RNA structure: experimental analysis

Current Opinion in Microbiology

Volumn 10, Issue 3, 2007, Pages 286-291

  Felden, Brice ^a  

^a UNIVERSITÉ DE RENNES 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEOPROTEIN; RNA;

CHEMICAL STRUCTURE; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; DENATURATION; ENZYME STRUCTURE; GENETIC ENGINEERING; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROKARYOTIC CELL; REVIEW; RIBOSOME; RNA ANALYSIS; RNA STRUCTURE; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA;

PROKARYOTA;

EID: 34250822304     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2007.05.001     Document Type: Review

References (21)

1. Pichon C., and Felden B. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci USA 102 (2005) 14249-14254. This study reports the identification of twelve novel RNAs that are expressed from the Staphylococcus aureus genome. For the sRNAs that are conserved throughout the bacterial phylogeny, their secondary structures were inferred by phylogenetic comparative methods. Some RNAs show large variations of expression among pathogenic strains, suggesting that they are involved in the regulation of staphylococcal virulence.
2. Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H., and Noller H.F. Crystal structure of the ribosome at 5.5 A resolution. Science 292 (2001) 883-896
3. Selmer M., Dunham C.M., Murphy IV F.V., Weixlbaumer A., Petry S., Kelley A.C., Weir J.R., and Ramakrishnan V. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006) 1935-1942. This study provides atomic details of the entire bacterial 70S ribosome bound to its ligands (mRNA and tRNAs in the A, P and E sites). The structure of the Thermus thermophilus ribosome complexed with mRNA and tRNAs was solved at 2.8 Å resolution. The structure reveals details of the interaction of the mRNA and tRNA ligands with the ribosome and the role of proteins and metal ions in the formation of intersubunit bridges.
4. Korostelev A., Trakhanov S., Laurberg M., and Noller H.F. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126 (2006) 1065-1077. This increased resolution 70S ribosome complex structure provides a enhanced view of the details of ribosome-tRNA interactions in the P and E sites. The structure provides new evidence that the ribosome and RNA substrates are dynamic with structural rearrangements during protein synthesis.
5. Mitra K., Schaffitzel C., Fabiola F., Chapman M.S., Ban N., and Frank J. Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements. Mol Cell 22 (2006) 533-543
6. Golas M.M., Sander B., Will C.L., Luhrmann R., and Stark H. Major conformational change in the complex SF3b upon integration into the spliceosomal U11/U12 di-snRNP as revealed by electron cryomicroscopy. Mol Cell 17 (2005) 869-883
7. Nonin-Lecomte S., Felden B., and Dardel F. NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation. Nucleic Acids Res 34 (2006) 1847-1853
8. Chowdhury S., Maris C., Allain F.H., and Narberhaus F. Molecular basis for temperature sensing by an RNA thermometer. EMBO J 25 (2006) 2487-2497
9. Lindell M., Brannvall M., Wagner E.G., and Kirsebom L.A. Lead(II) cleavage analysis of RNase P RNA in vivo. RNA 11 (2005) 1348-1354
10. Ryckelynck M., Masquida B., Giegé R., and Frugier M. An intricate RNA structure with two tRNA-derived motifs directs complex formation between yeast aspartyl-tRNA synthetase and its mRNA. J Mol Biol 354 (2005) 614-629
11. Adilakshmi T., Lease R.A., and Woodson S.A. Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation. Nucleic Acids Res 34 (2006) e64. A synchrotron X-ray beam was used to map the structure of two large RNAs in viable bacteria in situ. This study shows that short exposures to a synchrotron X-ray beam can footprint the tertiary structure and protein contacts of RNA-protein complexes with nucleotide resolution in living cells.
12. 2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc Natl Acad Sci USA 103 (2006) 14003-14008
13. Gagnon K.T., Zhang X., Agris P.F., and Maxwell E.S. Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodelling. J Mol Biol 362 (2006) 1025-1042
14. Jansen J.A., McCarthy T.J., Soukup G.A., and Soukup J.K. Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS ribozyme. Nat Struct Mol Biol 13 (2006) 517-523. NIAM and NAIS were used to identify backbone and nucleobase functional groups essential for the ligand-dependent function of a catalytic riboswitch that regulates amino sugar metabolism in some Gram-positive bacteria.
15. Gavory G., Symmons M.F., Krishnan Ghosh Y., Klenerman D., and Balasubramanian S. Structural analysis of the catalytic core of human telomerase RNA by FRET and molecular modeling. Biochemistry 45 (2006) 13304-13311
16. Lambert D., Heckman J.E., and Burke J.M. Three conserved guanosines approach the reaction site in native and minimal hammerhead ribozymes. Biochemistry 45 (2006) 7140-7147
17. 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. High-performance liquid chromatography (HPLC)/electrospray ionization mass spectrometry based methods were used to determine the complete modification map for the small ribosomal subunit from T. thermophilus. These results provide an example of the potential of LC/MS for extensive post-transcriptional modification mapping in large RNAs.
18. Yu E.T., Zhang Q., and Fabris D. Untying the FIV frameshifting pseudoknot structure by MS3D. J Mol Biol 345 (2005) 69-80
19. Kaur S., Gillet R., Li W., Gursky R., and Frank J. Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome. Proc Natl Acad Sci USA 103 (2006) 16484-16489. By cryo-EM, a density map for the pre-accommodated state of the tmRNA.SmpB.EF-Tu.70S ribosome complex shows two SmpB molecules bound per ribosome, one toward the A site on the 30S subunit side and the other bound to the 50S subunit near the GTPase-associated centre.
20. Antal M., Bordeau V., Douchin V., and Felden B. A small bacterial RNA regulates a putative ABC transporter. J Biol Chem 280 (2005) 7901-7908
21. Corvaisier S., Bordeau V., and Felden B. Inhibition of transfer messenger RNA aminoacylation and trans-translation by aminoglycoside antibiotics. J Biol Chem 278 (2003) 14788-14797