High-throughput preparation methods of crude extract for robust cell-free protein synthesis

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Kwon, Yong Chan ^a,b   Jewett, Michael C ^a,b,c  

^a Northwestern University   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL SIZE; CYTOLOGY; ESCHERICHIA COLI; HIGH THROUGHPUT SCREENING; METABOLISM; PROCEDURES; PROTEIN SYNTHESIS; ULTRASOUND;

CELL SIZE; ESCHERICHIA COLI; HIGH-THROUGHPUT SCREENING ASSAYS; PROTEIN BIOSYNTHESIS; SONICATION;

EID: 84923876698     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep08663     Document Type: Article

References (57)

1. Katzen, F., Chang, G. & Kudlicki, W. The past, present and future of cell-free protein synthesis. Trends Biotechnol. 23, 150-156 (2005).
2. Carlson, E. D., Gan, R., Hodgman, C. E. & Jewett, M. C. Cell-free protein synthesis: applications come of age. Biotechnol. Adv. 30, 1185-1194 (2012).
3. Hodgman, C. E. & Jewett, M. C. Cell-free synthetic biology: thinking outside the cell. Metab. Eng. 14, 261-269 (2012).
4. Caschera, F. & Noireaux, V. Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription-translation system. Biochimie 99, 162-168 (2014).
5. Zawada, J. F. et al. Microscale to manufacturing scale-up of cell-free cytokine production-a new approach for shortening protein production development timelines. Biotechnol. Bioeng. 108, 1570-1578 (2011).
6. Yin, G. et al. Aglycosylated antibodies and antibody fragments produced in a scalable in vitro transcription-translation system. mAbs 4, 217-225 (2012).
7. Lu, Y., Welsh, J. P. & Swartz, J. R. Production and stabilization of the trimeric influenza hemagglutinin stem domain for potentially broadly protective influenza vaccines. Proc. Natl. Acad. Sci. U. S. A. 111, 125-130 (2013).
8. Kanter, G. et al. Cell-free production of scFv fusion proteins: an efficient approach for personalized lymphoma vaccines. Blood 109, 3393-3399 (2007).
9. Lui, B. H., Cochran, J. R. & Swartz, J. R. Discovery of improved EGF agonists using a novel in vitro screening platform. J. Mol. Biol. 413, 406-415 (2011).
10. Stapleton, J. A. & Swartz, J. R. Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenases. PLoS one 5, e15275 (2010).
11. Loscha, K. V. et al. Multiple-site labeling of proteins with unnatural amino acids. Angew. Chem. -Int. Edit. 51, 2243-2246 (2012).
12. Bundy, B. C. & Swartz, J. R. Site-specific incorporation of p-propargyloxyphenylalanine in a cell-free environment for direct protein-protein click conjugation. Bioconjugate Chem. 21, 255-263 (2010).
13. Hong, S. H. et al. Cell-free protein synthesis from a release factor 1 deficient Escherichia coli activates efficient and multiple site-specific non-standard amino acid incorporation. ACS Synth. Biol. 3, 398-409 (2013).
14. Albayrak, C. & Swartz, J. R. Cell-free co-production of an orthogonal transfer RNA activates efficient site-specific non-natural amino acid incorporation. Nucleic Acids Res. 41, 5949-5963 (2013).
15. Hong, S. H., Kwon, Y. C. & Jewett, M. C. Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis. Front. Chem. 2, 34 (2014).
16. Singh-Blom, A., Hughes, R. A. & Ellington, A. D. An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins. J. Biotechnol. 178, 12-22 (2014).
17. Bundy, B. C., Franciszkowicz, M. J. & Swartz, J. R. Escherichia coli-based cell-free synthesis of virus-like particles. Biotechnol. Bioeng. 100, 28-37 (2008).
18. Patel, K. G.&Swartz, J. R. Surface functionalization of virus-like particles by direct conjugation using azide-alkyne click chemistry. Bioconjugate Chem. 22, 376-387 (2011).
19. Bundy, B. C. & Swartz, J. R. Efficient disulfide bond formation in virus-like particles. J. Biotechnol. 154, 230-239 (2011).
20. Shin, J., Jardine, P. &Noireaux, V. Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS Synth. Biol. 1, 408-413 (2012).
21. Kim, D. M. & Swartz, J. R. Efficient production of a bioactive, multiple disulfide-bonded protein using modified extracts of Escherichia coli. Biotechnol. Bioeng. 85, 122-129 (2004).
22. 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. 25, 589-593 (2009).
23. Matsuda, T., Watanabe, S. & Kigawa, T. Cell-free synthesis system suitable for disulfide-containing proteins. Biochem. Biophys. Res. Commun. 431, 296-301 (2013).
24. Kwon, Y. C. et al. Cloning-independent expression and analysis of omega-transaminases by use of a cell-free protein synthesis system. Appl. Environ. Microbiol. 76, 6295-6298 (2010).
25. Kwon, Y. C. et al. Integrating cell-free biosyntheses of heme prosthetic group and apoenzyme for the synthesis of functional P450 monooxygenase. Biotechnol. Bioeng. 110, 1193-1200 (2013).
26. Kim, T. W. et al. High-throughput in vitro glycoside hydrolase (HIGH) screening for enzyme discovery. Angew. Chem. -Int. Edit. 50, 11215-11218 (2011).
27. Boyer, M. E., Stapleton, J. A., Kuchenreuther, J. M., Wang, C. W. & Swartz, J. R. Cell-free synthesis and maturation of [FeFe] hydrogenases. Biotechnol. Bioeng. 99, 59-67 (2008).
28. Catherine, C., Lee, K. H., Oh, S. J. & Kim, D. M. Cell-free platforms for flexible expression and screening of enzymes. Biotechnol. Adv. 31, 797-803 (2013).
29. Klammt, C. et al. Evaluation of detergents for the soluble expression of alphahelical and beta-barrel-type integral membrane proteins by a preparative scale individual cell-free expression system. FEBS J. 272, 6024-6038 (2005).
30. Wuu, J. J. & Swartz, J. R. High yield cell-free production of integral membrane proteins without refolding or detergents. Biochim. Biophys. Acta 1778, 1237-1250 (2008).
31. Chalmeau, J., Monina, N., Shin, J., Vieu, C. & Noireaux, V. alpha-Hemolysin pore formation into a supported phospholipid bilayer using cell-free expression. Biochim. Biophys. Acta 1808, 271-278 (2011).
32. Jewett, M. C., Fritz, B. R., Timmerman, L. E. & Church, G. M. In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation. Mol. Syst. Biol. 9, 678 (2013).
33. Fritz, B. R. & Jewett, M. C. The impact of transcriptional tuning on in vitro integrated rRNA transcription and ribosome construction. Nucleic Acids Res. 42, 6774-6785 (2014).
34. Liu, Y., Fritz, B. R., Anderson, M. J., Schoborg, J. A. & Jewett, M. C. Characterizing and alleviating substrate limitations for improved in vitro ribosome construction. ACS Synth. Biol., doi:10.1021/sb5002467 (2014).
35. He, M. Cell-free protein synthesis: applications in proteomics and biotechnology. New Biotech. 25, 126-132 (2008).
36. Chappell, J., Jensen, K. & Freemont, P. S. Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology. Nucleic Acids Res. 41, 3471-3481 (2013).
37. Pardee, K. et al. Paper-based synthetic gene networks. Cell 159, 940-954 (2014).
38. Shimizu, Y. et al. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751-755 (2001).
39. Asahara, H. & Chong, S. In vitro genetic reconstruction of bacterial transcription initiation by coupled synthesis and detection of RNA polymerase holoenzyme. Nucleic Acids Res. 38, e141 (2010).
40. Zhou, Y. et al. Engineering bacterial transcription regulation to create a synthetic in vitro two-hybrid system for protein interaction assays. J. Am. Chem. Soc. 136, 14031-14038 (2014).
41. Wang, H. H. et al. Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synth. Biol. 1, 43-52 (2012).
42. Pratt, J. M. Coupled transcription-translation in prokaryotic cell-free systems. [Hames, B. D. & Higgins, S. J. (ed.)] [179-209] (IRL Press, New York, 1984).
43. Zubay, G. In vitro synthesis of protein in microbial systems. Annu. Rev. Genet. 7, 267-287 (1973).
44. Nirenberg, M. W. & Matthaei, J. H. The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc. Natl. Acad. Sci. U. S. A. 47, 1588-1602 (1961).
45. Kim, T. W. et al. Simple procedures for the construction of a robust and cost-effective cell-free protein synthesis system. J. Biotechnol. 126, 554-561 (2006).
46. Sun, Z. Z. et al. Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. J. Vis. Exp. 79, e50762 (2013).
47. Shrestha, P., Holland, T. M. & Bundy, B. C. Streamlined extract preparation for Escherichia coli-based cell-free protein synthesis by sonication or bead vortex mixing. Biotechniques 53, 163-174 (2012).
48. Hong, S. H. et al. Improving cell-free protein synthesis through genome engineering of Escherichia coli lacking release factor 1. ChemBioChem, In press, doi:10.1002/cbic.201402708 (2014).
49. Zawada, J. F. Preparation and testing of E. coli S30 in vitro transcription translation extracts. Methods Mol. Biol. 805, 31-41 (2012).
50. Piir, K., Paier, A., Liiv, A., Tenson, T. & Maivali, U. Ribosome degradation in growing bacteria. EMBO Rep. 12, 458-462 (2011).
51. Takahashi, M. K. et al. Rapidly Characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems. ACS Synth. Biol. doi:10.1021/sb400206c (2014).
52. Underwood, K. A., Swartz, J. R. & Puglisi, J. D. Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis. Biotechnol. Bioeng. 91, 425-435 (2005).
53. Calhoun, K. A. & Swartz, J. R. Energy systems for ATP regeneration in cell-free protein synthesis reactions. Methods Mol. Biol. 375, 3-17 (2007).
54. Kim, D. M. & Swartz, J. R. Prolonging cell-free protein synthesis by selective reagent additions. Biotechnol. Prog. 16, 385-390 (2000).
55. 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. 4, 220 (2008).
56. Swartz, J. R., Jewett, M. C. & Woodrow, K. A. Cell-free protein synthesis with prokaryotic combined transcription-translation. Methods Mol. Biol. 267, 169-182 (2004).
57. Kim, D. M., Kigawa, T., Choi, C. Y. & Yokoyama, S. A highly efficient cell-free protein synthesis system from Escherichia coli. Eur. J. Biochem. 239, 881-886 (1996).