Transforming synthetic biology with cell-free systems

Synthetic Biology

Volumn , Issue , 2013, Pages 277-301

  Ranji, Arnaz ^a   Wu, Jeffrey C ^b   Bundy, Bradley C ^b   Jewett, Michael C ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

^b BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

Cell free; DNA origami; Minimal cells; Nanomachines; Nucleic acid circuits; Protein evolution; Synthetic biology; Synthetic enzymatic pathways

Indexed keywords

EID: 84882708706     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-394430-6.00015-7     Document Type: Chapter

References (154)

1. Sacca B., Niemeyer C.M. DNA origami: the art of folding DNA. Angew Chem Int Ed Engl 2012, 51(1):58-66.
2. Zawada J.F., Yin G., Steiner A.R., Yang J., Naresh A., Roy S.M., et al. Microscale to manufacturing scale-up of cell-free cytokine production - a new approach for shortening protein production development timelines. BiotechBioeng 2011, 108(7):1570-1578.
3. Shimizu Y., Inoue A., Tomari Y., Suzuki T., Yokogawa T., Nishikawa K., et al. Cell-free translation reconstituted with purified components. Nat Biotechnol 2001, 19(8):751-755.
4. Carlson E.D., Gan R., Hodgman C.E., Jewett M.C. Cell-free protein synthesis: applications come of age. Biotechnol Adv 2012, 30(5):1185-1194. http://dx.doi.org/10.1016/j.biotechadv.2011.09.016.
5. Voloshin A.M., Swartz J.R. Efficient and scalable method for scaling up cell free protein synthesis in batch mode. Biotech Bioeng 2005, 91(4):516-521.
6. Saiki R.K., Gelfand D.H., Stoffel S., Scharf S.J., Higuchi R., Horn G.T., et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988, 239(4839):487-491.
7. Sousa R., Mukherjee S. T7 RNA polymerase. Prog Nucleic Acid Res Mol Biol 2003, 1-41.
8. Wang Y., Huang W., Sathitsuksanoh N., Zhu Z., Zhang Y.H.P. Biohydrogenation from biomass sugar mediated by in vitro synthetic enzymatic pathways. Chem Biol 2011, 18(3):372-380.
9. Zhang Y.H.P., Evans B.R., Mielenz J.R., Hopkins R.C., Adams M.W.W. High-yield hydrogen production from starch and water by a synthetic enzymatic pathway. PLoS One 2007, 2(5):e456.
10. Zhang Y.H.P., Myung S., You C., Zhu Z.G., Rollin J.A. Toward low-cost biomanufacturing through in vitro synthetic biology: bottom-up design. J Mater Chem 2011, 21(47):18877-18886.
11. Jewett M.C., Calhoun K.A., Voloshin A., Wuu J.J., Swartz J.R. An integrated cell-free metabolic platform for protein production and synthetic biology. Mol Syst Biol 2008, 4:220.
12. Kim J., White K.S., Winfree E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol 2006, 2:68.
13. Lesley S.A., Brow M.A., Burgess R.R. Use of in vitro protein synthesis from polymerase chain reaction-generated templates to study interaction of Escherichia coli transcription factors with core RNA polymerase and for epitope mapping of monoclonal antibodies. J Biol Chem 1991, 266(4):2632-2638.
14. Woodrow K.A., Airen I.O., Swartz J.R. Rapid expression of functional genomic libraries. J Proteome Res 2006, 5(12):3288-3300.
15. Park C.G., Kwon M.A., Song J.K., Kim D.M. Cell-free synthesis and multifold screening of Candida antarctica lipase B (CalB) variants after combinatorial mutagenesis of hot spots. Biotechnol Prog 2011, 27(1):47-53.
16. Alimov A.P., Khmelnitsky A., Simonenko P.N., Spirin A.S., Chetverin A.B. Cell-free synthesis and affinity isolation of proteins on a nanomole scale. Biotechniques 2000, 28(2):338-344.
17. Ahn J.-H., Keum J.-W., Kim D.-M. High-throughput, combinatorial engineering of initial codons for tunable expression of recombinant proteins. J Proteome Res 2008, 7(5):2107-2113.
18. Jewett M.C., Swartz J.R. Rapid expression and purification of 100nmol quantities of active protein using cell-free protein synthesis. Biotechnol Prog 2004, 20(1):102-109.
19. Kim T.-W., Oh I.-S., Ahn J.-H., Choi C.-Y., Kim D.-M. Cell-free synthesis and in situ isolation of recombinant proteins. Protein Expression Purif 2006, 45(2):249-254.
20. Bujara M., Schumperli M., Pellaux R., Heinemann M., Panke S. Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis. Nat Chem Biol 2011, 7(5):271-277.
21. Katzen F., Chang G., Kudlicki W. The past, present and future of cell-free protein synthesis. Trends Biotechnol 2005, 23(3):150-156.
22. Usón I., Sheldrick G.M. Advances in direct methods for protein crystallography. Curr Opin Struct Biol 1999, 9(5):643-648.
23. Kigawa T., Yamaguchi-Nunokawa E., Kodama K., Matsuda T., Yabuki T., Matsuda N., et al. Selenomethionine incorporation into a protein by cell-free synthesis. J Struct Funct Genomics 2002, 2(1):29-35.
24. Avenaud P., Castroviejo M., Claret S., Rosenbaum J., Mégraud F., Ménard A. Expression and activity of the cytolethal distending toxin of Helicobacter hepaticus. Biochem Biophys Res Commun 2004, 318(3):739-745.
25. Smith M.T., Varner C.T., Bush D.B., Bundy B.C. The incorporation of the A2 protein to produce novel Qβ virus-like particles using cell-free protein synthesis. Biotechnol Prog 2012, 28(2):549-555.
26. Wuu J.J., Swartz J.R. High yield cell-free production of integral membrane proteins without refolding or detergents. Biochim Biophys Acta 2008, 1778(5):1237-1250.
27. Lian J., Ma Y., Cai J., Wu M., Wang J., Wang X., et al. High-level expression of soluble subunit b of F1F0 ATP synthase in Escherichia coli cell-free system. Appl Microbiol Biotechnol 2009, 85(2):303-311.
28. Harris D.C., Jewett M.C. Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry. Curr Opin Biotechnol 2012, 23(5):672-678. http://dx.doi.org/10.1016/j.copbio.2012.02.002.
29. Bundy B.C., Swartz J.R. Site-specific incorporation of p-propargyloxyphenylalanine in a cell-free environment for direct protein-protein click conjugation. Bioconjug Chem 2010, 21(2):255-263.
30. Goerke A.R., Swartz J.R. High-level cell-free synthesis yields of proteins containing site-specific non-natural amino acids. BiotechBioeng 2009, 102(2):400-416.
31. Patel K.G., Swartz J.R. Surface functionalization of virus-like particles by direct conjugation using azide-alkyne click chemistry. Bioconjug Chem 2011, 22(3):376-387.
32. Forster A.C., Church G.M. Synthetic biology projects in vitro. Genome Res 2007, 17(1):1-6.
33. Carr P.A., Church G.M. Genome engineering. Nat Biotechnol 2009, 27(12):1151-1162.
34. Marshall W.S., Kaiser R.J. Recent advances in the high-speed solid phase synthesis of RNA. Curr Opin Chem Biol 2004, 8(3):222-229. http://dx.doi.org/10.1016/j.cbpa.2012.05.179.
35. Hockenberry A.J., Jewett M.C. Synthetic in vitro circuits. Curr Opin Chem Biol 2012, 16(3-4):253-259.
36. Adleman L.M. Molecular computation of solutions to combinatorial problems. Science 1994, 266(5187):1021-1024.
37. Seelig G., Soloveichik D., Zhang D.Y., Winfree E. Enzyme-free nucleic acid logic circuits. Science 2006, 314(5805):1585-1588.
38. Zhang D.Y., Turberfield A.J., Yurke B., Winfree E. Engineering entropy-driven reactions and networks catalyzed by DNA. Science 2007, 318(5853):1121-1125.
39. Qian L., Winfree E. A simple DNA gate motif for synthesizing large-scale circuits. J R Soc Interface 2011, 8(62):1281-1297.
40. Qian L., Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 2011, 332(6034):1196-1201.
41. Phillips A., Cardelli L. A programming language for composable DNA circuits. J R Soc Interface 2009, 6(Suppl 4):S419-S436.
42. Genot A.J., Bath J., Turberfield A.J. Reversible logic circuits made of DNA. J Am Chem Soc 2011, 133(50):20080-20083.
43. Li B., Ellington A.D., Chen X. Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res 2011, 39(16):e110.
44. Weigand J.E., Wittmann A., Suess B. RNA-based networks: using RNA aptamers and ribozymes as synthetic genetic devices. Methods Mol Biol 2012, 813:157-168.
45. Davidson E.A., Ellington A.D. Synthetic RNA circuits. Nat Chem Biol 2007, 3(1):23-28.
46. Montagne K., Plasson R., Sakai Y., Fujii T., Rondelez Y. Programming an in vitro DNA oscillator using a molecular networking strategy. Mol Syst Biol 2011, 7:466.
47. Kim J., Winfree E. Synthetic in vitro transcriptional oscillators. Mol Syst Biol 2011, 7:465.
48. Franco E., Friedrichs E., Kim J., Jungmann R., Murray R., Winfree E., et al. Timing molecular motion and production with a synthetic transcriptional clock. Proc Natl Acad Sci USA 2011, 108(40):E784-E793.
49. Benenson Y., Gil B., Ben-Dor U., Adar R., Shapiro E. An autonomous molecular computer for logical control of gene expression. Nature 2004, 429(6990):423-429.
50. Zhang D.Y., Seelig G. Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem 2011, 3(2):103-113.
51. Bath J., Turberfield A.J. DNA nanomachines. Nat Nano 2007, 2(5):275-284.
52. Yurke B., Turberfield A.J., Mills A.P., Simmel F.C., Neumann J.L. A DNA-fuelled molecular machine made of DNA. Nature 2000, 406(6796):605-608.
53. Dittmer W.U., Simmel F.C. Transcriptional control of DNA-based nanomachines. Nano Lett 2004, 4(4):689-691.
54. Dittmer W.U., Kempter S., Rädler J.O., Simmel F.C. Using gene regulation to program DNA-based molecular devices. Small 2005, 1(7):709-712.
55. Win M.N., Smolke C.D. Higher-order cellular information processing with synthetic RNA devices. Science 2008, 322(5900):456-460.
56. Seeman N.C. Nucleic acid junctions and lattices. J Theor Biol 1982, 99(2):237-247.
57. Shih W.M., Quispe J.D., Joyce G.F. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 2004, 427(6975):618-621.
58. Rothemund P.W. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440(7082):297-302.
59. Douglas S.M., Dietz H., Liedl T., Hogberg B., Graf F., Shih W.M. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 2009, 459(7245):414-418.
60. Han D., Pal S., Liu Y., Yan H. Folding and cutting DNA into reconfigurable topological nanostructures. Nature Nano 2010, 5(10):712-717.
61. Han D., Pal S., Nangreave J., Deng Z., Liu Y., Yan H. DNA origami with complex curvatures in three-dimensional space. Science 2011, 332(6027):342-346.
62. Douglas S.M., Marblestone A.H., Teerapittayanon S., Vazquez A., Church G.M., Shih W.M. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res 2009, 37(15):5001-5006.
63. Endo M., Katsuda Y., Hidaka K., Sugiyama H. A versatile DNA nanochip for direct analysis of DNA base-excision repair. Angew Chem Int Ed Engl 2010, 49(49):9412-9416.
64. Douglas S.M., Bachelet I., Church G.M. A logic-gated nanorobot for targeted transport of molecular payloads. Science 2012, 335(6070):831-834.
65. Shimizu Y., Kanamori T., Ueda T. Protein synthesis by pure translation systems. Methods 2005, 36(3):299-304.
66. Ohashi H., Kanamori T., Shimizu Y., Ueda T. A highly controllable reconstituted cell-free system - a breakthrough in protein synthesis research. Curr Pharm Biotechnol 2010, 11(3):267-271.
67. Hodgman C.E., Jewett M.C. Cell-free synthetic biology: thinking outside the cell. Metab Eng 2012, 14(3):261-269. http://dx.doi.org/10.1016/j.ymben.2011.09.002.
68. Swartz J. Developing cell-free biology for industrial applications. J Ind Microbiol Biot 2006, 33(7):476-485.
69. Guarino C., Delisa M.P. A prokaryote-based cell-free translation system that efficiently synthesizes glycoproteins. Glycobiology 2011, 22(5):596-601.
70. Uzawa T., Yamagishi A., Oshima T. Polypeptide synthesis directed by DNA as a messenger in cell-free polypeptide synthesis by extreme thermophiles, Thermus thermophilus HB27 and Sulfolobus tokodaii strain 7. J Biochem 2002, 131(6):849-853.
71. Madin K., Sawasaki T., Ogasawara T., Endo Y. A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes. Proc Natl Acad Sci USA 2000, 97(2):559-564.
72. Park N., Um S.H., Funabashi H., Xu J., Luo D. A cell-free protein-producing gel. Nat Mater 2009, 8(5):432-437.
73. Pelham H.R.B., Jackson R.J. An efficient mRNA-dependent translation system from reticulocyte lysates. Eur J Biochem 1976, 67(1):247-256.
74. Ryabova L.A., Ortlepp S.A., Baranovp V.I. Preparative synthesis of globin in a continuous cell-free translation system from rabbit reticulocytes. Nucleic Acids Res 1989, 17(11):4412.
75. Hancock J.F. Reticulocyte lysate assay for in vitro translation and posttranslational modification of ras proteins. Methods Enzymol 1995, 244:60-65.
76. Endo Y., Sawasaki T. Cell-free expression systems for eukaryotic protein production. Curr Opin Biotechnol 2006, 17(4):373-380.
77. Ezure T., Suzuki T., Shikata M., Ito M., Ando E.A. Cell-free protein synthesis system from insect cells. Cell-Free Protein Production 2010, 31-42. Humana Press. Y. Endo, T. Ueda, K. Takai (Eds.).
78. Tarui H., Murata M., Tani I., Imanishi S., Nishikawa S., Hara T. Establishment and characterization of cell-free translation/glycosylation in insect cell extract prepared with high pressure treatment. Appl Microbiol Biotechnol 2001, 55(4):446-453.
79. Suzuki T., Ito M., Ezure T., Shikata M., Ando E., Utsumi T., et al. Protein prenylation in an insect cell-free protein synthesis system and identification of products by mass spectrometry. Proteomics 2007, 7(12):1942-1950.
80. Suzuki T., Ito M., Ezure T., Shikata M., Ando E., Utsumi T., et al. N-terminal protein modifications in an insect cell-free protein synthesis system and their identification by mass spectrometry. Proteomics 2006, 6(16):4486-4495.
81. Sedov S.A., Belogurova N.G., Shipovskov S., Levashov A.V., Levashov P.A. Lysis of Escherichia coli cells by lysozyme: discrimination between adsorption and enzyme action. Colloids Surf B Biointerfaces 2011, 88(1):131-133.
82. Hu T., Li H.Y., Zhang X.Z., Luo H.J., Fu J.M. Toxic effect of NaCl on ion metabolism, antioxidative enzymes and gene expression of perennial ryegrass. Ecotoxicol Environ Saf 2011, 74(7):2050-2056.
83. te Velthuis A.J., van den Worm S.H., Sims A.C., Baric R.S., Snijder E.J., van Hemert M.J. Zn(2+) inhibits coronavirus and arterivirus RNA polymerase activity in vitro and zinc ionophores block the replication of these viruses in cell culture. PLoS Pathog 2010, 6(11):e1001176.
84. Jaenicke R. Protein folding: local structures, domains, subunits, and assemblies. Biochemistry 1991, 30(13):3147-3161.
85. Zlotnick A., Ceres P., Singh S., Johnson J.M. A small molecule inhibits and misdirects assembly of hepatitis B virus capsids. J Virol 2002, 76(10):4848-4854.
86. Bundy B.C., Franciszkowicz M.J., Swartz J.R. Escherichia coli-based cell-free synthesis of virus-like particles. BiotechBioeng 2008, 100(1):28-37.
87. Bundy B.C., Swartz J.R. Efficient disulfide bond formation in virus-like particles. J Biotechnol 2011, 154(4):230-239.
88. Ceres P., Zlotnick A. Weak protein-protein interactions are sufficient to drive assembly of hepatitis B virus capsids. Biochemistry 2002, 41(39):11525-11531.
89. Ezure T., Suzuki T., Shikata M., Ito M., Ando E., Nishimura O., et al. Expression of proteins containing disulfide bonds in an insect cell-free system and confirmation of their arrangements by MALDI-TOF MS. Proteomics 2007, 7(24):4424-4434.
90. Goerke A.R., Loening A.M., Gambhir S.S., Swartz J.R. Cell-free metabolic engineering promotes high-level production of bioactive gaussia princeps luciferase. Metab Eng 2008, 10(3-4):187-200.
91. Park C.G., Kim T.W., Oh I.S., Song J.K., Kim D.M. Expression of functional Candida antarctica lipase B in a cell-free protein synthesis system derived from Escherichia coli. Biotechnol Prog 2009, 25(2):589-593.
92. Betton J.-M., Miot M. Cell-free production of membrane proteins in the presence of detergents. Cell-Free Protein Synth 2008, Wiley-VCH Verlag GmbH & Co. KGaA, 165-178.
93. Gilbert G.P. Detergents for the stabilization and crystallization of membrane proteins. Methods 2007, 41(4):388-397.
94. Pedersen A., Hellberg K., Enberg J., Karlsson B.G. Rational improvement of cell-free protein synthesis. New Biotechnol 2011, 28(3):218-224.
95. Park K.-H., Billon-Denis E., Dahmane T., Lebaupain F., Pucci B., Breyton C., et al. In the cauldron of cell-free synthesis of membrane proteins: playing with new surfactants. New Biotechnol 2011, 28(3):255-261.
96. Hovijitra N.T., Wuu J.J., Peaker B., Swartz J.R. Cell-free synthesis of functional aquaporin Z in synthetic liposomes. Biotech Bioeng 2009, 104(1):40-49.
97. Um S.H., Lee J.B., Park N., Kwon S.Y., Umbach C.C., Luo D. Enzyme-catalysed assembly of DNA hydrogel. Nat Mater 2006, 5(10):797-801.
98. Park N., Kahn J.S., Rice E.J., Hartman M.R., Funabashi H., Xu J., et al. High-yield cell-free protein production from P-gel. Nat Protocols 2009, 4(12):1759-1770.
99. Chandra H., Srivastava S. Cell-free synthesis-based protein microarrays and their applications. Proteomics 2010, 10(4):717-730.
100. Ramachandran N., Hainsworth E., Bhullar B., Eisenstein S., Rosen B., Lau A.Y., et al. Self-assembling protein microarrays. Science 2004, 305(5680):86-90.
101. Goshima N., Kawamura Y., Fukumoto A., Miura A., Honma R., Satoh R., et al. Human protein factory for converting the transcriptome into an in vitro-expressed proteome. Nat Methods 2008, 5(12):1011-1017.
102. Zahnd C., Amstutz P., Pluckthun A. Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat Meth 2007, 4(3):269-279.
103. Zhu Y., Power B. Lab-on-a-chip in vitro compartmentalization technologies for protein studies. Protein-Protein Interaction 2008, 81-114. Springer, Berlin/Heidelberg. M. Werther, H. Seitz (Eds.).
104. Sepp A., Choo Y. Cell-free selection of zinc finger DNA-binding proteins using in vitro compartmentalization. J Mol Biol 2005, 354(2):212-219.
105. Fallah-Araghi A., Baret J.C., Ryckelynck M., Griffiths A.D. A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution. Lab Chip 2012, 12(5):882-891.
106. Agresti J.J., Antipov E., Abate A.R., Ahn K., Rowat A.C., Baret J.-C., et al. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci USA 2010, 107(9):4004-4009.
107. Wada A., Sawata S.Y., Ito Y. Ribosome display selection of a metal-binding motif from an artificial peptide library. Biotech Bioeng 2008, 101(5):1102-1107.
108. Yan X., Xu Z. Ribosome-display technology: applications for directed evolution of functional proteins. Drug Discov Today 2006, 11(19-20):911-916.
109. Zahnd C., Pecorari F., Straumann N., Wyler E., Pluckthun A. Selection and characterization of Her2 binding-designed ankyrin repeat proteins. J Biol Chem 2006, 281(46):35167-35175.
110. Hecht M.H., Das A., Go A., Bradley L.H., Wei Y. De novo proteins from designed combinatorial libraries. Protein Sci 2004, 13(7):1711-1723.
111. Ohta A., Yamagishi Y., Suga H. Synthesis of biopolymers using genetic code reprogramming. CurrOpinChem Biol 2008, 12(2):159-167.
112. Wang L., Xie J., Schultz P.G. Expanding the genetic code. Annu Rev Biophys Biomol Struct 2006, 35(1):225-249.
113. Xie J., Schultz P.G. A chemical toolkit for proteins - an expanded genetic code. Nat Rev Mol Cell Biol 2006, 7(10):775-782.
114. Ozawa K, Loscha KV, Kuppan KV, Loh CT, Dixon NE, Otting G. High-yield cell-free protein synthesis for site-specific incorporation of unnatural amino acids at multiple sites. Biochem Biophys Res Commun. 2012;418(4):652-656.
115. Johnson D.B.F., Xu J., Shen Z., Takimoto J.K., Schultz M.D., Schmitz R.J., et al. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat Chem Biol 2011, 7(11):779-786.
116. Buchner E. Alkoholischegahrung ohnehefezellen. BerChemGes 1897, 30:117-124.
117. Swartz J.R. Transforming biochemical engineering with cell-free biology. AIChE Journal 2012, 58(1):5-13.
118. Bujara M., Schümperli M., Billerbeck S., Heinemann M., Panke S. Exploiting cell-free systems: implementation and debugging of a system of biotransformations. BiotechBioeng 2010, 106(3):376-389.
119. Khalil A.S., Collins J.J. Synthetic biology: applications come of age. Nat Rev Genet 2010, 11(5):367-379.
120. Stano P. Minimal cells: relevance and interplay of physical and biochemical factors. Biotechnol J 2011, 6(7):850-859.
121. Forster A.C., Church G.M. Towards synthesis of a minimal cell. Mol Syst Biol 2006, 2:45.
122. Jewett M.C., Forster A.C. Update on designing and building minimal cells. Curr Opin Biotechnol 2010, 21(5):697-703.
123. Glass J.I., Assad-Garcia N., Alperovich N., Yooseph S., Lewis M.R., Maruf M., et al. Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 2006, 103(2):425-430.
124. Gibson D.G., Glass J.I., Lartigue C., Noskov V.N., Chuang R.Y., Algire M.A., et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010, 329(5987):52-56.
125. Noireaux V., Maeda Y.T., Libchaber A. Development of an artificial cell, from self-organization to computation and self-reproduction. Proc Natl Acad Sci USA 2011, 108(9):3473-3480.
126. Wochner A., Attwater J., Coulson A., Holliger P. Ribozyme-catalyzed transcription of an active ribozyme. Science 2011, 332(6026):209-212.
127. Szostak J.W., Bartel D.P., Luisi P.L. Synthesizing life. Nature 2001, 409(6818):387-390.
128. Stano P., Luisi P.L. Achievements and open questions in the self-reproduction of vesicles and synthetic minimal cells. Chem Commun (Camb) 2010, 46(21):3639-3653.
129. Kuruma Y., Stano P., Ueda T., Luisi P.L. A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells. Biochim Biophys Acta 2009, 1788(2):567-574.
130. Kurihara K., Tamura M., Shohda K., Toyota T., Suzuki K., Sugawara T. Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA. Nat Chem 2011, 3(10):775-781.
131. Caschera F., Sunami T., Matsuura T., Suzuki H., Hanczyc M.M., Yomo T. Programmed vesicle fusion triggers gene expression. Langmuir 2011, 27(21):13082-13090.
132. Noireaux V., Libchaber A. A vesicle bioreactor as a step toward an artificial cell assembly. Proc Natl Acad Sci USA 2004, 101(51):17669-17674.
133. Asahara H., Chong S. In vitro genetic reconstruction of bacterial transcription initiation by coupled synthesis and detection of RNA polymerase holoenzyme. Nucleic Acids Res 2010, 38(13):e141.
134. Murtas G., Kuruma Y., Bianchini P., Diaspro A., Luisi P.L. Protein synthesis in liposomes with a minimal set of enzymes. Biochem Biophys Res Commun 2007, 363(1):12-17.
135. Kuruma Y., Nishiyama K., Shimizu Y., Muller M., Ueda T. Development of a minimal cell-free translation system for the synthesis of presecretory and integral membrane proteins. Biotechnol Prog 2005, 21(4):1243-1251.
136. Kita H., Matsuura T., Sunami T., Hosoda K., Ichihashi N., Tsukada K., et al. Replication of genetic information with self-encoded replicase in liposomes. Chembiochem 2008, 9(15):2403-2410.
137. Oberholzer T., Wick R., Luisi P.L., Biebricher C.K. Enzymatic RNA replication in self-reproducing vesicles: an approach to a minimal cell. Biochem Biophys Res Commun 1995, 207(1):250-257.
138. Liu D.V., Zawada J.F., Swartz J.R. Streamlining Escherichia coli S30 extract preparation for economical cell-free protein synthesis. Biotechnol Prog 2005, 21(2):460-465.
139. Kim T.W., Keum J.W., Oh I.S., Choi C.Y., Park C.G., Kim D.M. Simple procedures for the construction of a robust and cost-effective cell-free protein synthesis system. J Biotechnol 2006, 126(4):554-561.
140. Shrestha P., Holland T., Bundy B.C. Streamlined extract preparation for Escherichia coli-based cell-free protein synthesis by sonication or bead vortex mixing. BioTechniques 2012, 53(3):163-174.
141. Airen IO, Swartz JR, eds. Functional Genomic Analysis of Escherichia Coli Using Sequenctial Cell-Free Protein Synthesis. Salt Lake City, UT; 2010: AIChE Annual Meeting.
142. Santacoloma P.A., Sin G., Gernaey K.V., Woodley J.M. Multienzyme-catalyzed processes: next-generation biocatalysis. Org Process Res Dev 2011, 15(1):203-212.
143. Du L., Gao R., Forster A.C. Engineering multigene expression in vitro and in vivo with small terminators for T7 RNA polymerase. Biotech Bioeng 2009, 104(6):1189-1196.
144. Du L., Villarreal S., Forster A.C. Multigene expression in vivo: supremacy of large versus small terminators for T7 RNA polymerase. BiotechBioeng 2012, 109(4):1043-1050.
145. Wang H.H., Huang P., Xu G., Haas W., Marblestone A., Li J., et al. Multiplexed in vivo his-tagging of enzyme pathways for in vitro single-pot multieznyme catalysis. ACS Synth Biol 2012, 1(2):43-52.
146. Sheldon R.A. Enzyme immobilization: the quest for optimum performance. Adv Synth Catal 2007, 349(8-9):1289-1307.
147. Jewett M.C., Swartz J.R. Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis. Biotech Bioeng 2004, 86(1):19-26.
148. Ryabova L.A., Vinokurov L.M., Shekhovtsova E.A., Alakhov Y.B., Spirin A.S. Acetyl phosphate as an energy source for bacterial cell-free translation systems. Anal Biochem 1995, 226(1):184-186.
149. Calhoun K.A., Swartz J.R. Energizing cell-free protein synthesis with glucose metabolism. Biotech Bioeng 2005, 90(5):606-613.
150. Kim T.W., Oh I.S., Keum J.W., Kwon Y.C., Byun J.Y., Lee K.H., et al. Prolonged cell-free protein synthesis using dual energy sources: combined use of creatine phosphate and glucose for the efficient supply of ATP and retarded accumulation of phosphate. Biotech Bioeng 2007, 97(6):1510-1515.
151. Ma R., Yang Z., Huang L., Zhu X., Kai L., Cai J., et al. Construction of an efficient Escherichia coli cell-free system for in vitro expression of several kinds of proteins. Eng Life Sci 2010, 10(4):333-338.
152. Ezure T., Suzuki T., Higashide S., Shintani E., Endo K., Kobayashi S-I, et al. Cell-free protein synthesis system prepared from insect cells by freeze-thawing. Biotechnol Prog 2006, 22(6):1570-1577.
153. Ueda T., Kanamori T., Ohashi H. Ribosome display with the PURE technology. Cell-Free Protein Production 2010, 219-225. Humana Press. Y. Endo, T. Ueda, K. Takai (Eds.).
154. Hino M., Kataoka M., Kajimoto K., Yamamoto T., Kido J.-I., Shinohara Y., et al. Efficiency of cell-free protein synthesis based on a crude cell extract from Escherichia coli, wheat germ, and rabbit reticulocytes. J Biotechnol 2008, 133(2):183-189.