell 163:4866–79
    [Google Scholar]
  66. 66. 
    Schöneberg J, Pavlin MR, Yan S, Righini M, Lee IH et al. 2018. ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science 362:64211423–28
    [Google Scholar]
  67. 67. 
    Exterkate M, Caforio A, Stuart MCA, Driessen AJM 2018. Growing membranes in vitro by continuous phospholipid biosynthesis from free fatty acids. ACS Synth. Biol. 7:1153–65
    [Google Scholar]
  68. 68. 
    Bhattacharya A, Brea RJ, Niederholtmeyer H, Devaraj NK 2019. A minimal biochemical route towards de novo formation of synthetic phospholipid membranes. Nat. Commun. 10:300
    [Google Scholar]
  69. 69. 
    Shin JS, Pierce NA. 2004. A synthetic DNA walker for molecular transport. J. Am. Chem. Soc. 126:3510834–35
    [Google Scholar]
  70. 70. 
    Omabegho T, Sha R, Seeman NC 2009. A bipedal DNA Brownian motor with coordinated legs. Science 324:592367–71
    [Google Scholar]
  71. 71. 
    Venkataraman S, Dirks RM, Rothemund PWK, Winfree E, Pierce NA 2007. An autonomous polymerization motor powered by DNA hybridization. Nat. Nanotechnol. 2:490–94
    [Google Scholar]
  72. 72. 
    Zhang Y, McMullen A, Pontani LL, He X, Sha R et al. 2017. Sequential self-assembly of DNA functionalized droplets. Nat. Commun. 8:21
    [Google Scholar]
  73. 73. 
    Parolini L, Mognetti BM, Kotar J, Eiser E, Cicuta P, Di Michele L 2015. Volume and porosity thermal regulation in lipid mesophases by coupling mobile ligands to soft membranes. Nat. Commun. 6:5948
    [Google Scholar]
  74. 74. 
    Kurokawa C, Fujiwara K, Morita M, Kawamata I, Kawagishi Y et al. 2017. DNA cytoskeleton for stabilizing artificial cells. PNAS 114:287228–33
    [Google Scholar]
  75. 75. 
    Joesaar A, Yang S, Bögels B, van der Linden A, Pieters P et al. 2019. DNA-based communication in populations of synthetic protocells. Nat. Nanotechnol. 14:369–78
    [Google Scholar]
  76. 76. 
    Rothemund PWK. 2006. Folding DNA to create nanoscale shapes and patterns. Nature 440:7082297–302
    [Google Scholar]
  77. 77. 
    Douglas SM, Dietz H, Liedl T, Hogberg B, Graf F, Shih WM 2009. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459:414–18
    [Google Scholar]
  78. 78. 
    Dietz H, Douglas SM, Shih WM 2009. Folding DNA into twisted and curved nanoscale shapes. Science 325:59415–30
    [Google Scholar]
  79. 79. 
    Woo S, Rothemund PWK. 2011. Programmable molecular recognition based on the geometry of DNA nanostructures. Nature Chem 3:620–27
    [Google Scholar]
  80. 80. 
    Gerling T, Wagenbauer KF, Neuner AM, Dietz H 2015. Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components. Science 347:62291446–52
    [Google Scholar]
  81. 81. 
    Daljit Singh JK, Luu MT, Abbas A, Wickham SFJ 2018. Switchable DNA-origami nanostructures that respond to their environment and their applications. Biophys. Rev. 10:51283–93
    [Google Scholar]
  82. 82. 
    Wei B, Dai M, Yin P 2012. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485:623–26
    [Google Scholar]
  83. 83. 
    Ke Y, Ong LL, Shih WM, Yin P 2012. Three-dimensional structures self-assembled from DNA bricks. Science 338:61111177–83
    [Google Scholar]
  84. 84. 
    Langecker M, Arnaut V, Martin TG, List J, Renner S et al. 2012. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338:6109932–36
    [Google Scholar]
  85. 85. 
    Göpfrich K, Li CY, Ricci M, Bhamidimarri SP, Yoo J et al. 2016. Large-conductance transmembrane porin made from DNA origami. ACS Nano 10:98207–14
    [Google Scholar]
  86. 86. 
    Yang Y, Wang J, Shigematsu H, Xu W, Shih WM et al. 2016. Self-assembly of size-controlled liposomes on DNA nanotemplates. Nat. Chem. 8:476–83
    [Google Scholar]
  87. 87. 
    Zhang Z, Yang Y, Pincet F, Llaguno MC, Lin C 2017. Placing and shaping liposomes with reconfigurable DNA nanocages. Nat. Chem. 9:653–59
    [Google Scholar]
  88. 88. 
    Franquelim HG, Khmelinskaia A, Sobczak JP, Dietz H, Schwille P 2018. Membrane sculpting by curved DNA origami scaffolds. Nat. Commun. 9:811
    [Google Scholar]
  89. 89. 
    Ke G, Liu M, Jiang S, Qi X, Yang YR et al. 2016. Directional regulation of enzyme pathways through the control of substrate channeling on a DNA origami scaffold. Angew. Chem. 55:267483–86
    [Google Scholar]
  90. 90. 
    Zadorin AS, Rondelez Y, Gines G, Dilhas V, Urtel G et al. 2017. Synthesis and materialization of a reaction–diffusion French flag pattern. Nat. Chem. 9:990–96
    [Google Scholar]
  91. 91. 
    Chatterjee G, Dalchau N, Muscat RA, Phillips A, Seelig G 2017. A spatially localized architecture for fast and modular DNA computing. Nat. Nanotechnol. 12:920–27
    [Google Scholar]
  92. 92. 
    Srinivas N, Parkin J, Seelig G, Winfree E, Soloveichik D 2017. Enzyme-free nucleic acid dynamical systems. Science 358:6369eaal2052
    [Google Scholar]
  93. 93. 
    Kim J, White KS, Winfree E 2006. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol. Syst. Biol. 2:68
    [Google Scholar]
  94. 94. 
    Kim J, Winfree E. 2011. Synthetic in vitro transcriptional oscillators. Mol. Syst. Biol. 7:465
    [Google Scholar]
  95. 95. 
    Weitz M, Kim J, Kapsner K, Winfree E, Franco E, Simmel FC 2014. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. Nat. Chem. 6:295–302
    [Google Scholar]
  96. 96. 
    Baccouche A, Montagne K, Padirac A, Fujii T, Rondelez Y 2014. Dynamic DNA-toolbox reaction circuits: a walkthrough. Methods 67:2234–49
    [Google Scholar]
  97. 97. 
    Montagne K, Plasson R, Sakai Y, Fujii T, Rondelez Y 2011. Programming an in vitro DNA oscillator using a molecular networking strategy. Mol. Syst. Biol. 7:466
    [Google Scholar]
  98. 98. 
    Gines G, Zadorin AS, Galas JC, Fujii T, Estevez-Torres A, Rondelez Y 2017. Microscopic agents programmed by DNA circuits. Nat. Nanotechnol. 12:351–59
    [Google Scholar]
  99. 99. 
    Ishihama Y, Schmidt T, Rappsilber J, Mann M, Harlt FU et al. 2008. Protein abundance profiling of the Escherichia coli cytosol. BMC Genom 9:102
    [Google Scholar]
  100. 100. 
    Kigawa T, Yabuki T, Matsuda N, Matsuda T, Nakajima R et al. 2004. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J. Struct. Funct. Genom. 5:1–263–68
    [Google Scholar]
  101. 101. 
    Nirenberg MW, Matthaei JH. 1961. The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. PNAS 47:101588–602
    [Google Scholar]
  102. 102. 
    Caschera F, Noireaux V. 2015. A cost-effective polyphosphate-based metabolism fuels an all E. coli cell-free expression system. Metab. Eng. 27:29–37
    [Google Scholar]
  103. 103. 
    Jewett MC, Calhoun KA, Voloshin A, Wuu JJ, Swartz JR 2008. An integrated cell-free metabolic platform for protein production and synthetic biology. Mol. Syst. Biol. 4:220
    [Google Scholar]
  104. 104. 
    Caschera F, Noireaux V. 2014. Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription–translation system. Biochimie 99:162–68
    [Google Scholar]
  105. 105. 
    Kai L, Roos C, Haberstock S, Proverbio D, Ma Y et al. 2012. Systems for the cell-free synthesis of proteins. Methods Mol. Biol. 800:201–25
    [Google Scholar]
  106. 106. 
    Foshag D, Henrich E, Hiller E, Schäfer M, Kerger C et al. 2018. The E. coli S30 lysate proteome: a prototype for cell-free protein production. New Biotechnol 40:245–60
    [Google Scholar]
  107. 107. 
    Garenne D, Beisel CL, Noireaux V 2019. Characterization of the all-E. coli transcription–translation system myTXTL by mass spectrometry. Rapid Commun. Mass Spectrom. 33:111036–48
    [Google Scholar]
  108. 108. 
    Garamella J, Marshall R, Rustad M, Noireaux V 2016. The all E. coli TX-TL Toolbox 2.0: a platform for cell-free synthetic biology. ACS Synth. Biol. 5:4344–55
    [Google Scholar]
  109. 109. 
    Vilkhovoy M, Horvath N, Shih CH, Wayman JA, Calhoun K et al. 2018. Sequence specific modeling of E. coli cell-free protein synthesis. ACS Synth. Biol. 7:81844–57
    [Google Scholar]
  110. 110. 
    Shin J, Noireaux V. 2012. An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. ACS Synth. Biol. 1:129–41
    [Google Scholar]
  111. 111. 
    Chappell J, Jensen K, Freemont PS 2013. Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology. Nucleic Acids Res 41:53471–81
    [Google Scholar]
  112. 112. 
    Shin J, Jardine P, Noireaux V 2012. Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS Synth. Biol. 1:9408–13
    [Google Scholar]
  113. 113. 
    Rustad M, Eastlund A, Marshall R, Jardine P, Noireaux V 2017. Synthesis of infectious bacteriophages in an E. coli-based cell-free expression system. J. Vis. Exp. 126:e56144
    [Google Scholar]
  114. 114. 
    Westbrook A, Tang X, Marshall R, Maxwell CS, Chappell J et al. 2019. Distinct timescales of RNA regulators enable the construction of a genetic pulse generator. Biotechnol. Bioeng. 116:51139–51
    [Google Scholar]
  115. 115. 
    Rues RB, Henrich E, Boland C, Caffrey M, Bernhard F 2016. Cell-free production of membrane proteins in Escherichia coli lysates for functional and structural studies. Methods Mol. Biol. 1432:1–21
    [Google Scholar]
  116. 116. 
    Rues RB, Gräwe A, Henrich E, Bernhard F 2017. Membrane protein production in E. coli lysates in presence of preassembled nanodiscs. Methods Mol. Biol. 1586:291–312
    [Google Scholar]
  117. 117. 
    Matsubayashi H, Kuruma Y, Ueda T 2014. In vitro synthesis of the E. coli Sec translocon from DNA. Angew. Chem. 53:297535–38
    [Google Scholar]
  118. 118. 
    Majumder S, Garamella J, Wang YL, Denies M, Noireaux V, Liu AP 2017. Cell-sized mechanosensitive and biosensing compartment programmed with DNA. Chem. Commun. 53:537349–52
    [Google Scholar]
  119. 119. 
    Berhanu S, Ueda T, Kuruma Y 2019. Artificial photosynthetic cell producing energy for protein synthesis. Nat. Commun. 10:1325
    [Google Scholar]
  120. 120. 
    Ho KKY, Lee JW, Durand G, Majumder S, Liu AP 2017. Protein aggregation with poly(vinyl) alcohol surfactant reduces double emulsion-encapsulated mammalian cell-free expression. PLOS ONE 12:3e0174689
    [Google Scholar]
  121. 121. 
    Goerke AR, Swartz JR. 2008. Development of cell-free protein synthesis platforms for disulfide bonded proteins. Biotechnol. Bioeng. 99:2351–67
    [Google Scholar]
  122. 122. 
    Jaroentomeechai T, Stark JC, Natarajan A, Glasscock CJ, Yates LE et al. 2018. Single-pot glycoprotein biosynthesis using a cell-free transcription–translation system enriched with glycosylation machinery. Nat. Commun. 9:2686
    [Google Scholar]
  123. 123. 
    Brödel AK, Wüstenhagen DA, Kubick S 2014. Cell-free protein synthesis systems derived from cultured mammalian cells. Methods Mol. Biol. 1261:129–40
    [Google Scholar]
  124. 124. 
    Chemla Y, Ozer E, Schlesinger O, Noireaux V, Alfonta L 2015. Genetically expanded cell-free protein synthesis using endogenous pyrrolysyl orthogonal translation system. Biotechnol. Bioeng. 112:81663–72
    [Google Scholar]
  125. 125. 
    Martin RW, Des Soye BJ, Kwon YC, Kay J, Davis RG et al. 2018. Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids. Nat. Commun. 9:1203
    [Google Scholar]
  126. 126. 
    Doerr A, de Reus E, van Nies P, van der Haar M, Wei K et al. 2019. Modelling cell-free RNA and protein synthesis with minimal systems. Phys. Biol. 16:2025001
    [Google Scholar]
  127. 127. 
    Moore SJ, MacDonald JT, Wienecke S, Ishwarbhai A, Tsipa A et al. 2018. Rapid acquisition and model-based analysis of cell-free transcription–translation reactions from nonmodel bacteria. PNAS 115:19E4340–49
    [Google Scholar]
  128. 128. 
    Failmezger J, Scholz S, Blombach B, Siemann-Herzberg M 2018. Cell-free protein synthesis from fast-growing Vibrio natriegens. Front. . Microbiol 9:1146
    [Google Scholar]
  129. 129. 
    Des Soye BJ, Davidson SR, Weinstock MT, Gibson DG, Jewett MC 2018. Establishing a high-yielding cell-free protein synthesis platform derived from Vibrio natriegens. ACS Synth. . Biol 7:92245–55
    [Google Scholar]
  130. 130. 
    Moore SJ, Lai HE, Needham H, Polizzi KM, Freemont PS 2017. Streptomyces venezuelae TX-TL—a next generation cell-free synthetic biology tool. Biotechnol. J. 12:41600678
    [Google Scholar]
  131. 131. 
    Kelwick R, Webb AJ, MacDonald JT, Freemont PS 2016. Development of a Bacillus subtilis cell-free transcription–translation system for prototyping regulatory elements. Metab. Eng. 38:370–81
    [Google Scholar]
  132. 132. 
    Buntru M, Vogel S, Stoff K, Spiegel H, Schillberg S 2015. A versatile coupled cell-free transcription–translation system based on tobacco BY-2 cell lysates. Biotechnol. Bioeng. 112:5867–78
    [Google Scholar]
  133. 133. 
    Stech M, Quast RB, Sachse R, Schulze C, Wüstenhagen DA, Kubick S 2014. A continuous-exchange cell-free protein synthesis system based on extracts from cultured insect cells. PLOS ONE 9:5e96635
    [Google Scholar]
  134. 134. 
    Gan R, Jewett MC. 2014. A combined cell-free transcription–translation system from Saccharomyces cerevisiae for rapid and robust protein synthesis. Biotechnol. J. 9:5641–51
    [Google Scholar]
  135. 135. 
    Collias D, Marshall R, Collins SP, Beisel CL, Noireaux V 2019. An educational module to explore CRISPR technologies with a cell-free transcription–translation system. Synth. Biol. 4:1ysz005
    [Google Scholar]
  136. 136. 
    Stark JC, Huang A, Hsu KJ, Dubner RS, Forbrook J et al. 2019. BioBits Health: classroom activities exploring engineering, biology, and human health with fluorescent readouts. ACS Synth. Biol. 8:51001–9
    [Google Scholar]
  137. 137. 
    Sun ZZ, Yeung E, Hayes CA, Noireaux V, Murray RM 2014. Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system. ACS Synth. Biol. 3:6387–97
    [Google Scholar]
  138. 138. 
    Takahashi MK, Hayes CA, Chappell J, Sun ZZ, Murray RM et al. 2015. Characterizing and prototyping genetic networks with cell-free transcription–translation reactions. Methods 86:60–72
    [Google Scholar]
  139. 139. 
    De Los Santos ELC, Meyerowitz JT, Mayo SL, Murray RM 2016. Engineering transcriptional regulator effector specificity using computational design and in vitro rapid prototyping: developing a vanillin sensor. ACS Synth. Biol. 5:4287–95
    [Google Scholar]
  140. 140. 
    Marshall R, Maxwell CS, Collins SP, Jacobsen T, Luo ML et al. 2018. Rapid and scalable characterization of CRISPR technologies using an E. coli cell-free transcription–translation system. Mol. Cell. 69:1146–57
    [Google Scholar]
  141. 141. 
    Wandera KG, Collins SP, Wimmer F, Marshall R, Noireaux V, Beisel CL 2019. An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system. Methods 172:4250
    [Google Scholar]
  142. 142. 
    Wojtkowiak D, Georgopoulos C, Zylicz M 1993. Isolation and characterization of ClpX, a new ATP-dependent specificity component of the Clp protease of Escherichia coli. J. Biol. . Chem 268:3022609–17
    [Google Scholar]
  143. 143. 
    Niederholtmeyer H, Sun ZZ, Hori Y, Yeung E, Verpoorte A et al. 2015. Rapid cell-free forward engineering of novel genetic ring oscillators. eLife 4:e09771
    [Google Scholar]
  144. 144. 
    Karzbrun E, Tayar AM, Noireaux V, Bar-Ziv RH 2014. Programmable on-chip DNA compartments as artificial cells. Science 345:6198829–32
    [Google Scholar]
  145. 145. 
    Caschera F, Karim AS, Gazzola G, D'Aquino AE, Packard NH, Jewett MC 2018. High-throughput optimization cycle of a cell-free ribosome assembly and protein synthesis system. ACS Synth. Biol. 7:122841–53
    [Google Scholar]
  146. 146. 
    Rustad M, Eastlund A, Jardine P, Noireaux V 2018. Cell-free TXTL synthesis of infectious bacteriophage T4 in a single test tube reaction. Synth. Biol. 3:1ysy002
    [Google Scholar]
  147. 147. 
    Van Nies P, Westerlaken I, Blanken D, Salas M, Mencía M, Danelon C 2018. Self-replication of DNA by its encoded proteins in liposome-based synthetic cells. Nat. Commun. 9:1583
    [Google Scholar]
  148. 148. 
    Kuruma Y, Stano P, Ueda T, Luisi PL 2009. A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells. Biochim. Biophys. Acta Biomembr. 1788:2567–74
    [Google Scholar]
  149. 149. 
    Scott A, Noga MJ, De Graaf P, Westerlaken I, Yildirim E, Danelon C 2016. Cell-free phospholipid biosynthesis by gene-encoded enzymes reconstituted in liposomes. PLOS ONE 11:10e0163058
    [Google Scholar]
  150. 150. 
    Kay JE, Jewett MC. 2015. Lysate of engineered Escherichia coli supports high-level conversion of glucose to 2,3-butanediol. Metab. Eng. 32:133–42
    [Google Scholar]
  151. 151. 
    Majumder S, Wubshet N, Liu AP 2019. Encapsulation of complex solutions using droplet microfluidics towards the synthesis of artificial cells. J. Micromechanics Microengineering 29:083001
    [Google Scholar]
  152. 152. 
    Supramaniam P, Ces O, Salehi-Reyhani A 2019. Microfluidics for artificial life: techniques for bottom-up synthetic biology. Micromachines 10:5E299
    [Google Scholar]
  153. 153. 
    Tayar AM, Karzbrun E, Noireaux V, Bar-Ziv RH 2017. Synchrony and pattern formation of coupled genetic oscillators on a chip of artificial cells. PNAS 114:4411609–14
    [Google Scholar]
  154. 154. 
    Tayar AM, Karzbrun E, Noireaux V, Bar-Ziv RH 2015. Propagating gene expression fronts in a one-dimensional coupled system of artificial cells. Nat. Phys. 11:1037–41
    [Google Scholar]
  155. 155. 
    Gerber D, Maerkl SJ, Quake SR 2009. An in vitro microfluidic approach to generating protein-interaction networks. Nat. Methods 6:171–74
    [Google Scholar]
  156. 156. 
    Fordyce PM, Gerber D, Tran D, Zheng J, Li H et al. 2010. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat. Biotechnol. 28:9970–75
    [Google Scholar]
  157. 157. 
    Einav S, Gerber D, Bryson PD, Sklan EH, Elazar M et al. 2008. Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis. Nat. Biotechnol. 2:6(91019–27
    [Google Scholar]
  158. 158. 
    Glick Y, Ben-Ari Y, Drayman N, Pellach M, Neveu G et al. 2016. Pathogen receptor discovery with a microfluidic human membrane protein array. PNAS 113:164344–49
    [Google Scholar]
  159. 159. 
    Kipper S, Frolov L, Guy O, Pellach M, Glick Y et al. 2017. Control and automation of multilayered integrated microfluidic device fabrication. Lab Chip 17:557–66
    [Google Scholar]
  160. 160. 
    Jacobs ML, Boyd MA, Kamat NP 2019. Diblock copolymers enhance folding of a mechanosensitive membrane protein during cell-free expression. PNAS 116:104031–36
    [Google Scholar]
  161. 161. 
    Vogele K, Frank T, Gasser L, Goetzfried MA, Hackl MW et al. 2018. Towards synthetic cells using peptide-based reaction compartments. Nat. Commun. 9:3862
    [Google Scholar]
  162. 162. 
    Dupin A, Simmel FC. 2019. Signalling and differentiation in emulsion-based multi-compartmentalized in vitro gene circuits. Nat. Chem. 4:e09771
    [Google Scholar]
  163. 163. 
    Efrat Y, Tayar AM, Daube SS, Levy M, Bar-Ziv RH 2018. Electric-field manipulation of a compartmentalized cell-free gene expression reaction. ACS Synth. Biol. 7:81829–33
    [Google Scholar]
  164. 164. 
    Noireaux V, Libchaber A. 2004. A vesicle bioreactor as a step toward an artificial cell assembly. PNAS 101:5117669–74
    [Google Scholar]
  165. 165. 
    Oberholzer T, Nierhaus KH, Luisi PL 1999. Protein expression in liposomes. Biochem. Biophys. Res. Commun. 261:2238–41
    [Google Scholar]
  166. 166. 
    Ishikawa K, Sato K, Shima Y, Urabe I, Yomo T 2004. Expression of a cascading genetic network within liposomes. FEBS Lett 576:3387–90
    [Google Scholar]
  167. 167. 
    Adamala KP, Martin-Alarcon DA, Guthrie-Honea KR, Boyden ES 2017. Engineering genetic circuit interactions within and between synthetic minimal cells. Nat. Chem. 9:431–39
    [Google Scholar]
  168. 168. 
    Stano P. 2019. Gene expression inside liposomes: from early studies to current protocols. Chemistry 25:337798–814
    [Google Scholar]
  169. 169. 
    Lentini R, Martín NY, Forlin M, Belmonte L, Fontana J et al. 2017. Two-way chemical communication between artificial and natural cells. ACS Cent. Sci. 3:2117–23
    [Google Scholar]
  170. 170. 
    Maeda YT, Nakadai T, Shin J, Uryu K, Noireaux V, Libchaber A 2012. Assembly of MreB filaments on liposome membranes: a synthetic biology approach. ACS Synth. Biol. 1:253–59
    [Google Scholar]
  171. 171. 
    Furusato T, Horie F, Matsubayashi HT, Amikura K, Kuruma Y, Ueda T 2018. De novo synthesis of basal bacterial cell division proteins FtsZ, FtsA, and ZipA inside giant vesicles. ACS Synth. Biol. 7:4953–61
    [Google Scholar]
  172. 172. 
    Garamella J, Majumder S, Liu AP, Noireaux V 2019. An adaptive synthetic cell based on mechanosensing, biosensing, and inducible gene circuits. ACS Synth. Biol. 8:81913–20
    [Google Scholar]
  173. 173. 
    Majumder S, Willey PT, DeNies MS, Liu AP, Luxton GWG 2019. A synthetic biology platform for the reconstitution and mechanistic dissection of LINC complex assembly. J. Cell Sci. 132:jcs219451
    [Google Scholar]
  174. 174. 
    Fujii S, Matsuura T, Yomo T 2015. Membrane curvature affects the formation of α-hemolysin nanopores. ACS Chem. Biol. 10:71694–701
    [Google Scholar]
  175. 175. 
    Nishimura K, Matsuura T, Nishimura K, Sunami T, Suzuki H, Yomo T 2012. Cell-free protein synthesis inside giant unilamellar vesicles analyzed by flow cytometry. Langmuir 28:228426–32
    [Google Scholar]
  176. 176. 
    Dopp JL, Tamiev DD, Reuel NF 2019. Cell-free supplement mixtures: elucidating the history and biochemical utility of additives used to support in vitro protein synthesis in E. coli extract. Biotechnol. Adv. 37:1246–58
    [Google Scholar]
  177. 177. 
    Sun ZZ, Hayes CA, Shin J, Caschera F, Murray RM, Noireaux V 2013. Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. J. Vis. Exp. 79:e50762
    [Google Scholar]
  178. 178. 
    Gräwe A, Dreyer A, Vornholt T, Barteczko U, Buchholz L et al. 2019. A paper-based, cell-free biosensor system for the detection of heavy metals and date rape drugs. PLOS ONE 14:3e0210940
    [Google Scholar]
  179. 179. 
    Wang S, Majumder S, Emery NJ, Liu AP 2018. Simultaneous monitoring of transcription and translation in mammalian cell-free expression in bulk and in cell-sized droplets. Synth. Biol. 3:1ysy005
    [Google Scholar]
  180. 180. 
    Lu Y, Chan W, Ko BY, VanLang CC, Swartz JR 2015. Assessing sequence plasticity of a virus-like nanoparticle by evolution toward a versatile scaffold for vaccines and drug delivery. PNAS 112:4012360–65
    [Google Scholar]
  181. 181. 
    Pardee K, Green AA, Takahashi MK, Braff D, Lambert G et al. 2016. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165:51255–66
    [Google Scholar]
/content/journals/10.1146/annurev-bioeng-092019-111110
Loading
/content/journals/10.1146/annurev-bioeng-092019-111110
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error