Chapter 2 Development of Key Technologies for High-Throughput Cell-Free Protein Production with the Extract from Wheat Embryos

Advances in Protein Chemistry and Structural Biology

Volumn 75, Issue C, 2008, Pages 53-84

  Takai, Kazuyuki ^a   Sawasaki, Tatsuya ^a   Endo, Yaeta ^a  

^a EHIME UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT EXTRACT; VEGETABLE PROTEIN;

BIOSYNTHESIS; HIGH THROUGHPUT SCREENING; ISOLATION AND PURIFICATION; METHODOLOGY; PRENATAL DEVELOPMENT; REVIEW; WHEAT;

HIGH-THROUGHPUT SCREENING ASSAYS; PLANT EXTRACTS; PLANT PROTEINS; TRITICUM;

EID: 76649137521     PISSN: 18761623     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-3233(07)75002-7     Document Type: Review

References (84)

1. Abe M., Ohno S., Yokogawa T., Nakanishi T., Arisaka F., Hosoya T., Hiramatsu T., Suzuki M., Ogasawara T., Sawasaki T., Nishikawa K., Kitamura M., Hori H., and Endo Y. Detection of structural changes in a cofactor binding protein by using a wheat germ cell-free protein synthesis system coupled with unnatural amino acid probing. Proteins 67 (2007) 643-652
2. Abraham A.K., Olsnes S., and Pihl A. Fidelity of protein synthesis in vitro is increased in the presence of spermidine. FEBS Lett. 101 (1979) 93-96
3. Ahn J., Chu H., Kim T., Oh I., Choi C., Hahn G., Park C., and Kim D. 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 (2005) 1346-1352
4. Alekhina O.M., Vassilenko K.S., and Spirin A.S. Translation of non-capped mRNAs in a eukaryotic cell-free system: Acceleration of initiation rate in the course of polysome formation. Nucleic Acids Res. 35 (2007) 6547-6559
5. Alkalaeva E.Z., Pisarev A.V., Frolova L.Y., Kisselev L.L., and Pestova T.V. In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3. Cell 125 (2006) 1125-1136
6. Coleman W.H., and Roberts W.K. Factor requirements for the tritin inactivation of animal cell ribosomes. Biochim. Biophys. Acta 654 (1981) 57-66
7. Endo Y., and Sawasaki T. Cell-free expression systems for eukaryotic protein production. Curr. Opin. Biotechnol. 17 (2006) 373-380
8. Endo Y., and Tsurugi K. RNA N-glycosidase activity of ricin A-chain. Mechanism of action of the toxic lectin ricin on eukaryotic ribosomes. J. Biol. Chem. 262 (1987) 8128-8130
9. Endo Y., Mitsui K., Motizuki M., and Tsurugi K. The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes. The site and the characteristics of the modification in 28 S ribosomal RNA caused by the toxins. J. Biol. Chem. 262 (1987) 5908-5912
10. Endo Y., Otsuzuki S., Ito K., and Miura K. Production of an enzymatic active protein using a continuous flow cell-free translation system. J. Biotechnol. 25 (1992) 221-230
11. Erickson A.H., and Blobel G. Cell-free translation of messenger RNA in a wheat germ system. Methods Enzymol. 96 (1983) 38-50
12. Gallie D.R. A tale of two termini: A functional interaction between the termini of an mRNA is a prerequisite for efficient translation initiation. Gene 216 (1998) 1-11
13. Gallie D.R., and Walbot V. Identification of the motifs within the tobacco mosaic virus 5′-leader responsible for enhancing translation. Nucleic Acids Res. 20 (1992) 4631-4638
14. Gallie D.R., Sleat D.E., Watts J.W., Turner P.C., and Wilson T.M. The 5′-leader sequence of tobacco mosaic virus RNA enhances the expression of foreign gene transcripts in vitro and in vivo. Nucleic Acids Res. 15 (1987) 3257-3273
15. Hirano N., Sawasaki T., Tozawa Y., Endo Y., and Takai K. Tolerance for random recombination of domains in prokaryotic and eukaryotic translation systems: Limited interdomain misfolding in a eukaryotic translation system. Proteins 64 (2006) 343-354
16. Igarashi K., Hashimoto S., Miyake A., Kashiwagi K., and Hirose S. Increase of fidelity of polypeptide synthesis by spermidine in eukaryotic cell-free systems. Eur. J. Biochem. 128 (1982) 597-604
17. Ishihara G., Goto M., Saeki M., Ito K., Hori T., Kigawa T., Shirouzu M., and Yokoyama S. Expression of G protein coupled receptors in a cell-free translational system using detergents and thioredoxin-fusion vectors. Protein Expr. Purif. 41 (2005) 27-37
18. Ishikawa K., Watanabe M., Kuroita T., Uchiyama I., Bujnicki J.M., Kawakami B., Tanokura M., and Kobayashi I. Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5′-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi. Nucleic Acids Res. 33 (2005) e112
19. Ito K., and Igarashi K. The increase by spermidine of fidelity of protamine synthesis in a wheat-germ cell-free system. Eur. J. Biochem. 156 (1986) 505-510
20. Jackson M., Pratt J.M., and Holland I.B. Enhanced polypeptide synthesis programmed by linear DNA fragments in cell-free extracts lacking exonuclease V. FEBS Lett. 163 (1983) 221-224
21. Jelenc P.C., and Kurland C.G. Nucleoside triphosphate regeneration decreases the frequency of translation errors. Proc. Natl Acad. Sci. USA 76 (1979) 3174-3178
22. Jun S.Y., Kang S.H., and Lee K. Continuous-exchange cell-free protein synthesis using PCR-generated DNA and an RNase E-deficient extract. BioTechniques 44 (2008) 387-391
23. Kainosho M., Torizawa T., Iwashita Y., Terauchi T., Mei Ono A., and Güntert P. Optimal isotope labelling for NMR protein structure determinations. Nature 440 (2006) 52-57
24. Kamura N., Sawasaki T., Kasahara Y., Takai K., and Endo Y. Selection of 5′-untranslated sequences that enhance initiation of translation in a cell-free protein synthesis system from wheat embryos. Bioorg. Med. Chem. Lett. 15 (2005) 5402-5406
25. Kanno T., Kasai K., Ikejiri-Kanno Y., Wakasa K., and Tozawa Y. In vitro reconstitution of rice anthranilate synthase: Distinct functional properties of the alpha subunits OASA1 and OASA2. Plant Mol. Biol. 54 (2004) 11-22
26. Kanno T., Komatsu A., Kasai K., Dubouzet J.G., Sakurai M., Ikejiri-Kanno Y., Wakasa K., and Tozawa Y. Structure-based in vitro engineering of the anthranilate synthase, a metabolic key enzyme in the plant tryptophan pathway. Plant Physiol. 138 (2005) 2260-2268
27. Kanno T., Kitano M., Kato R., Omori A., Endo Y., and Tozawa Y. Sequence specificity and efficiency of protein N-terminal methionine elimination in wheat-embryo cell-free system. Protein Expr. Purif. 52 (2007) 59-65
28. Kawasaki T., Gouda M.D., Sawasaki T., Takai K., and Endo Y. Efficient synthesis of a disulfide-containing protein through a batch cell-free system from wheat germ. Eur. J. Biochem. 270 (2003) 4780-4786
29. Kigawa T., and Yokoyama S. A continuous cell-free protein synthesis system for coupled transcription-translation. J. Biochem. 110 (1991) 166-168
30. Kigawa T., Yabuki T., Yoshida Y., Tsutsui M., Ito Y., Shibata T., and Yokoyama S. Cell-free production and stable-isotope labeling of milligram quantities of proteins. FEBS Lett. 442 (1999) 15-19
31. Kim D.-M., Kigawa T., Choi C.-Y., and Yokoyama S. A highly efficient cell-free protein synthesis system from Escherichia coli. Eur. J. Biochem. 239 (1996) 881-886
32. Klammt C., Löhr F., Schäfer B., Haase W., Dötsch V., Rüterjans H., Glaubitz C., and Bernhard F. High level cell-free expression and specific labeling of integral membrane proteins. Eur. J. Biochem. 271 (2004) 568-580
33. Klammt C., Schwarz D., Fendler K., Haase W., Dötsch V., and Bernhard F. Evaluation of detergents for the soluble expression of alpha-helical and beta-barrel-type integral membrane proteins by a preparative scale individual cell-free expression system. FEBS J. 272 (2005) 6024-6038
34. Klammt C., Schwarz D., Löhr F., Schneider B., Dötsch V., and Bernhard F. Cell-free expression as an emerging technique for the large scale production of integral membrane protein. FEBS J. 273 (2006) 4141-4153
35. Klammt C., Schwarz D., Eifler N., Engel A., Piehler J., Haase W., Hahn S., Dötsch V., and Bernhard F. Cell-free production of G protein-coupled receptors for functional and structural studies. J. Struct. Biol. 158 (2007) 482-493
36. Kobayashi T., Kodani Y., Nozawa A., Endo Y., and Sawasaki T. DNA-binding profiling of human hormone nuclear receptors via fluorescence correlation spectroscopy in a cell-free system. FEBS Lett. 582 (2008) 2737-2744
37. Kohno T. Production of proteins for NMR studies using the wheat germ cell-free system. Methods Mol. Biol. 310 (2005) 169-185
38. Kohno T., and Endo Y. Production of protein for nuclear magnetic resonance study using the wheat germ cell-free system. Methods Mol. Biol. 375 (2007) 257-272
39. Kopeina G.S., Afonina Z.A., Gromova K.V., Shirokov V.A., Vasiliev V.D., and Spirin A.S. Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA. Nucleic Acids Res. 36 (2008) 2476-2488
40. Kurland C.G. Translational accuracy in vitro. Cell 28 (1982) 201-202
41. Lingappa J.R., Hill R.L., Wong M.L., and Hegde R.S. A multistep, ATP-dependent pathway for assembly of human immunodeficiency virus capsids in a cell-free system. J. Cell Biol. 136 (1997) 567-581
42. Lingappa J.R., Newman M.A., Klein K.C., and Dooher J.E. Comparing capsid assembly of primate lentiviruses and hepatitis B virus using cell-free systems. Virology 333 (2005) 114-123
43. Madin K., Sawasaki T., Ogasawara T., and 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 97 (2000) 559-564
44. Mangus D.A., Evans M.C., and Jacobson A. Poly(A)-binding proteins: Multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol. 4 (2003) 223
45. Marcus A., and Feeley J. Activation of protein synthesis in the imbibitions phase of seed germination. Proc. Natl Acad. Sci. USA 51 (1964) 1075-1079
46. Martemyanov K.A., Spirin A.S., and Gudkov A.T. Direct expression of PCR products in a cell-free transcription/translation system: Synthesis of antibacterial peptide cecropin. FEBS Lett. 414 (1997) 268-270
47. Masaoka T., Nishi M., Ryo A., Endo Y., and Sawasaki T. The wheat germ cell-free based screening of protein substrates of calcium/calmodulin-dependent protein kinase II delta. FEBS Lett. 582 (2008) 1795-1801
48. Massiah A.J., and Hartley M.R. Wheat ribosome-inactivating proteins: Seed and leaf forms with different specificities and cofactor requirements. Planta 197 (1995) 633-640
49. 7G46) methyltransferase (Trm8-Trm82 complex) in a wheat germ cell-free translation system. J. Biotechnol. 133 (2008) 453-460
50. Michel-Reydellet N., Woodrow K., and Swartz J. 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
51. Miyazono K., Watanabe M., Kosinski J., Ishikawa K., Kamo M., Sawasaki T., Nagata J.M., Bujnicki J.M., Endo Y., Tanokura M., and Kobayashi I. Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res. 35 (2007) 1908-1918
52. Morita E.H., Sawasaki T., Tanaka R., Endo Y., and Kohno T. A wheat germ cell-free system is a novel way to screen protein folding and function. Protein Sci. 12 (2003) 1216-1221
53. 15N HSQC spectra with a wheat germ cell-free protein synthesis system. J. Biomol. NMR 30 (2004) 37-45
54. Netzer W.J., and Hartl F.U. Recombination of protein domains facilitated by co-translational folding in eukaryotes. Nature 388 (1997) 343-349
55. Noren C.J., Anthony-Cahill S.J., Griffith M.C., and Schultz P.G. A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244 (1989) 182-188
56. Nozawa A., Nanamiya H., Miyata T., Linka N., Endo Y., Weber A.P.M., and Tozawa Y. A cell-free translation and proteoliposome reconstitution system for functional analysis of plant solute transporters. Plant Cell Physiol. 48 (2007) 1815-1820
57. Ogasawara T., Sawasaki T., Morishita R., Ozawa A., Madin K., and Endo Y. A new class of enzyme acting on damaged ribosomes: Ribosomal RNA apurinic site specific lyase found in wheat germ. EMBO J. 18 (1999) 6522-6531
58. Ozawa A., Sawasaki T., Takai K., Uchiumi T., Hori H., and Endo Y. RALyase; a terminator of elongation function of depurinated ribosomes. FEBS Lett. 555 (2003) 455-458
59. Park S.W., Vepachedu R., Sharma N., and Vivanco J.M. Ribosome-inactivating proteins in plant biology. Planta 219 (2004) 1093-1096
60. Pavlov M.Y., and Ehrenberg M. Rate of translation of natural mRNAs in an optimized in vitro system. Arch. Biochem. Biophys. 328 (1996) 9-16
61. Pisarev A.V., Hellen C.U.T., and Pestova T.V. Recycling of eukaryotic posttermination ribosomal complexes. Cell 131 (2007) 286-299
62. Qin Y., Polacek N., Vesper O., Staub E., Einfeldt E., Wilson D.N., and Nierhaus K.H. The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell 127 (2006) 721-733
63. Roberts B.E., and Paterson B.M. Efficient translation of tobacco mosaic virus RNA and rabbit globin 9S RNA in a cell-free system from commercial wheat germ. Proc. Natl Acad. Sci. USA 70 (1973) 2330-2334
64. Sawasaki T., and Endo Y. Protein expression in the wheat-germ cell-free system. In: Dyson M.R., and Durocher Y. (Eds). Expression Systems. The METHODS EXPRESS series (2007), Scion Publishing Ltd, Bloxham, Oxfordshire, UK 87-108
65. Sawasaki T., Ogasawara T., Morishita R., and Endo Y. A cell-free protein synthesis system for high-throughput proteomics. Proc. Natl Acad. Sci. USA 99 (2002) 14652-14657
66. Sawasaki T., Hasegawa Y., Tsuchimochi M., Kamura N., Ogasawara T., Kuroita T., and Endo Y. A bilayer cell-free protein synthesis system for high-throughput screening of gene products. FEBS Lett. 514 (2002) 102-105
67. Sawasaki T., Hasegawa Y., Morishita R., Seki M., Shinozaki K., and Endo Y. Genome-scale, biochemical annotation method based on the wheat germ cell-free protein synthesis system. Phytochemistry 65 (2004) 1549-1555
68. Sawasaki T., Kamura N., Matsunaga S., Saeki M., Tsuchimochi M., Morishita R., and Endo Y. Arabidopsis HY5 protein functions as a DNA-binding tag for purification and functional immobilization of proteins on agarose/DNA microplate. FEBS Lett. 582 (2008) 221-228
69. Sawasaki T., Nishihara M., and Endo Y. RIP and RALyase cleave the sarcin/ricin domain, a critical domain for ribosome function, during senescence of wheat coleoptiles. Biochem. Biophys. Res. Commun. 370 (2008) 561-565
70. Schatz P.J. Use of peptide libraries to map the substrate specificity of a peptide-modifying enzyme: A 13 residue consensus peptide specifies biotinylation in Escherichia coli. Biotechnology (N.Y.) 11 (1993) 1138-1143
71. Shimizu Y., Inoue A., Tomari Y., Suzuki T., Yokogawa T., Nishikawa K., and Ueda T. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19 (2001) 751-755
72. Spirin A.S., Baranov V.I., Ryabova L.A., Ovodov S.Y., and Alakhov Y.B. A continuous cell-free translation system capable of producing polypeptides in high yield. Science 242 (1988) 1162-1164
73. Stewart T.S., Hruby D.E., Sharma O.K., and Roberts W.K. An ATP-dependent inhibition of protein synthesis in ascites cell extracts by wheat germ protein. Biochim. Biophys. Acta 479 (1977) 31-38
74. Stirpe F. Ribosome-inactivating proteins. Toxicon 44 (2004) 371-383
75. Tanguay R.L., and Gallie D.R. Isolation and characterization of the 102-kilodalton RNA-binding protein that binds to the 5′ and 3′ translational enhancers of tobacco mosaic virus RNA. J. Biol. Chem. 271 (1996) 14316-14322
76. Taylor B.E., and Irvin J.D. Depurination of plant ribosomes by pokeweed antiviral protein. FEBS Lett. 273 (1990) 144-146
77. Trbovic N., Klammt C., Koglin A., Löhr F., Bernhard F., and Dötsch V. Efficient strategy for the rapid backbone assignment of membrane proteins. J. Am. Chem. Soc. 127 (2005) 13504-13505
78. Tsuboi T., Takeo S., Iriko H., Jin L., Tsuchimochi M., Matsuda S., Han E.T., Otsuki H., Kaneko J., Sattabongkot J., Udomsangpetch R., Sawasaki T., Torii M., and Endo Y. Wheat germ cell-free system-based production of malaria proteins for discovery of novel vaccine candidates. Infect. Immun. 76 (2008) 1702-1708
79. Vinarov D.A., Lytle B.L., Peterson F.C., Tyler E.M., Volkman B.F., and Markley J.L. Cell-free protein production and labeling protocol for NMR-based structural proteomics. Nat. Methods 1 (2004) 149-153
80. Vinarov D.A., Loushin Newman C.L., and Markley J.L. Wheat germ cell-free platform for eukaryotic protein production. FEBS J. 273 (2006) 4160-4169
81. Wagner E.G., Jelenc P.C., Ehrenberg M., and Kurland C.G. Rate of elongation of polyphenylalanine in vitro. Eur. J. Biochem. 122 (1982) 193-197
82. Wells D.R., Tanguay R.L., Le H., and Gallie D.R. HSP101 functions as a specific translational regulatory protein whose activity is regulated by nutrient status. Genes Dev. 12 (1998) 3236-3251
83. Yabuki T., Motoda Y., Hanada K., Nunokawa E., Saito M., Seki E., Inoue M., Kigawa T., and Yokoyama S. A robust two-step PCR method of template DNA production for high-throughput cell-free protein synthesis. J. Struct. Funct. Genomics 8 (2007) 173-191
84. Yang H.L., Ivashkiv L., Chen H.Z., Zubay G., and Cashel M. Cell-free coupled transcription-translation system for investigation of linear DNA segments. Proc. Natl Acad. Sci. USA 77 (1980) 7029-7033