Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering

Biological Procedures Online

Volumn 6, Issue 1, 2004, Pages 35-54

  Antoun, Ayman ^a   Pavlov, Michael Y ^a   Tenson, Tanel ^b   Ehrenberg, Måns ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF TARTU   (Estonia)

Author keywords

Prokaryotic initiation factor 2; Radiation; Ribosomes; Scattering

Indexed keywords

GUANOSINE TRIPHOSPHATE; INITIATION FACTOR 1; INITIATION FACTOR 2; INITIATION FACTOR 3; MESSENGER RNA;

ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; EUBACTERIUM; LIGHT SCATTERING; MATHEMATICAL COMPUTING; MOLECULAR MECHANICS; MOLECULAR WEIGHT; NONHUMAN; PROTEIN SYNTHESIS; RIBOSOME SUBUNIT; RNA TRANSLATION;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 2342547059     PISSN: 14809222     EISSN: None     Source Type: Journal    
DOI: 10.1251/bpo71     Document Type: Article

References (39)

1. Gualerzi CO, Pon CL. Initiation of mRNA translation in prokaryotes. Biochemistry 1990; 29:5881-5889.
2. Pestova TV, Hellen CU. The structure and function of initiation factors in eukaryotic protein synthesis. Cell Mol Life Sci 2000; 57:651-674.
3. Roll-Mecak A, Shin BS, Dever TE, Burley SK. Engaging the ribosome: universal IFs of translation. Trends Biochem Sci 2001; 26:705-709.
4. Kyrpides NC, Woese CR. Universally conserved translation initiation factors. Proc Natl Acad Sci USA 1998; 95:224-228.
5. Pestova TV, Kolupaeva VG. The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev 2002; 16:2906-2922.
6. Kisselev L, Ehrenberg M, Frolova L. Termination of translation: interplay of mRNA, rRNAs and release factors? Embo J 2003; 22:175-182.
7. Freistroffer DV, Pavlov MY, MacDougall J, Buckingham RH, 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 1997; 16:4126-4133.
8. Zavialov AV, Buckingham RH, Ehrenberg M. A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 2001; 107:115-124.
9. Zavialov AV, Mora L, Buckingham RH, Ehrenberg M. Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3. Mol Cell 2002; 10:789-798.
10. Karimi R, Pavlov MY, Buckingham RH, Ehrenberg M. Novel roles for classical factors at the interface between translation termination and initiation. Mol Cell 1999; 3:601-609.
11. Antoun A, Pavlov MY, Andersson K, Tenson T, Ehrenberg M. The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis. Embo J 2003; 22:5593-5601.
12. Grunberg-Manago M, Dessen P, Pantaloni D, Godefroy-Colburn T, Wolfe AD, Dondon J. Light-scattering studies showing the effect of initiation factors on the reversible dissociation of Escherichia coli ribosomes. J Mol Biol 1975; 94:461-478.
13. Wishnia A, Boussert A, Graffe M, Dessen PH, Grunberg-Manago M. Kinetics of the reversible association of ribosomal subunits: stopped-flow studies of the rate law and of the effect of Mg2+. In: J Mol Biol, vol. 93. pp. 499-415; 1975: 499-415.
14. Blumberg BM, Nakamoto T, Kezdy FJ. Kinetics of initiation of bacterial protein synthesis. Proc Natl Acad Sci USA 1979; 76:251-255.
15. Pestova TV, Lomakin IB, Lee JH, Choi SK, Dever TE, Hellen CU. The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature 2000; 403:332-335.
16. Noll M, Hapke B, Noll H. Structural dynamics of bacterial ribosomes. II. Preparation and characterization of ribosomes and subunits active in the translation of natural messenger RNA. J Mol Biol 1973; 80:519-529.
17. Jelenc PC, Kurland CG. Nucleoside triphosphate regeneration decreases the frequency of translation errors. Proc Natl Acad Sci USA 1979; 76:3174-3178.
18. Pavlov MY, Freistroffer DV, MacDougall J, Buckingham RH, Ehrenberg M. Fast recycling of Escherichia coli ribosomes requires both ribosome recycling factor (RRF) and release factor RF3. Embo J 1997; 16:4134-4141.
19. Rodnina MV, Wintermeyer W. GTP consumption of elongation factor Tu during translation of heteropolymeric mRNAs. Proc Natl Acad Sci USA 1995; 92:1945-1949.
20. Soffientini A, Lorenzetti R, Gastaldo L, Parlett JH, Spurio R, La Teana A, Islam K. Purification procedure for bacterial translational initiation factors IF2 and IF3. Protein Expr Purif 1994; 5:118-124.
21. Ehrenberg M, Bilgin N, Kurland C. Design and use of a fast and accurate in vitro translation system. In: Ribosomes and Protein Synthesis. A practical Approach. pp. 101-128. Oxford: Oxford University Press; 1990: 101-128.
22. Marquardt DW. An algorithm for least squares estimation of nonlinear parameters. J Soc Ind Appl Math 1963; 11: 431-441.
23. Cenatiempo Y, Deville F, Dondon J, Grunberg-Manago M, Sacerdot C, Hershey JW, Hansen HF, Petersen HU, Clark BF, Kjeldgaard M, et al. The protein synthesis initiation factor 2 G-domain. Study of a functionally active C-terminal 65-kilodalton fragment of IF2 from Escherichia coli. Biochemistry 1987; 26:5070-5076.
24. Sacerdot C, Vachon G, Laalami S, Morel-Deville F, Cenatiempo Y, Grunberg-Manago M. Both forms of translational initiation factor IF2 (alpha and beta) are required for maximal growth of Escherichia coli. Evidence for two translational initiation codons for IF2 beta. J Mol Biol 1992; 225:67-80.
25. Tomsic J, Vitali LA, Daviter T, Savelsbergh A, Spurio R, Striebeck P, Wintermeyer W, Rodnina MV, Gualerzi CO. Late events of translation initiation in bacteria: a kinetic analysis. Embo J 2000; 19:2127-2136.
26. Ingraham JL, Maaloe O, Neidhardt FC. Growth of the Bacterial Cell. Sunderland, MA 01375, USA: Sinauer Associates Inc.; 1983.
27. Farewell A, Neidhardt FC. Effect of temperature on in vivo protein synthetic capacity in Escherichia coli. J Bacteriol 1998; 180:4704-4710.
28. Meinnel T, Blanquet S. Maturation of pre-tRNA(fMet) by Escherichia coli RNase P is specified by a guanosine of the 5′ -flanking sequence. J Biol Chem 1995; 270:15908-15914.
29. Sambrook J, Russell D. Preparation and transformation of competent Ecoli using callcium chloride. In: Molecular Cloning (A Laboratory Manual) Edited by Spedding G. pp. 116-118. New York: Cold Spring Harbor Laboratory Press; 2001: 116-118.
30. Dubnoff JS, Maitra U. Isolation and properties of polypeptide chain initiation factor FII from Escherichia coli: evidence for a dual function. Proc Natl Acad Sci U S A 1971; 68:318-323.
31. Ramesh V, Gite S, Li Y, RajBhandary UL. Suppressor mutations in Escherichia coli methionyl-tRNA formyltransferase: role of a 16-amino acid insertion module in initiator tRNA recognition. Proc Natl Acad Sci USA 1997; 94:13524-13529.
32. Gillam IC, Tener GM. The Use of BD-Cellulose in Separating Transfer RNAs. Methods in Enzymology 1971; 20:55-71.
33. Rodnina MV, Semenkov YP, Wintermeyer W. Purification of fMet-tRNA(fMet) by fast protein liquid chromatography. Anal Biochem 1994; 219:380-381.
34. Forster AC, Weissbach H, Blacklow SC. A simplified reconstitution of mRNA-directed peptide synthesis: activity of the epsilon enhancer and an unnatural amino acid. Anal Biochem 2001; 297:60-70.
35. Cantor CR, Schimmel PR. Light Scattering. In: Biophysical Chemistry. pp. 838-842. New York: W.H. Freeman and Company; 1980: 838-842.
36. van Holde KE. Scattering. In: Physical Biochemistry. pp. 209-224. Englewwood Cliffd, NJ 0732: Prentice-Hall; 1985: 209-224.
37. Belloni L. Interacting monodisperse and polydisperse spheres. In: Neutron, X-Ray and Light Scattering Edited by Linder P, Zemb T. pp. 135-155. Amsterdam: Elsevier Science; 1991: 135-155.
38. Velev OD, Kaler EW, Lenhoff AM. Protein interactions in solution characterized by light and neutron scattering: comparison of lysozyme and chymotrypsinogen. Biophys J 1998; 75:2682-2697.
39. Wen J, Arakawa T, Philo JS. Size-exclusion chromatography with on-line light-scattering, absorbance, and refractive index detectors for studying proteins and their interactions. Anal Biochem 1996; 240:155-166.