Engine out of the chassis: Cell-free protein synthesis and its uses

FEBS Letters

Volumn 588, Issue 2, 2014, Pages 261-268

  Rosenblum, Gabriel ^a   Cooperman, Barry S ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Cell free protein synthesis; High throughput; Transcription; Translation

Indexed keywords

4 ACETYLPHENYLALANINE; AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; AMINOACYL TRANSFER RNA; BACTERIAL TOXIN; CIRCULAR DNA; DNA FRAGMENT; NONNATURAL AMINO ACID; PHENYLALANINE TRANSFER RNA; PLASMID DNA; PLASMINOGEN ACTIVATOR; PSEUDOURIDINE; RNA POLYMERASE; UNCLASSIFIED DRUG; VIRUS MESSENGER RNA;

5' UNTRANSLATED REGION; AMINO ACID SUBSTITUTION; ANALYTICAL EQUIPMENT; ARTIFICIAL MEMBRANE; CELL FREE PROTEIN SYNTHESIS; CELL FREE PROTEIN SYNTHESIS KIT; CELL FREE SYSTEM; FLUORESCENCE; GENE AMPLIFICATION; GENE INTERACTION; GENE SEQUENCE; GENETIC TRANSCRIPTION; HUMAN; IN VIVO STUDY; INTERNAL RIBOSOME ENTRY SITE; ISOTOPE LABELING; MEMBRANE PERMEABILITY; MOLECULAR CLONING; NONHUMAN; OXIDATION REDUCTION REACTION; OXIDATIVE PHOSPHORYLATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN AGGREGATION; PROTEIN CLEAVAGE; PROTEIN ENGINEERING; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEIN SYNTHESIS; REVIEW; RIBOSOME; RIBOSOME NASCENT CHAIN COMPLEX; RNA BINDING; RNA STRUCTURE; RNA TRANSLATION; TEMPERATURE DEPENDENCE;

CELL-FREE PROTEIN SYNTHESIS; HIGH THROUGHPUT; TRANSCRIPTION; TRANSLATION;

ANIMALS; CELL-FREE SYSTEM; GENETIC ENGINEERING; HUMANS; PROTEIN BIOSYNTHESIS;

EID: 84892365296     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2013.10.016     Document Type: Review

References (80)

1. J.K. DeVries, and G. Zubay DNA-directed peptide synthesis. II. The synthesis of the alpha-fragment of the enzyme beta-galactosidase Proc. Natl. Acad. Sci. USA 57 1967 1010 1012
2. M.W. Nirenberg, and J.H. Matthaei The dependence of cell-free protein synthesis in E. Coli upon naturally occurring or synthetic polyribonucleotides Proc. Natl. Acad. Sci. USA 47 1961 1588 1602
3. G. Zubay In vitro synthesis of protein in microbial systems Annu. Rev. Genet. 7 1973 267 287
4. S. Mureev, O. Kovtun, U.T. Nguyen, and K. Alexandrov Species-independent translational leaders facilitate cell-free expression Nat. Biotechnol. 27 2009 747 752
5. T. Ezure et al. Cell-free protein synthesis system prepared from insect cells by freeze-thawing Biotechnol. Prog. 22 2006 1570 1577
6. T. Sawasaki, R. Morishita, M.D. Gouda, and Y. Endo Methods for high-throughput materialization of genetic information based on wheat germ cell-free expression system Methods Mol. Biol. 375 2007 95 106
7. H.R. Pelham, and R.J. Jackson An efficient mRNA-dependent translation system from reticulocyte lysates Eur. J. Biochem. 67 1976 247 256
8. S. Mikami, T. Kobayashi, M. Masutani, S. Yokoyama, and H. Imataka A human cell-derived in vitro coupled transcription/translation system optimized for production of recombinant proteins Protein Expr. Purif. 62 2008 190 198
9. D.M. Kim, and J.R. Swartz Prolonging cell-free protein synthesis with a novel ATP regeneration system Biotechnol. Bioeng. 66 1999 180 188
10. N. Michel-Reydellet, K. Woodrow, and J. Swartz Increasing PCR fragment stability and protein yields in a cell-free system with genetically modified Escherichia coli extracts J. Mol. Microbiol. Biotechnol. 9 2005 26 34
11. X. Jiang, K. Oohira, Y. Iwasaki, H. Nakano, S. Ichihara, and T. Yamane Reduction of protein degradation by use of protease-deficient mutants in cell-free protein synthesis system of Escherichia coli J. Biosci. Bioeng. 93 2002 151 156
12. G. Yin, and J.R. Swartz Enhancing multiple disulfide bonded protein folding in a cell-free system Biotechnol. Bioeng. 86 2004 188 195
13. D.M. Kim, and J.R. Swartz Efficient production of a bioactive, multiple disulfide-bonded protein using modified extracts of Escherichia coli Biotechnol. Bioeng. 85 2004 122 129
14. K.A. Underwood, J.R. Swartz, and J.D. Puglisi Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis Biotechnol. Bioeng. 91 2005 425 435
15. E. Mikamo-Satoh, A. Takagi, H. Tanaka, T. Matsumoto, T. Nishihara, and T. Kawai Profiling of gene-dependent translational progress in cell-free protein synthesis by real-space imaging Anal. Biochem. 394 2009 275 280
16. R.Y. Tsien The green fluorescent protein Annu. Rev. Biochem. 67 1998 509 544
17. G. Rosenblum, C. Chen, J. Kaur, X. Cui, Y.E. Goldman, and B.S. Cooperman Real-time assay for testing components of protein synthesis Nucleic Acids Res. 40 2012 e88
18. J. Shin, and V. Noireaux Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system J. Biol. Eng. 4 2010 9
19. H.L. Yang, L. Ivashkiv, H.Z. Chen, G. Zubay, and M. Cashel Cell-free coupled transcription-translation system for investigation of linear DNA segments Proc. Natl. Acad. Sci. USA 77 1980 7029 7033
20. S.Y. Jun, S.H. Kang, and K.H. Lee Continuous-exchange cell-free protein synthesis using PCR-generated DNA and an RNase E-deficient extract Biotechniques 44 2008 387 391
21. A.V. Kralicek, M. Radjainia, N.A. Mohamad Ali, C. Carraher, R.D. Newcomb, and A.K. Mitra A PCR-directed cell-free approach to optimize protein expression using diverse fusion tags Protein Expr. Purif. 80 2011 117 124
22. P.S. Wu, K. Ozawa, S.P. Lim, S.G. Vasudevan, N.E. Dixon, and G. Otting Cell-free transcription/translation from PCR-amplified DNA for high-throughput NMR studies Angew. Chem., Int. Ed. Engl. 46 2007 3356 3358
23. Y. Shimizu, A. Inoue, Y. Tomari, T. Suzuki, T. Yokogawa, K. Nishikawa, and T. Ueda Cell-free translation reconstituted with purified components Nat. Biotechnol. 19 2001 751 755
24. H. Asahara, and S. Chong In vitro genetic reconstruction of bacterial transcription initiation by coupled synthesis and detection of RNA polymerase holoenzyme Nucleic Acids Res. 38 2010 e141
25. Y. Zhou, H. Asahara, E.A. Gaucher, and S. Chong Reconstitution of translation from Thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components Nucleic Acids Res. 40 2012 7932 7945
26. K. Madin, T. Sawasaki, T. Ogasawara, and Y. Endo 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 97 2000 559 564
27. K. Kariko, H. Muramatsu, F.A. Welsh, J. Ludwig, H. Kato, S. Akira, and D. Weissman Incorporation of pseudouridine into mRNA yields superior non-immunogenic vector with increased translational capacity and biological stability Mol. Ther. 16 2008 1833 1840
28. A. Bugaut, and S. Balasubramanian 5′-UTR RNA G-quadruplexes: translation regulation and targeting Nucleic Acids Res. 40 2012 4727 4741
29. M. Mandal, and R.R. Breaker Adenine riboswitches and gene activation by disruption of a transcription terminator Nat. Struct. Mol. Biol. 11 2004 29 35
30. M. Mandal, M. Lee, J.E. Barrick, Z. Weinberg, G.M. Emilsson, W.L. Ruzzo, and R.R. Breaker A glycine-dependent riboswitch that uses cooperative binding to control gene expression Science 306 2004 275 279
31. G. Rosenblum et al. Quantifying elongation rhythm during full-length protein synthesis J. Am. Chem. Soc. 135 2013 11322 11329
32. W.C. Winkler, A. Nahvi, A. Roth, J.A. Collins, and R.R. Breaker Control of gene expression by a natural metabolite-responsive ribozyme Nature 428 2004 281 286
33. C. Yanofsky Attenuation in the control of expression of bacterial operons Nature 289 1981 751 758
34. J. Shine, and L. Dalgarno The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites Proc. Natl. Acad. Sci. USA 71 1974 1342 1346
35. M. Dreyfus What constitutes the signal for the initiation of protein synthesis on Escherichia coli mRNAs? J. Mol. Biol. 204 1988 79 94
36. V. Vimberg, A. Tats, M. Remm, and T. Tenson Translation initiation region sequence preferences in Escherichia coli BMC Mol. Biol. 8 2007 100
37. S.K. Jang, H.G. Krausslich, M.J. Nicklin, G.M. Duke, A.C. Palmenberg, and E. Wimmer A segment of the 5′ non-translated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation J. Virol. 62 1988 2636 2643
38. J. Pelletier, and N. Sonenberg Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA Nature 334 1988 320 325
39. M.B. Iskakova, W. Szaflarski, M. Dreyfus, J. Remme, and K.H. Nierhaus Troubleshooting coupled in vitro transcription-translation system derived from Escherichia coli cells: synthesis of high-yield fully active proteins Nucleic Acids Res. 34 2006 e135
40. L. Kai, V. Dotsch, R. Kaldenhoff, and F. Bernhard Artificial environments for the co-translational stabilization of cell-free expressed proteins PLoS ONE 8 2013 e56637
41. Y. Sasaki, W. Asayama, T. Niwa, S. Sawada, T. Ueda, H. Taguchi, and K. Akiyoshi Amphiphilic polysaccharide nanogels as artificial chaperones in cell-free protein synthesis Macromol. Biosci. 11 2011 814 820
42. T. Niwa, T. Kanamori, T. Ueda, and H. Taguchi Global analysis of chaperone effects using a reconstituted cell-free translation system Proc. Natl. Acad. Sci. USA 109 2012 8937 8942
43. L.A. Ryabova, D. Desplancq, A.S. Spirin, and A. Pluckthun Functional antibody production using cell-free translation: effects of protein disulfide isomerase and chaperones Nat. Biotechnol. 15 1997 79 84
44. A.M. Voloshin, and J.R. Swartz Efficient and scalable method for scaling up cell free protein synthesis in batch mode Biotechnol. Bioeng. 91 2005 516 521
45. A.S. Spirin, V.I. Baranov, L.A. Ryabova, S.Y. Ovodov, and Y.B. Alakhov A continuous cell-free translation system capable of producing polypeptides in high yield Science 242 1988 1162 1164
46. T. Kigawa, and S. Yokoyama A continuous cell-free protein synthesis system for coupled transcription-translation J. Biochem. 110 1991 166 168
47. T. Sawasaki, Y. Hasegawa, M. Tsuchimochi, N. Kamura, T. Ogasawara, T. Kuroita, and Y. Endo A bilayer cell-free protein synthesis system for high-throughput screening of gene products FEBS Lett. 514 2002 102 105
48. J.F. Zawada et al. Microscale to manufacturing scale-up of cell-free cytokine production - a new approach for shortening protein production development timelines Biotechnol. Bioeng. 108 2011 1570 1578
49. E.D. Carlson, R. Gan, C.E. Hodgman, and M.C. Jewett Cell-free protein synthesis: applications come of age Biotechnol. Adv. 30 2011 1185 1194
50. M. Watanabe, K. Miyazono, M. Tanokura, T. Sawasaki, Y. Endo, and I. Kobayashi Cell-free protein synthesis for structure determination by X-ray crystallography Methods Mol. Biol. 607 2010 149 160
51. Z. Xu, H. Chen, X. Yin, N. Xu, and P. Cen High-level expression of soluble human beta-defensin-2 fused with green fluorescent protein in Escherichia coli cell-free system Appl. Biochem. Biotechnol. 127 2005 53 62
52. P. Renesto, and D. Raoult From genes to proteins: in vitro expression of rickettsial proteins Ann. N.Y. Acad. Sci. 990 2003 642 652
53. K.A. Martemyanov, V.A. Shirokov, O.V. Kurnasov, A.T. Gudkov, and A.S. Spirin Cell-free production of biologically active polypeptides: application to the synthesis of antibacterial peptide cecropin Protein Expr. Purif. 21 2001 456 461
54. J.P. Welsh, J. Bonomo, and J.R. Swartz Localization of BiP to translating ribosomes increases soluble accumulation of secreted eukaryotic proteins in an Escherichia coli cell-free system Biotechnol. Bioeng. 108 2011 1739 1748
55. A.L. Fink Protein aggregation: folding aggregates, inclusion bodies and amyloid Fold Des. 3 1998 R9 R23
56. M.C. Jewett, B.R. Fritz, L.E. Timmerman, and G.M. Church In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation Mol. Syst. Biol. 9 2013 678
57. N. Vazquez-Laslop, H. Ramu, D. Klepacki, K. Kannan, and A.S. Mankin The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide EMBO J. 29 2010 3108 3117
58. L. Gorini, and E. Kataja Phenotypic repair by streptomycin of defective genotypes in E. Coli Proc. Natl. Acad. Sci. USA 51 1964 487 493
59. R. Rosset, and L. Gorini A ribosomal ambiguity mutation J. Mol. Biol. 39 1969 95 112
60. O. Rackham, and J.W. Chin A network of orthogonal ribosome xmRNA pairs Nat. Chem. Biol. 1 2005 159 166
61. A. Katranidis et al. Fast biosynthesis of GFP molecules: a single-molecule fluorescence study Angew. Chem., Int. Ed. Engl. 48 2009 1758 1761
62. M. Dorywalska, S.C. Blanchard, R.L. Gonzalez, H.D. Kim, S. Chu, and J.D. Puglisi Site-specific labeling of the ribosome for single-molecule spectroscopy Nucleic Acids Res. 33 2005 182 189
63. A. Petrov, and J.D. Puglisi Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations Nucleic Acids Res. 38 2010 e143
64. J. Hanes, and A. Pluckthun In vitro selection and evolution of functional proteins by using ribosome display Proc. Natl. Acad. Sci. USA 94 1997 4937 4942
65. M.S. Evans, K.G. Ugrinov, M.A. Frese, and P.L. Clark Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro Nat. Methods 2 2005 757 762
66. C.C. Liu, and P.G. Schultz Adding new chemistries to the genetic code Annu. Rev. Biochem. 79 2010 413 444
67. L. Wang, A. Brock, B. Herberich, and P.G. Schultz Expanding the genetic code of Escherichia coli Science 292 2001 498 500
68. L. Wang, and P.G. Schultz Expanding the genetic code Angew. Chem., Int. Ed. Engl. 44 2004 34 66
69. D.E. Agafonov, Y. Huang, M. Grote, and M. Sprinzl Efficient suppression of the amber codon in E. Coli in vitro translation system FEBS Lett. 579 2005 2156 2160
70. S. Sando, A. Ogawa, T. Nishi, M. Hayami, and Y. Aoyama In vitro selection of RNA aptamer against Escherichia coli release factor 1 Bioorg. Med. Chem. Lett. 17 2007 1216 1220
71. C. Albayrak, and J.R. Swartz Cell-free co-production of an orthogonal transfer RNA activates efficient site-specific non-natural amino acid incorporation Nucleic Acids Res. 41 2013 5949 5963
72. D.B. Johnson et al. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites Nat. Chem. Biol. 7 2011 779 786
73. 2O J. Biomol. NMR 50 2011 35 42
74. K. Ozawa, P.S. Wu, N.E. Dixon, and G. Otting N-labelled proteins by cell-free protein synthesis. Strategies for high-throughput NMR studies of proteins and protein-ligand complexes FEBS J. 273 2006 4154 4159
75. M. Takeda, and M. Kainosho Cell-free protein synthesis using E. Coli cell extract for NMR studies Adv. Exp. Med. Biol. 992 2012 167 177
76. J.H. Ahn, M.Y. Hwang, I.S. Oh, K.M. Park, G.H. Hahn, C.Y. Cho, and D.M. Kim Preparation method for Escherichia coli S30 extracts completely dependent upon tRNA addition to catalyze cell-free protein synthesis Biotechnol. Bioprocess Eng. 11 2006 420 424
77. R.J. Jackson, S. Napthine, and I. Brierley Development of a tRNA-dependent in vitro translation system RNA 7 2001 765 773
78. T. Yokogawa, Y. Kitamura, D. Nakamura, S. Ohno, and K. Nishikawa Optimization of the hybridization-based method for purification of thermostable tRNAs in the presence of tetraalkylammonium salts Nucleic Acids Res. 38 2010 e89
79. E.M. Phizicky, and J.D. Alfonzo Do all modifications benefit all tRNAs? FEBS Lett. 584 2010 265 271
80. M.B. Hoagland, M.L. Stephenson, J.F. Scott, L.I. Hecht, and P.C. Zamecnik A soluble ribonucleic acid intermediate in protein synthesis J. Biol. Chem. 231 1958 241 257