The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold

FEBS Letters

Volumn 585, Issue 7, 2011, Pages 1049-1053

  Lee, Chul Won ^a   Li, Lichun ^b   Giedroc, David P ^a  

^a INDIANA UNIVERSITY   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Coronavirus; Mouse hepatitis virus; Nuclear magnetic resonance; RNA tetraloop; SARS; Solution structure

Indexed keywords

5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SARS CORONAVIRUS; VIRUS REPLICATION;

5' UNTRANSLATED REGIONS; BASE PAIRING; BASE SEQUENCE; CONSERVED SEQUENCE; INVERTED REPEAT SEQUENCES; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; RNA, VIRAL; SARS VIRUS; SOLUTIONS; STRUCTURE-ACTIVITY RELATIONSHIP;

CORONAVIRUS; MURINE HEPATITIS VIRUS; SARS CORONAVIRUS;

EID: 79953254138     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2011.03.002     Document Type: Article

References (31)

1. S. Raman, P. Bouma, G.D. Williams, and D.A. Brian Stem-loop III in the 5′ untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication J. Virol. 77 2003 6720 6730 (Pubitemid 36666866)
2. S. Raman, and D.A. Brian Stem-loop IV in the 5′ untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication J. Virol. 79 2005 12434 12446 (Pubitemid 41346106)
3. S.J. Goebel, T.B. Miller, C.J. Bennett, K.A. Bernard, and P.S. Masters A hypervariable region within the 3′ cis-acting element of the murine coronavirus genome is nonessential for RNA synthesis but affects pathogenesis J. Virol. 81 2007 1274 1287 (Pubitemid 46167848)
4. R. Zust, T.B. Miller, S.J. Goebel, V. Thiel, and P.S. Masters Genetic interactions between an essential 3′ cis-acting RNA pseudoknot, replicase gene products, and the extreme 3′ end of the mouse coronavirus genome J. Virol. 82 2008 1214 1228
5. P. Liu, L. Li, S.C. Keane, D. Yang, J.L. Leibowitz, and D.P. Giedroc Mouse hepatitis virus stem-loop 2 adopts a uYNMG(U)a-like tetraloop structure that is highly functionally tolerant of base substitutions J. Virol. 83 2009 12084 12093
6. C.J. Budzilowicz, S.P. Wilczynski, and S.R. Weiss Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3′ end of the viral mRNA leader sequence J. Virol. 53 1985 834 840 (Pubitemid 15173289)
7. G. van Marle, J.C. Dobbe, A.P. Gultyaev, W. Luytjes, W.J. Spaan, and E.J. Snijder Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences Proc. Natl. Acad. Sci. USA 96 1999 12056 12061 (Pubitemid 29502857)
8. A.O. Pasternak, E. van den Born, W.J. Spaan, and E.J. Snijder The stability of the duplex between sense and antisense transcription-regulating sequences is a crucial factor in arterivirus subgenomic mRNA synthesis J. Virol. 77 2003 1175 1183 (Pubitemid 36055540)
9. S. Zuniga, I. Sola, S. Alonso, and L. Enjuanes Sequence motifs involved in the regulation of discontinuous coronavirus subgenomic RNA synthesis J. Virol. 78 2004 980 994 (Pubitemid 38067619)
10. B. Yount, R.S. Roberts, L. Lindesmith, and R.S. Baric Rewiring the severe acute respiratory syndrome coronavirus (SARS-CoV) transcription circuit: engineering a recombination-resistant genome Proc. Natl. Acad. Sci. USA 103 2006 12546 12551 (Pubitemid 44267295)
11. P. Liu, L. Li, J.J. Millership, H. Kang, J.L. Leibowitz, and D.P. Giedroc A U-turn motif-containing stem-loop in the coronavirus 5′ untranslated region plays a functional role in replication RNA 13 2007 763 780 (Pubitemid 46641536)
12. S.C. Chen, and R.C. Olsthoorn Group-specific structural features of the 5′-proximal sequences of coronavirus genomic RNAs Virology 401 2010 29 41
13. L. Li, H. Kang, P. Liu, N. Makkinje, S.T. Williamson, J.L. Leibowitz, and D.P. Giedroc Structural lability in stem-loop 1 drives a 5′ UTR-3′ UTR interaction in coronavirus replication J. Mol. Biol. 377 2008 790 803
14. H. Kang, M. Feng, M.E. Schroeder, D.P. Giedroc, and J.L. Leibowitz Putative cis-acting stem-loops in the 5′ untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their mouse hepatitis virus counterparts J. Virol. 80 2006 10600 10614 (Pubitemid 44628906)
15. C. Hsiao, S. Mohan, E. Hershkovitz, A. Tannenbaum, and L.D. Williams Single nucleotide RNA choreography Nucleic Acids Res. 34 2006 1481 1491
16. F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer, and A. Bax NMRPipe: a multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6 1995 277 293
17. Goddard, T.D., Kneller, D.G. SPARKY 3, University of California, San Francisco.
18. B.A. Johnson, and R.A. Blevins NMR view: a computer program for the visualization and analysis of NMR data J. Biomol. NMR 5 1994 603 614
19. B. Furtig, C. Richter, J. Wohnert, and H. Schwalbe NMR spectroscopy of RNA Chembiochem 4 2003 936 962 (Pubitemid 37267582)
20. P. Guntert Automated NMR structure calculation with CYANA Methods Mol. Biol. 278 2004 353 378
21. T. Herrmann, P. Guntert, and K. Wuthrich Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA J. Mol. Biol. 319 2002 209 227 (Pubitemid 34729497)
22. F.C. Oberstrass, A. Lee, R. Stefl, M. Janis, G. Chanfreau, and F.H. Allain Shape-specific recognition in the structure of the Vts1p SAM domain with RNA Nat. Struct. Mol. Biol. 13 2006 160 167 (Pubitemid 43214720)
23. C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clore The Xplor-NIH NMR molecular structure determination package J. Magn. Reson. 160 2003 65 73
24. G.M. Clore, and J. Kuszewski Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation J. Am. Chem. Soc. 125 2003 1518 1525 (Pubitemid 36206232)
25. X.J. Lu, and W.K. Olson 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures Nat. Protoc. 3 2008 1213 1227
26. The PyMOL Molecular Graphics System, Version1.2r3pre, Schrödinger, LLC.
27. I.L. Hofacker Vienna RNA secondary structure server Nucleic Acids Res. 31 2003 3429 3431 (Pubitemid 37442172)
28. P. Thulasi, L.K. Pandya, and B.M. Znosko Thermodynamic characterization of RNA triloops Biochemistry 49 2010 9058 9062
29. B.T. Wimberly, D.E. Brodersen, W.M. Clemons Jr., R.J. Morgan-Warren, A.P. Carter, C. Vonrhein, T. Hartsch, and V. Ramakrishnan Structure of the 30S ribosomal subunit Nature 407 2000 327 339
30. A.P. Carter, W.M. Clemons, D.E. Brodersen, R.J. Morgan-Warren, B.T. Wimberly, and V. Ramakrishnan Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics Nature 407 2000 340 348
31. D.O. Campbell, and P. Legault Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping Biochemistry 44 2005 4157 4170 (Pubitemid 40403955)