Streamlined extract preparation for Escherichia coli-based cell-free protein synthesis by sonication or bead vortex mixing

BioTechniques

Volumn 53, Issue 3, 2012, Pages 163-174

  Shrestha, Prashanta ^a   Holland, Troy Michael ^a   Bundy, Bradley Charles ^a  

^a Department of Electrical and Computer Engineering   (United States)

Author keywords

Bead mill; Cell free; Cell free protein synthesis; CFPS; Escherichia coli; Extracts preparation; In vitro protein synthesis; Sonication; Vortex mixing

Indexed keywords

LYSOZYME; RNA POLYMERASE;

ARTICLE; BACTERIAL STRAIN; BEAD VORTEX MIXING; BIOTECHNOLOGICAL PROCEDURES; CELL FREE SYSTEM; CELL VIABILITY; ESCHERICHIA COLI; FERMENTATION TECHNIQUE; FREEZE THAWING; NONHUMAN; PH; PROTEIN PURIFICATION; PROTEIN SYNTHESIS; TEMPERATURE SENSITIVITY; ULTRASOUND;

BIOTECHNOLOGY; CELL CULTURE TECHNIQUES; CELL EXTRACTS; CELL-FREE SYSTEM; COLD TEMPERATURE; ESCHERICHIA COLI PROTEINS; FERMENTATION; MURAMIDASE; SONICATION;

ESCHERICHIA COLI; PROKARYOTA;

EID: 84866397327     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/0000113924     Document Type: Article

References (53)

1. Bretthauer, R.K., L. Marcus, J. Chaloupka, H.O. Halvorson, and R.M. Bock. 1963. Amino acid incorporation into protein by cell-free extracts of yeast. Biochemistry 2:1079-1084.
2. Zubay, G. 1973. In vitro synthesis of protein in microbial systems. Annu. Rev. Genet. 7:267-287.
3. Pratt, J.M. 1984. Coupled transcription-translation in prokarytoic cell-free systems, p. 179-209. In B.D. Hames, S.J. Higgins (Eds.), Transcription and Translation: A Practical Approach. IRL Press, New York.
4. Kigawa, T., T. Yabuki, N. Matsuda, T. Matsuda, R. Nakajima, A. Tanaka, and S. Yokoyama. 2004. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J. Struct. Funct. Genomics 5:63-68.
5. Liu, D.V., J.F. Zawada, and J.R. Swartz. 2005. Streamlining Escherichia coli S30 extract preparation for economical cell-free protein synthesis. Biotechnol. Prog. 21:460-465.
6. Kim, T.W., J.W. Keum, I.S. Oh, C.Y. Choi, C.G. Park, and D.M. Kim. 2006. Simple procedures for the construction of a robust and cost-effective cell-free protein synthesis system. J. Biotechnol. 126:554-561.
7. Yang, W.C., K.G. Patel, H.E. Wong, and J.R. Swartz. 2012. Simplifying and streamlining Escherichia coli-based cell-free protein synthesis. Biotechnol. Prog. 28:413-420.
8. Ezure, T., T. Suzuki, S. Higashide, E. Shintani, K. Endo, S. Kobayashi, M. Shikata, M. Ito, et al. 2006. Cell-free protein synthesis system prepared from insect cells by freeze-thawing. Biotechnol. Prog. 22:1570-1577.
9. Takai, K., T. Sawasaki, and Y. Endo. 2010. Practical cell-free protein synthesis system using purified wheat embryos. Nat. Protocols 5:227-238.
10. Nirenberg, M.W. 1963. Cell-free protein synthesis directed by messenger RNA. Methods Enzymol. 6:17-23.
11. Avenaud, P., M. Castroviejo, S. Claret, J. Rosenbaum, F. Megraud, and A. Menard. 2004. Expression and activity of the cytolethal distending toxin of Helicobacter hepaticus. Biochem. Biophys. Res. Commun. 318:739-745.
12. Smith, M.T., C.T. Varner, D.B. Bush, and B.C. Bundy. 2012. The incorporation of the A2 protein to produce novel Qbeta virus-like particles using cell-free protein synthesis. Biotechnol. Prog. 28:549-555.
13. Bundy, B.C., M.J. Franciszkowicz, and J.R. Swartz. 2008. Escherichia coli-based cell-free synthesis of virus-like particles. Biotechnol. Bioeng. 100:28-37.
14. Bundy, B.C. and J.R. Swartz. 2011. Efficient disulfide bond formation in virus-like particles. J. Biotechnol. 154:230-239.
15. Isaksson, L., J. Enberg, R. Neutze, B. Göran Karlsson, and A. Pedersen. 2012. Expression screening of membrane proteins with cell-free protein synthesis. Protein Expr. Purif. 82:218-225.
16. Hovijitra, N.T., J.J. Wuu, B. Peaker, and J.R. Swartz. 2009. Cell-free synthesis of functional aquaporin Z in synthetic liposomes. Biotechnol. Bioeng. 104:40-49.
17. Klammt, C., F. Lohr, B. Schafer, W. Haase, V. Dotsch, H. Ruterjans, C. Glaubitz, and F. Bernhard. 2004. High level cell-free expression and specific labeling of integral membrane proteins. Eur. J. Biochem. 271:568-580.
18. Bundy, B.C. and J.R. Swartz. 2010. Site-specific incorporation of p-propargyloxyphenylalanine in a cell-free environment for direct protein-protein click conjugation. Bioconjug. Chem. 21:255-263.
19. Muranaka, N., M. Miura, H. Taira, and T. Hohsaka. 2007. Incorporation of unnatural non-α-amino acids into the N terminus of proteins in a cell-free translation system. Chembiochem 8:1650-1653.
20. Ozawa, K., K.V. Loscha, K.V. Kuppan, C.T. Loh, N.E. Dixon, and G. Otting. 2012. High-yield cell-free protein synthesis for site-specific incorporation of unnatural amino acids at two sites. Biochem. Biophys. Res. Commun. 418:652-656.
21. Patel, K.G. and J.R. Swartz. 2011. Surface functionalization of virus-like particles by direct conjugation using azide-alkyne click chemistry. Bioconjug. Chem. 22:376-387.
22. Woodrow, K.A. and J.R. Swartz. 2007. A sequential expression system for high-throughput functional genomic analysis. Proteomics 7:3870-3879.
23. Hanes, J. and A. Plückthun. 1997. In vitro selection and evolution of functional proteins by using ribosome display. Proc. Natl. Acad. Sci. USA 94:4937-4942.
24. Stapleton, J.A. and J.R. Swartz. 2010. Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenases. PLoS One 5:e15275.
25. Fallah-Araghi, A., J.C. Baret, M. Ryckelynck, and A.D. Griffiths. 2012. A completely in vitro ultra high-throughput droplet-based microfluidic screening system for protein engineering and directed evolution. Lab Chip 12:882-891.
26. Beebe, E.T., S. Makino, A. Nozawa, Y. Matsubara, R.O. Frederick, J.G. Primm, M.A. Goren, and B.G. Fox. 2011. Robotic large-scale application of wheat cell-free translation to structural studies including membrane proteins. N Biotechnol 28:239-249.
27. Zubay, G. 1973. In vitro synthesis of protein in microbial systems. Annu. Rev. Genet. 7:267-287.
28. Anderson, C.W., J.W. Straus, and B.S. Dudock. 1983. Preparation of a cell-free protein-synthesizing system from wheat germ. Methods Enzymol. 101:635-644.
29. Spirin, A.S., V.I. Baranov, L.A. Ryabova, S.Y. Ovodov, and Y.B. Alakhov. 1988. A continuous cell-free translation system capable of producing polypeptides in high yield. Science 242:1162-1164.
30. Calhoun, K.A. and J.R. Swartz. 2005. An economical method for cell-free protein synthesis using glucose and nucleoside monophosphates. Biotechnol. Prog. 21:1146-1153.
31. Calhoun, K.A. and J.R. Swartz. 2005. Energizing cell-free protein synthesis with glucose metabolism. Biotechnol. Bioeng. 90:606-613.
32. Kim, T.W., J.W. Keum, I.S. Oh, C.Y. Choi, H.C. Kim, and D.M. Kim. 2007. An economical and highly productive cell-free protein synthesis system utilizing fructose-1,6-bisphosphate as an energy source. J. Biotechnol. 130:389-393.
33. Jewett, M.C. and J.R. Swartz. 2004. Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis. Biotechnol. Bioeng. 86:19-26.
34. Jewett, M.C., K.A. Calhoun, A. Voloshin, J.J. Wuu, and J.R. Swartz. 2008. An integrated cell-free metabolic platform for protein production and synthetic biology. Mol. Syst. Biol. 4:220.
35. Jun, S.Y., S.H. Kang, and K.H. Lee. 2008. Continuous-exchange cell-free protein synthesis using PCR-generated DNA and an RNase E-deficient extract. BioTechniques 44:387-391.
36. Lesley, S.A., M.A. Brow, and R.R. Burgess. 1991. 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. 266:2632-2638.
37. Carlson, E.D., R. Gan, C.E. Hodgman, and M.C. Jewett. 2011. Cell-free protein synthesis: applications come of age. Biotechnol. Adv. 30:1185-1194.
38. Ahn, J.H., H.S. Chu, T.W. Kim, I.S. Oh, C.Y. Choi, G.H. Hahn, C.G. Park, and D.M. Kim. 2005. Cell-free synthesis of recombinant proteins from PCR-amplified genes at a comparable productivity to that of plasmid-based reactions. Biochem. Biophys. Res. Commun. 338:1346-1352.
39. Young, T.S., I. Ahmad, J.A. Yin, and P.G. Schultz. 2010. An enhanced system for unnatural amino acid mutagenesis in E. coli. J. Mol. Biol. 395:361-374.
40. Simpson, R.J. 2010. Large-scale extraction of recombinant proteins from bacteria. Cold Spring Harb. Protoc. 2010:pdb. prot5484.
41. Jiang, Y.-X., J.-G. Wu, K.-Q. Yu, C.-X. Ai, F. Zou, and H.-W. Zhou. 2011. Integrated lysis procedures reduce extraction biases of microbial DNA from mangrove sediment. J. Biosci. Bioeng. 111:153-157.
42. Johnson, B.H. and M.H. Hecht. 1994. Recombinant proteins can be isolated from E. coli cells by repeated cycles of freezing and thawing. Biotechnology (N Y) 12:1357-1360.
43. Harlow, E. and D. Lane. 2006. Immunoprecipitation: lysing bacteria by sonication. Cold Spring Harb. Protoc. 2006:pdb. prot4532.
44. Benov, L. and J. Al-Ibraheem. 2002. Disrupting Escherichia coli: a comparison of methods. J. Biochem. Mol. Biol. 35:428-431.
45. Breiling, A. and V. Orlando. 2006. Chromatin immunoprecipitation (ChIP) of protein complexes: mapping of genomic targets of nuclear proteins in cultured cells. Cold Spring Harb. Protoc. 2006:pdb. prot4560.
46. Simpson, R.J. 2010. Small-scale extraction of recombinant proteins from bacteria. Cold Spring Harb. Protoc. 2010:pdb. prot5483.
47. Futai, M. 1974. Orientation of membrane vesicles from Escherichia coli prepared by different procedures. J. Membr. Biol. 15:15-28.
48. Ho, C.W., W.S. Tan, W.B. Yap, T.C. Ling, and B.T. Tey. 2008. Comparative evaluation of different cell disruption methods for the release of recombinant hepatitis B core antigen from Escherichia coli. Biotechnol. Bioprocess Eng. 13:577-583.
49. Hummel, W. and M.-R. Kula. 1989. Simple method for small-scale disruption of bacteria and yeasts. J. Microbiol. Methods 9:201-209.
50. Miller, D.N., J.E. Bryant, E.L. Madsen, and W.C. Ghiorse. 1999. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65:4715-4724.
51. Kim, D.M., T. Kigawa, C.Y. Choi, and S. Yokoyama. 1996. A highly efficient cell-free protein synthesis system from Escherichia coli. Eur. J. Biochem. 239:881-886.
52. Zheng, H., J. Yin, Z. Gao, H. Huang, X. Ji, and C. Dou. 2011. Disruption of Chlorella vulgaris cells for the release of biodiesel-producing lipids: a comparison of grinding, ultrasonication, bead milling, enzymatic lysis, and microwaves. Appl. Biochem. Biotechnol. 164:1215-1224.
53. Doulah, M.S. 1977. Mechanism of disintegration of biological cells in ultrasonic cavitation. Biotechnol. Bioeng. 19:649-660.