Biophysical studies of bacterial ribosome assembly

Current Opinion in Structural Biology

Volumn 18, Issue 3, 2008, Pages 299-304

  Williamson, James R ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN SUBUNIT; RIBOSOME PROTEIN; RIBOSOME RNA;

BACTERIAL METABOLISM; BINDING SITE; CAULOBACTER CRESCENTUS; CELL GROWTH; ESCHERICHIA COLI; GENE MUTATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN MODIFICATION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; QUANTITATIVE ANALYSIS; REVIEW; RIBOSOME; RNA BINDING; RNA CONFORMATION; RNA PROCESSING; RNA TRANSCRIPTION;

BACTERIA; BIOPHYSICS; MASS SPECTROMETRY; RIBOSOMES;

BACTERIA (MICROORGANISMS);

EID: 44949210279     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2008.05.001     Document Type: Review

References (30)

1. Paul B.J., Ross W., Gaal T., and Gourse R.L. rRNA transcription in Escherichia coli. Annu Rev Genet 38 (2004) 749-770
2. Zengel J.M., and Lindahl L. Diverse mechanisms for regulating ribosomal-protein synthesis in Escherichia coli. Progress in Nucleic Acid Research and Molecular Biology vol 47 (1994) 331-370
3. Kaczanowska M., and Ryden-Aulin M. Ribosome biogenesis and the translation process in Escherichia coli. Microbiol Mol Biol Rev 71 (2007) 477
4. Wilson D.N., and Nierhaus K.H. The weird and wonderful world of bacterial ribosome regulation. Crit Rev Biochem Mol Biol 42 (2007) 187-219
5. Chow C.S., Larnichhane T.N., and Mahto S.K. Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications. ACS Chem Biol 2 (2007) 610-619
6. Polevoda B., and Sherman F. Methylation of proteins involved in translation. Mol Microbiol 65 (2007) 590-606
7. Srivastava A.K., and Schlessinger D. Mechanism and regulation of bacterial ribosomal-RNA processing. Annu Rev Microbiol 44 (1990) 105-129
8. Running W.E., Ravipaty S., Karty J.A., and Reilly J.P. A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus. J Proteome Res 6 (2007) 337-347
9. Jiang M.X., Datta K., Walker A., Strahler J., Bagamasbad P., Andrews P.C., and Maddock J.R. The Escherichia coli GTPase CgtA(E) is involved in late steps of large ribosome assembly. J Bacteriol 188 (2006) 6757-6770
10. Jiang M., Sullivan S.M., Walker A.K., Strahler J.R., Andrews P.C., and Maddock J.R. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J Bacteriol 189 (2007) 3434-3444
11. Talkington M.W.T., Siuzdak G., and Williamson J.R. An assembly landscape for the 30S ribosomal subunit. Nature 438 (2005) 628-632
12. McCloskey J.A., and Rozenski J. The small subunit rRNA modification database. Nucleic Acids Res 33 (2005) D135-D138
13. Guymon R., Pomerantz S.C., Crain P.F., and McCloskey J.A. Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: the complete modification map of 16S rRNA of Thermus thermophilus. Biochemistry 45 (2006) 4888-4899
14. Andersen N.M., and Douthwaite S. YebU is a m(5)C methyltransferase specific for 16 S rRNA nucleotide 1407. J Mol Biol 359 (2006) 777-786
15. Videler H., Ilag L.L., McKay A.R.C., Hanson C.L., and Robinson C.V. Mass spectrometry of intact ribosomes. FEBS Lett 579 (2005) 943-947
16. Yamamoto T., Izumi S., and Gekko K. Mass spectrometry of hydrogen/deuterium exchange in 70S ribosomal proteins from E. coli. FEBS Lett 580 (2006) 3638-3642
17. Suh M.J., Pourshahian S., and Limbach P.A. Developing limited proteolysis and mass spectrometry for the characterization of ribosome topography. J Am Soc Mass Spectrom 18 (2007) 1304-1317
18. Beardsley R.L., Running W.E., and Reilly J.P. Probing the structure of the Caulobacter crescentus ribosome with chemical labeling and mass spectrometry. J Proteome Res 5 (2006) 2935-2946
19. Sanbonmatsu K.Y., Joseph S., and Tung C.S. Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A 102 (2005) 15854-15859
20. Stagg S.M., Mears J.A., and Harvey S.C. A structural model for the assembly of the 30 S subunit of the ribosome. J Mol Biol 328 (2003) 49-61
21. Held W.A., Ballou B., Mizushima S., and Nomura M. Assembly mapping of 30 S ribosomal proteins from Escherichia coli. Further studies. J Biol Chem 249 (1974) 3103-3111
22. Trylska J., McCammon J.A., and Brooks C.L. Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. J Am Chem Soc 127 (2005) 11125-11133
23. Hamacher K., Trylska J., and McCammon J.A. Dependency map of proteins in the small ribosomal subunit. PLoS Comput Biol 2 (2006) 80-87
24. Liiv A., and Remme J. Importance of transient structures during post-transcriptional refolding of the pre-23 S rRNA and ribosomal large subunit assembly. J Mol Biol 342 (2004) 725-741
25. Adilakshmi T., Ramaswamy P., and Woodson S.A. Protein-independent folding pathway of the 16 S rRNA 5′ domain. J Mol Biol 351 (2005) 508-519
26. Holmes K.L., and Culver G.M. Mapping structural differences between 30S ribosomal subunit assembly intermediates. Nat Struct Mol Biol 11 (2004) 179-186
27. Holmes K.L., and Culver G.M. Analysis of conformational changes in 16S rRNA during the course of 30 S subunit assembly. J Mol Biol 354 (2005) 340-357
28. Dutca L.M., Jagannathan I., Grondek J.F., and Culver G.M. Temperature-dependent RNP conformational rearrangements: analysis of binary complexes of primary binding proteins with 16 S rRNA. J Mol Biol 368 (2007) 853-869
29. Gutell R.R. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Res 22 (1994) 3502-3507
30. Wimberly B.T., Brodersen D.E., Clemons W.M., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., and Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature 407 (2000) 327-339