Domain II plays a crucial role in the function of ribosome recycling factor

Biochemical Journal

Volumn 393, Issue 3, 2006, Pages 767-777

  Guo, Peng ^a   Zhang, Liqiang ^a   Zhang, Hongjie ^a   Feng, Vanning ^a   Jing, Guozhong ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

Domain function; Domain swaps; Elongation factor (EF G); Escherichia coli; Ribosome recycling factor (RRF); Thermoanaerobacter tengcongensis

Indexed keywords

BIOASSAY; COMPLEXATION; DISSOCIATION; ESCHERICHIA COLI; RECYCLING;

DOMAIN FUNCTION; DOMAIN SWAPS; ELONGATION FACTOR (EF-G); RIBOSOME RECYCLING FACTOR (RRF); THERMOANAEROBACTER TENGCONGENSIS;

CELLS;

ELONGATION FACTOR G; RIBOSOME RECYCLING FACTOR;

ARTICLE; BACTERIAL STRAIN; CHIMERA; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN STRUCTURE; RIBOSOME; THERMOANAEROBACTER; THERMOANAEROBACTER TENGCONGENSIS; WILD TYPE;

AMINO ACID SEQUENCE; CLONING, MOLECULAR; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHENOTYPE; POLYRIBOSOMES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; RIBOSOMAL PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TEMPERATURE; THERMOANAEROBACTER; TIME FACTORS;

BACTERIA (MICROORGANISMS); CHIMAERIFORMES; ESCHERICHIA COLI; THERMOANAEROBACTER; THERMOANAEROBACTER TENGCONGENSIS;

EID: 31544450994     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20050780     Document Type: Article

References (46)

1. Freistroffer, D. V., Pavlov, M. Y., MacDougall, J., Buckingham, R. H. and Ehrenberg, M. (1997) 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, 4126-4133
2. Zavialov, A. V., Buckingham, R. H. and Ehrenberg, M. (2001) A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 107, 115-124
3. Zavialov, A. V., Mora, L., Buckingham, R. H. and Ehrenberg, M. (2002) Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3. Mol. Cell 10, 789-798
4. Janosi, L., Hara, H., Zhang, S. and Kaji, A. (1996) Ribosome recycling by ribosome recycling factor (RRF)- an important but overlooked step of protein synthesis. Adv. Biophys. 32, 121-201
5. Janosi, L., Ricker, R. and Kaji, A. (1996) Dual functions of ribosome recycling factor in protein biosynthesis: disassembling the termination complex and preventing translational errors. Biochimie 78, 959-969
6. Pavlov, M. Y., Freistroffer, D., MacDougall, J., Buckingham, R. H. and Ehrenberg, M. (1997) Fast recycling of Escherichia coli ribosomes requires both ribosome recycling factor (RRF) and release factor RF3. EMBO J. 16, 4134-4141
7. Karimi, R., Pavlov, M. Y, Buckingham, R. H. and Ehrenberg, M. (1999) Novel roles for classical factors at the interface between translation termination and initiation. Mol. Cell 3, 601-609
8. Lancaster, L., Kiel, M. C., Kaji, A. and Noller, H. F. (2002) Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing. Cell 111, 129-140
9. Agrawal, R. K., Sharma, M. R., Kiel, M. C., Hirokawa, G., Booth, T. M., Spahn, C. M. et al. (2004) Visualization of ribosome-recycling factor on the Escherichia coli 70 S ribosome: function implications. Proc. Natl. Acad. Sci. U.S.A. 101, 8900-8905
10. Fujiwara, T, Ito, K., Yamami, T. and Nakamura, Y. (2004) Ribosome recycling factor disassembles the posttermination ribosomal complex independent of the ribosomal translocase activity of elongation factor G. Mo. Microbiol. 53, 517-528
11. Kiel, M. C., Raj, V. S., Kaji, H. and Kaji, A. (2003) Release of ribosome-bound ribosome recycling factor by elongation factor G. J. Biol. Chem. 278, 48041-48050
12. Peske, R, Rodnina, M. V. and Wintermeyer, W. (2005) Sequence of steps in ribosome recycling as defined by kinetic analysis. Mol. Cell 18, 403-412
13. Zavialov, A. V., Hauryliuk, V. V. and Ehrenberg, M. (2005) Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G. Mol. Cell 18, 675-686
14. Hirokawa, G., Nijman, R. M., Raj, V. S., Kaji, H., Igarashi, K. and Kaji, A. (2005) The role of ribosome recycling factor in dissociation of 70 S ribosomes into subunits. RNA 11, 1317-1328
15. Toyoda, T., Tin, O. R, Ito, K., Fujiwara, T, Kumasaka, T, Yamamoto, M., Garber, M. B. and Nakamura, Y. (2000) Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch. RNA 6, 1432-1444
16. Nakano, H., Yoshida, T, Uchiyama, S., Kawachi, M., Matsuo, H., Kato, T, Ohshima, A., Yamaichi, Y, Honda, T., Kato, H. et al. (2003) Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium. J. Biol. Chem. 278, 3427-3436
17. Selmer, M., Al-Karadaghi, S., Hirokawa, G., Kaji, A. and Liljas, A. (1999) Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic. Science (Washington D.C.) 286, 2349-2352
18. Kim, K. K., Min, K. and Suh, S. W. (2000) Crystal structure of the ribosome recycling factor from Escherichia coli. EMBO J. 19, 2362-2370
19. Nakano, H., Uchiyama, S., Yoshida, T., Ohkubo, T., Kato, H., Yamagata, Y. and Kobayashi, Y. (2002) Crystallization and preliminary X-ray crystallographic studies of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly. Acta Crystallogr. D Biol. 58, 124-126
20. Yoshida, T, Uchiyama, S., Nakano, H., Kashimori, H., Kijima, H., Ohshima, T., Saihara, Y, Ishino, T, Shimahara, H., Yoshida, T. et al. (2001) Solution structure of the ribosome recycling factor from Aquifex aeolicus. Biochemistry 40, 2387-2396
21. Saikrishnan, K., Kalapala, S. K., Varshney, U. and Vijayan, M. (2005) X-ray structural studies of Mycobacterium tuberculosis RRF and a comparative study of RRFs of known structure. Molecular plasticity and biological implications. J. Mol. Biol. 345, 29-38
22. Rao, A. R. and Varshney, U. (2001) Specific interaction between the ribosome recycling factor and the elongation factor G from Mycobacterium tuberculosis mediates peptidyl-tRNA release and ribosome recycling in Escherichia coli. EMBO J. 20, 2977-2986
23. Ito, K., Fujiwara, T., Toyoda, T. and Nakamura, Y. (2002) Elongation factor G participates in ribosome disassembly by interacting with ribosome recycling factor at their tRNA-mimicry domains. Mol. Cell 9, 1263-1272
24. Guo, P., Zhang, L. Q., Qi, Z., Chen, R. S. and Jing, G. Z. (2005) Expression in Escherichia coli, purification and characterization of Thermoanaerobacter tengcongensis ribosome recycling factor. J. Biochem. (Tokyo) 138, 89-94
25. Sambrook, J., Fritsch, E. F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
26. Zhang, X. L., Guo, P. and Jing, G. Z. (2003) A vector with the downstream box of the initiation codon can highly enhance protein expression in Escherichia coli. Biotech. Lett. 25, 755-760
27. Bao, Q., Tian, Y., Li, W., Xu, Z., Xuan, Z., Hu, S., Dong, W., Yang, J., Chen, Y, Xue, Y. et al. (2002) A complete sequence of the. T tengcongensis genome. Genome Res. 12, 689-700
28. Ichikawa, S. and Kaji, A. (1989) Molecular cloning and expression of ribosome releasing factor. J. Biol. Chem. 264, 20054-20059
29. Zengel, J. M., Archer, R. H. and Lindahl, L. (1984) The nucleotide sequence of the Escherichia coli fus gene coding for elongation factor G. Nucleic Acids Res. 12, 2181-2192
30. Horton, R. M., Cai, Z., Ho, S. N. and Pease, L. R. (1990) Gene splicing by overlap extension: Tailor-made genes using the polymerase chain reaction. Biotechniques 8, 528-535
31. Feng, Y M., Zhang, Y.M. and Jing, G. Z. (2002) Soluble expression in Escherichia coli, purification and characterization of a human TF-1 cell apoptosis-related protein TFAR19. Protein Exp. Purif. 25, 323-329
32. Zhou, B. and Jing, G. Z. (1998) Determination of protein extinction coefficients by alkaline hydrolysis. Progr. Biochem. Biophys. 26, 384-387
33. Tai, P. and Davis, B. (1979) Isolation of polysomes free of initiation factors. Methods Enzymol. 59, 362-371
34. Jelenc, P. C. (1980) Rapid purification of highly active ribosomes from Escherichia coli. Anal. Biochem. 105, 369-374
35. Hirashima, A. and Kaji, A. (1972) Factor-dependent release of ribosomes from messenger RNA: requirement for two heat-stable factors. J. Mol. Biol. 65, 43-58
36. Ohnishi, M., Janosi, L., Shuda, M., Matsumoto, H., Terawaki, T. and Kaji, A. (1999) Molecular cloning, sequencing purification and characterization of Pseudomonas aeruginosa ribosome recycling factor. J. Bacteriol. 181, 1281-1291
37. Hirokawa, G., Kiel, M. C., Muto, A., Selmer, M., Raj, V. S., Liljas, A., Igarashi, K., Kaji, H. and Kaji, A. (2002) Post-termination complex disassembly by ribosome recycling factor, a functional tRNA mimic. EMBO J. 21, 2272-2281
38. Janosi, L., Shimizu, I. and Kaji, A. (1994) Ribosome recycling factor (ribosome releasing factor) is essential for bacterial growth. Proc. Natl. Acad. Sci. U.S.A. 91, 4249-4253
39. Janosi, L., Mottagui-Tabar, S., Isaksson, L. A., Sekine, Y., Ohtsubo, E., Zhang, S., Goon, S., Nelken, S., Shuda, M. and Kaji, A. (1998) Evidence for in vivo ribosome recycling, the fourth step in protein biosynthesis. EMBOJ. 17, 1141-1151
40. Fujiwara, T., Ito, K., Nakayashiki, T. and Nakamura, Y. (1999) Amber mutations in ribosome recycling factors of Escherichia coli and Thermus themophilus: evidence for C-terminal modulator element. FEBS Lett. 447, 297-302
41. Yamami, T., Ito, K., Fujiwara, T. and Nakamura, Y. (2005) Heterologous expression of Aquifex aeolicus ribosome recycling factor in Escherichia coli is dominant lethal by forming a complex that lacks functional co-ordination for ribosome disassembly. Mol. Microbiol. 55, 150-161
42. Rodnina, M. V., Savelsbergh, A., Katunin, V. I. and Wintermeyer, W. (1997) Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature (London) 385, 37-41
43. Agrawal, R. K., Penczek, P., Grassucci, R. A. and Frank, J. (1998) Visualization of elongation factor G on the Escherichia coli 70 S ribosome: the mechanism of translocation. Proc. Natl. Acad. Sci. U.S.A. 95, 6134-6138
44. Wilson, D. N., Schluenzen, F., Harms, J. M., Yoshida, T., Ohkubo, T., Albrecht, R., Buerger, J., Kobayashi, Y. and Fucini, P. (2005) X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on 50S ribosomal subunit. EMBO J. 24, 251-260
45. Gao, N., Zavialov, A. V., Li, W., Sengupta, J., Valle, M., Gursky, R. P., Ehrenberg, M. and Frank, J. (2005) Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Molo. Cell 18, 663-674
46. Ishino, T., Atarashi, K., Uchiyama, S., Yamami, T., Saihara, Y., Yoshida, T., Hara, H., Yokose, K., Kobayashi, Y. and Nakamura, Y. (2000) Interaction of ribosome recycling factor and elongation factor EF-G with E. coli ribosomes studied by the surface plasmon resonance technique. Genes to Cells 5, 953-963