Real-Time Single-Molecule Observation of Green Fluorescent Protein Synthesis by Immobilized Ribosomes

Methods in Molecular Biology

Volumn 778, Issue , 2011, Pages 215-228

  Iizuka, Ryo ^a   Funatsu, Takashi ^a   Uemura, Sotaro ^b  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

Green fluorescent protein; Protein folding; Ribosome display; SecM; Single molecule fluorescence imaging; Total internal reflection fluorescence microscopy; Translation; Translation arrest

Indexed keywords

GREEN FLUORESCENT PROTEIN;

ARTICLE; BIOLOGICAL MODEL; FLUORESCENCE MICROSCOPY; METABOLISM; METHODOLOGY; PROTEIN FOLDING; RIBOSOME;

GREEN FLUORESCENT PROTEINS; MICROSCOPY, FLUORESCENCE; MODELS, BIOLOGICAL; PROTEIN FOLDING; RIBOSOMES;

EID: 80054772954     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-261-8_14     Document Type: Chapter

References (27)

1. Fedorov, A. N., and Baldwin, T. O. (1997) Cotranslational protein folding. J. Biol. Chem. 272, 32715–32718.
2. Uemura, S., Iizuka, R., Ueno, T., Shimizu, Y., Taguchi, H., Ueda, T., Puglisi, J. D., and Funatsu, T. (2008) Single molecule imaging of full protein synthesis by immobilized ribosomes. Nucleic Acids Res. 36, e70.
3. Nakatogawa, H., and Ito, K. (2002) The ribosomal exit tunnel functions as a discriminating gate. Cell 108, 629–636.
4. Ban, N., Nissen, P., Hansen, J., Moore, P. B., and Steitz, T. A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920.
5. Nissen, P., Hansen, J., Ban, N., Moore, P. B., and Steitz, T. A. (2000) The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930.
6. Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H., and Noller, H. F. (2001) Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883–896.
7. Dorywalska, M., Blanchard, S. C., Gonzalez, R. L., Kim, H. D., Chu, S., and Puglisi, J. D. (2005) Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res. 33, 182–189.
8. Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., and Ueda, T. (2001) Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751–755.
9. Shimizu, Y., Kanamori, T., and Ueda, T. (2005) Protein synthesis by pure translation systems. Methods 36, 299–304.
10. Kolb, V. A., Makeyev, E. V., Ward, W. W., and Spirin, A. S. (1996) Synthesis and maturation of green fluorescent protein in a cell-free translation. Biotechnol. Lett. 18, 1447–1452.
11. Jermutus, L., Kolly, R., Földes-Papp, Z., Hanes, J., Rigler, R., and Plückthun, A. (2002) Ligand binding of a ribosome-displayed protein detected in solution at the single molecule level by fluorescence correlation spectroscopy. Eur. Biophys. J. 31, 179–184.
12. Ito, Y., Suzuki, M., and Husimi, Y. (1999) A novel mutant of green fluorescent protein with enhanced sensitivity for microanalysis at 488 nm excitation. Biochem. Biophys. Res. Commun. 264, 556–560.
13. Patterson, G. H., Knobel, S. M., Sharif, W. D., Kain, S. R., and Piston, D. W. (1997) Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. Biophys. J. 73, 2782–2790.
14. Crameri, A., Whitehorn, E. A., Tate, E., and Stemmer, W. P. (1996) Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat. Biotechnol. 14, 315–319.
15. Matsuura, T., and Plückthun, A. (2003) Selection based on the folding properties of proteins with ribosome display. FEBS Lett. 539, 24–28.
16. Matsuura, T., Yanagida, H., Ushioda, J., Urabe, I., and Yomo, T. (2007) Nascent chain, mRNA, and ribosome complexes generated by a pure translation system. Biochem. Biophys. Res. Commun. 352, 372–377.
17. Evans, M. S., Ugrinov, K. G., Frese, M. A., and Clark, P. L. (2005) Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro. Nat. Methods 2, 757–762.
18. Muto, H., Nakatogawa, H., and Ito, K. (2006) Genetically encoded but nonpolypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall. Mol. Cell 22, 545–552.
19. Ohashi, H., Shimizu, Y., Ying, B. W., and Ueda, T. (2007) Efficient protein selection based on ribosome display system with purified components. Biochem. Biophys. Res. Commun. 352, 270–276.
20. Hayes, C. S., Bose, B., and Sauer, R. T. (2002) Proline residues at the C-terminus of nascent chains induce SsrA-tagging during transla tion termination. J. Biol. Chem. 277, 33825–33832.
21. Hayes, C. S., and Sauer, R. T. (2003) Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol. Cell 12, 903–911.
22. Powers, T., and Noller, H. F. (1991) A functional pseudoknot in 16S ribosomal RNA. EMBO J. 10, 2203–2214.
23. Chalfie, M., Tu, Y., Euskirchen, G., Ward, W. W., and Prasher, D. C. (1994) Green fluorescent protein as a marker for gene expression. Science 263, 802–805.
24. Forrer, P., and Jaussi, R. (1998) High-level expression of soluble heterologous proteins in the cytoplasm of Escherichia coli by fusion to the bacteriophage lambda head protein D. Gene 224, 45–52.
25. Yang, F., Forrer, P., Dauter, Z., Conway, J. F., Cheng, N., Cerritelli, M. E., Steven, A. C., Plückthun, A., and Wlodawer, A. (2000) Novel fold and capsid-binding properties of the l-phage display platform protein gpD. Nat. Struct. Biol. 7, 230–237.
26. Olins, P. O., and Rangwala, S. H. (1989) A novel sequence element derived from bacteriophage T7 mRNA acts as an enhancer of translation of the lacZ gene in Escherichia coli. J. Biol. Chem. 264, 16973–16976.
27. Selvin, P. R., and Ha, T. (2007) Single-Molecule Techniques. Cold Spring Harbor Laboratory Press, NY.