A Highly Purified, Fluorescently Labeled In Vitro Translation System for Single-Molecule Studies of Protein Synthesis

Methods in Enzymology

Volumn 472, Issue , 2010, Pages 221-259

  Fei, Jingyi ^a   Wang, Jiangning ^a   Sternberg, Samuel H ^a,b   MacDougall, Daniel D ^a   Elvekrog, Margaret M ^a   Pulukkunat, Dileep K ^a   Englander, Michael T ^a   Gonzalez, Ruben L ^a  

^a Howard Hughes Medical Institute   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENCE RESONANCE ENERGY TRANSFER; IN VITRO STUDY; PROTEIN SYNTHESIS; ARTICLE; BIOASSAY; CHEMICAL STRUCTURE; CHEMISTRY; INSTRUMENTATION; METABOLISM; METHODOLOGY; RIBOSOME;

FLUORESCENT DYE; PROTEIN; RNA;

BIOLOGICAL ASSAY; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; MOLECULAR STRUCTURE; PROTEIN BIOSYNTHESIS; PROTEINS; RIBOSOMES; RNA;

EID: 77957036693     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)72008-5     Document Type: Chapter

References (99)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., Basic local alignment search tool. J. Mol. Biol. 215 (1990), 403–410.
2. Antoun, A., Pavlov, Michael Y., Tenson, Tanel, Ehrenberg, M., Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering. Biol. Proced. Online 6 (2004), 35–54.
3. Aoki, H., Adams, S.L., Turner, M.A., Ganoza, M.C., Molecular characterization of the prokaryotic efp gene product involved in a peptidyltransferase reaction. Biochimie 79 (1997), 7–11.
4. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L., Mori, H., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol. Syst. Biol., 2, 2006, 0008.
5. Bastiaens, P.I., Jovin, T.M., Microspectroscopic imaging tracks the intracellular processing of a signal transduction protein: Fluorescent-labeled protein kinase C beta I. Proc. Natl. Acad. Sci. USA 93 (1996), 8407–8412.
6. Blanchard, S.C., Single-molecule observations of ribosome function. Curr. Opin. Struct. Biol. 19 (2009), 103–109.
7. Blanchard, S.C., Gonzalez, R.L., Kim, H.D., Chu, S., Puglisi, J.D., tRNA selection and kinetic proofreading in translation. Nat. Struct. Mol. Biol. 11 (2004), 1008–1014.
8. Blanchard, S.C., Kim, H.D., Gonzalez, R.L. Jr., Puglisi, J.D., Chu, S., tRNA dynamics on the ribosome during translation. Proc. Natl. Acad. Sci. USA 101 (2004), 12893–12898.
9. Bochner, B.R., Ames, B.N., Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography. J. Biol. Chem. 257 (1982), 9759–9769.
10. Brandi, L., Marzi, S., Fabbretti, A., Fleischer, C., Hill, W.E., Gualerzi, C.O., Lodmell, J.S., The translation initiation functions of IF2: Targets for thiostrepton inhibition. J. Mol. Biol. 335 (2004), 881–894.
11. Cammack, K.A., Wade, H.E., The sedimentation behaviour of ribonuclease-active and -inactive ribosomes from bacteria. Biochem. J. 96 (1965), 671–680.
12. Carbon, J., David, H., Studies on the thionucleotides in transfer ribonucleic acid. Addition of N-ethylmaleimide and formation of mixed disulfides with thiol compounds. Biochemistry 7 (1968), 3851–3858.
13. Chambliss, G.H., Henkin, T.M., Leventhal, J.M., Bacterial in vitro protein-synthesizing systems. Methods Enzymol. 101 (1983), 598–605.
14. Clemens, M.J., Targets and mechanisms for the regulation of translation in malignant transformation. Oncogene 23 (2004), 3180–3188.
15. Datsenko, K.A., Wanner, B.L., One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97 (2000), 6640–6645.
16. Daviter, T., Gromadski, K.B., Rodnina, M.V., The ribosome's response to codon-anticodon mismatches. Biochimie 88 (2006), 1001–1011.
17. DeLano, W., The PyMOL Molecular Graphics System., 2008, DeLano Scientific LLC, Palo Alto, CA http://www.pymol.org.
18. Dincbas-Renqvist, V., Engstrom, A., Mora, L., Heurgue-Hamard, V., Buckingham, R., Ehrenberg, M., A post-translational modification in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation. EMBO J. 19 (2000), 6900–6907.
19. Dorywalska, M., Blanchard, S.C., Gonzalez, R.L., Kim, H.D., Chu, S., Puglisi, J.D., Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res. 33 (2005), 182–189.
20. Dubnoff, J.S., Maitra, U., Moldave, Kivie, Lawrence, G., Isolation and properties of protein factors involved in polypeptide chain initiation in Escherichia coli. Methods Enzymol. 20 (1971), 248–261.
21. Elbing, K., Brent, R., Escherichia coli, plasmids, and bacteriophages. Curr. Protoc. Mol. Biol. 59 (2002), 1.1.1–1.1.7.
22. Ermolenko, D.N., Majumdar, Z.K., Hickerson, R.P., Spiegel, P.C., Clegg, R.M., Noller, H.F., Observation of intersubunit movement of the ribosome in solution using FRET. J. Mol. Biol. 370 (2007), 530–540.
23. Fei, J., Kosuri, P., MacDougall, D.D., Gonzalez, R.L., Jr., Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol. Cell 30 (2008), 348–359.
24. Fei, J., Bronson, J.E., Hofman, J.M., Srinivas, R.L., Wiggins, C.H., Gonzalez, R.L.J., Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc. Natl. Acad. Sci. USA 106 (2009), 15702–15707.
25. Forchhammer, K., Leinfelder, W., Bock, A., Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein. Nature 342 (1989), 453–456.
26. Fourmy, D., Mechulam, Y., Brunie, S., Blanquet, S., Fayat, G., Identification of residues involved in the binding of methionine by Escherichia coli methionyl-tRNA synthetase. FEBS Lett. 292 (1991), 259–263.
27. Frank, J., Gonzalez, R.L., Jr., Structure and dynamics of a processive Brownian motor: The translating ribosome. Annu. Rev. Biochem., 2010 doi: 10.1146/annurev-biochem-060408-173330.
28. Fredrick, K., Noller, H., Catalysis of ribosomal translocation by sparsomycin. Science 300 (2003), 1159–1162.
29. Freistroffer, D.V., Pavlov, M.Y., MacDougall, J., Buckingham, R.H., Ehrenberg, M., Release factor RF3 in E.coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner. EMBO J. 16 (1997), 4126–4133.
30. Gallagher, S.R., One-dimensional SDS gel electrophoresis of proteins. Curr. Protoc. Mol. Biol., 75, 2006, 10-2A-1 10-2A-37.
31. Goldberg, R.B., Bender, R.A., Streicher, S.L., Direct selection for P1-sensitive mutants of enteric bacteria. J. Bacteriol. 118 (1974), 810–814.
32. Gonzalez, R.L. Jr., Chu, S., Puglisi, J.D., Thiostrepton inhibition of tRNA delivery to the ribosome. RNA 13 (2007), 2091–2097.
33. Guex, N., Peitsch, M.C., SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18 (1997), 2714–2723.
34. Ha, T., Single-molecule fluorescence resonance energy transfer. Methods 25 (2001), 78–86.
35. Hapke, B., Noll, H., Structural dynamics of bacterial ribosomes. IV. Classification of ribosomes by subunit interaction. J. Mol. Biol. 105 (1976), 97–109.
36. Hartz, D., McPheeters, D.S., Traut, R., Gold, L., Extension inhibition analysis of translation initiation complexes. Methods Enzymol. 164 (1988), 419–425.
37. Hartz, D., McPheeters, D.S., Gold, L., Selection of the initiator tRNA by Escherichia coli initiation factors. Genes Dev. 3 (1989), 1899–1912.
38. Heurgue-Hamard, V., Champ, S., Engstrom, A., Ehrenberg, M., Buckingham, R.H., The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J. 21 (2002), 769–778.
39. Hirokawa, G., Nijman, R.M., Raj, V.S., Kaji, H., Igarashi, K., Kaji, A., The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits. RNA 11 (2005), 1317–1328.
40. Hoffmann, A., Roeder, R.G., Purification of his-tagged proteins in non-denaturing conditions suggests a convenient method for protein interaction studies. Nucleic Acids Res. 19 (1991), 6337–6338.
41. Hohng, S., Joo, C., Ha, T., Single-molecule three-color FRET. Biophys. J. 87 (2004), 1328–1337.
42. Jelenc, P.C., Kurland, C.G., Nucleoside triphosphate regeneration decreases the frequency of translation errors. Proc. Natl. Acad. Sci. USA 76 (1979), 3174–3178.
43. Joseph, S., Noller, H.F., EF-G-catalyzed translocation of anticodon stem-loop analogs of transfer RNA in the ribosome. EMBO J. 17 (1998), 3478–3483.
44. Kapp, L.D., Lorsch, J.R., The molecular mechanics of eukaryotic translation. Annu. Rev. Biochem. 73 (2004), 657–704.
45. Korostelev, A., Ermolenko, D.N., Noller, H.F., Structural dynamics of the ribosome. Curr. Opin. Chem. Biol. 12 (2008), 674–683.
46. Lakowicz, J.R., Principles of Fluorescence Spectroscopy. 1999, Springer, New York, NY.
47. Lee, T.H., Blanchard, S.C., Kim, H.D., Puglisi, J.D., Chu, S., The role of fluctuations in tRNA selection by the ribosome. Proc. Natl. Acad. Sci. USA 104 (2007), 13661–13665.
48. Li, W., Agirrezabala, X., Lei, J., Bouakaz, L., Brunelle, J.L., Ortiz-Meoz, R.F., Green, R., Sanyal, S., Ehrenberg, M., Frank, J., Recognition of aminoacyl-tRNA: A common molecular mechanism revealed by cryo-EM. EMBO J. 27 (2008), 3322–3331.
49. Liljas, A., Structural Aspects of Protein Synthesis. 2004, World Scientific Publishing Co. Pte. Ltd., Singapore.
50. Liu, C., Wang, R., Varlamova, O., Leyh, T.S., Regulating energy transfer in the ATP sulfurylase-GTPase system. Biochemistry 37 (1998), 3886–3892.
51. Maar, D., Liveris, D., Sussman, J.K., Ringquist, S., Moll, I., Heredia, N., Kil, A., Blasi, U., Schwartz, I., Simons, R.W., A single mutation in the IF3 N-terminal domain perturbs the fidelity of translation initiation at three levels. J. Mol. Biol. 383 (2008), 937–944.
52. Marshall, R.A., Aitken, C.E., Dorywalska, M., Puglisi, J.D., Translation at the single-molecule level. Annu. Rev. Biochem. 77 (2008), 177–203.
53. Marshall, R.A., Dorywalska, M., Puglisi, J.D., Irreversible chemical steps control intersubunit dynamics during translation. Proc. Natl. Acad. Sci. USA 105 (2008), 15364–15369.
54. Marshall, R.A., Aitken, C.E., Puglisi, J.D., GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Mol. Cell 35 (2009), 37–47.
55. McKenna, S.A., Kim, I., Puglisi, E.V., Lindhout, D.A., Aitken, C.E., Marshall, R.A., Puglisi, J.D., Purification and characterization of transcribed RNAs using gel filtration chromatography. Nat. Protoc. 2 (2007), 3270–3277.
56. Milligan, J.F., Groebe, D.R., Witherell, G.W., Uhlenbeck, O.C., Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15 (1987), 8783–8798.
57. Mohr, D., Wintermeyer, W., Rodnina, M.V., GTPase activation of elongation factors Tu and G on the ribosome. Biochemistry 41 (2002), 12520–12528.
58. Moore, D.D., Commonly used reagents and equipment. Curr. Protoc. Mol. Biol., 35, 2000, A.2.5.
59. Moore, S., Sauer, R.T., P1vir phage transduction http://openwetware.org/wiki/Sauer:P1vir_phage_transduction, 2009.
60. Mora, L., Heurgue-Hamard, V., de Zamaroczy, M., Kervestin, S., Buckingham, R.H., Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo. J. Biol. Chem. 282 (2007), 35638–35645.
61. Munro, J.B., Altman, R.B., O'Connor, N., Blanchard, S.C., Identification of two distinct hybrid state intermediates on the ribosome. Mol. Cell 25 (2007), 505–517.
62. Odom, O.W., Picking, W.D., Hardesty, B., Movement of tRNA but not the nascent peptide during peptide bond formation on ribosomes. Biochemistry 29 (1990), 10734–10744.
63. Ogle, J.M., Ramakrishnan, V., Structural insights into translational fidelity. Annu. Rev. Biochem. 74 (2005), 129–177.
64. Pavlov, M.Y., Ehrenberg, M., Rate of translation of natural mRNAs in an optimized in vitro system. Arch. Biochem. Biophys. 328 (1996), 9–16.
65. Peske, F., Rodnina, M.V., Wintermeyer, W., Sequence of steps in ribosome recycling as defined by kinetic analysis. Mol. Cell 18 (2005), 403–412.
66. Plumbridge, J.A., Baumert, H.G., Ehrenberg, M., Rigler, R., Characterisation of a new, fully active fluorescent derivative of E. coli tRNA Phe. Nucleic Acids Res. 8 (1980), 827–843.
67. Powers, T., Noller, H.F., A functional pseudoknot in 16S ribosomal RNA. EMBO J. 10 (1991), 2203–2214.
68. Qin, Y., Polacek, N., Vesper, O., Staub, E., Einfeldt, E., Wilson, D.N., Nierhaus, K.H., The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell 127 (2006), 721–733.
69. Raleigh, E.A., Elbing, K., Brent, R., Escherichia coli, plasmids, and bacteriophages. Curr. Protoc. Mol. Biol. 59 (2002), 1.4.1–1.4.14.
70. Recht, M.I., Douthwaite, S., Dahlquist, K.D., Puglisi, J.D., Effect of mutations in the A site of 16S rRNA on aminoglycoside antibiotic-ribosome interaction. J. Mol. Biol. 286 (1999), 33–43.
71. Robertson, J.M., Wintermeyer, W., Effect of translocation on topology and conformation of anticodon and D loops of tRNAPhe. J. Mol. Biol. 151 (1981), 57–79.
72. Roy, R., Hohng, S., Ha, T., A practical guide to single-molecule FRET. Nat. Methods 5 (2008), 507–516.
73. Sasse, J., Gallagher, S.R., Staining proteins in gels. Curr. Protoc. Mol. Biol. 85 (2009), 10.6.1–10.6.27.
74. Schmitt, E., Blanquet, S., Mechulam, Y., Crystallization and preliminary X-ray analysis of Escherichia coli methionyl-tRNAMet(f) formyltransferase complexed with formyl-methionyl-tRNAMet(f). Acta Crystallogr. Sect. D Biol. Crystallogr. 55:Pt 1 (1999), 332–334.
75. Schneider, R.J., Mohr, I., Translation initiation and viral tricks. Trends Biochem. Sci. 28 (2003), 130–136.
76. Schuette, J.C., Murphy, F.V.t., Kelley, A.C., Weir, J.R., Giesebrecht, J., Connell, S.R., Loerke, J., Mielke, T., Zhang, W., Penczek, P.A., Ramakrishnan, V., Spahn, C.M., GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J. 28 (2009), 755–765.
77. Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M., Cate, J.H.D., Structures of the bacterial ribosome at 3.5 A resolution. Science 310 (2005), 827–834.
78. Selmer, M., Dunham, C.M., Murphy, F.V.t., Weixlbaumer, A., Petry, S., Kelley, A.C., Weir, J.R., Ramakrishnan, V., Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006), 1935–1942.
79. Seshadri, A., Varshney, U., Mechanism of recycling of post-termination ribosomal complexes in eubacteria: A new role of initiation factor 3. J. Biosci. 31 (2006), 281–289.
80. Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., Ueda, T., Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19 (2001), 751–755.
81. Simonian, M.H., Smith, J.A., Spectrophotometric and colorimetric determination of protein concentration. Curr. Protoc. Mol. Biol., 76, 2006, 10-1A-2 10-1A-9.
82. Slatko, B.E., Albright, L.M., Denaturing gel electrophoresis for sequencing. Curr. Protoc. Mol. Biol. 16 (1992), 7.6.1–7.6.13.
83. Sonenberg, N., Hinnebusch, A.G., Regulation of translation initiation in eukaryotes: Mechanisms and biological targets. Cell 136 (2009), 731–745.
84. Spahn, C.M., Blaha, G., Agrawal, R.K., Penczek, P., Grassucci, R.A., Trieber, C.A., Connell, S.R., Taylor, D.E., Nierhaus, K.H., Frank, J., Localization of the ribosomal protection protein tet(o) on the ribosome and the mechanism of tetracycline resistance. Mol. Cell 7 (2001), 1037–1045.
85. Stark, H., Rodnina, M.V., Wieden, H.J., Zemlin, F., Wintermeyer, W., van Heel, M., Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Nat. Struct. Biol. 9 (2002), 849–854.
86. Sternberg, S.H., Fei, J., Prywes, N., McGrath, K.A., Gonzalez, R.L., Jr., Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Nat. Struct. Mol. Biol. 16 (2009), 861–868.
87. Thompson, J.D., Higgins, D.G., Gibson, T.J., CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994), 4673–4680.
88. Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J., Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat. Struct. Mol. Biol. 10 (2003), 899–906.
89. Villa, E., Sengupta, J., Trabuco, L.G., LeBarron, J., Baxter, W.T., Shaikh, T.R., Grassucci, R.A., Nissen, P., Ehrenberg, M., Schulten, K., Frank, J., Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc. Natl. Acad. Sci. USA 106 (2009), 1063–1068.
90. Wagner, E.G., Jelenc, P.C., Ehrenberg, M., Kurland, C.G., Rate of elongation of polyphenylalanine in vitro. Eur. J. Biochem. 122 (1982), 193–197.
91. Wall, J.D., Harriman, P.D., Phage P1 mutants with altered transducing abilities for Escherichia coli. Virology 59 (1974), 532–544.
92. Weinger, J.S., Parnell, K.M., Dorner, S., Green, R., Strobel, S.A., Substrate-assisted catalysis of peptide bond formation by the ribosome. Nat. Struct. Mol. Biol. 11 (2004), 1101–1106.
93. Wilson, K., Preparation of genomic DNA from bacteria. Curr. Protoc. Mol. Biol., 1987, 2.4.1–2.4.2.
94. Wilson, D.N., Blaha, G., Connell, S.R., Ivanov, P.V., Jenke, H., Stelzl, U., Teraoka, Y., Nierhaus, K.H., Protein synthesis at atomic resolution: Mechanistics of translation in the light of highly resolved structures for the ribosome. Curr. Protein Pept. Sci. 3 (2002), 1–53.
95. Wyatt, J.R., Chastain, M., Puglisi, J.D., Synthesis and purification of large amounts of RNA oligonucleotides. BioTechniques 11 (1991), 764–769.
96. Youngman, E.M., Brunelle, J.L., Kochaniak, A.B., Green, R., The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell 117 (2004), 589–599.
97. Zavialov, A.V., Buckingham, R.H., Ehrenberg, M., A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 107 (2001), 115–124.
98. Zavialov, A.V., Hauryliuk, V.V., Ehrenberg, M., Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G. Mol. Cell 18 (2005), 675–686.
99. Zhuang, X., Bartley, L.E., Babcock, H.P., Russell, R., Ha, T., Herschlag, D., Chu, S., A single-molecule study of RNA catalysis and folding. Science 288 (2000), 2048–2051.