Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch

Nucleic Acids Research

Volumn 35, Issue 2, 2007, Pages 572-583

  Noeske, Jonas ^a   Buck, Janina ^a   Fürtig, Boris ^a   Nasiri, Hamid R ^a   Schwalbe, Harald ^a   Wöhnert, Jens ^b  

^a GOETHE UNIVERSITY   (Germany)

^b UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE; HYPOXANTHINE; MAGNESIUM; MESSENGER RNA; MUTANT PROTEIN; TRANSCRIPTION TERMINATION FACTOR RHO;

5' UNTRANSLATED REGION; ARTICLE; BASE PAIRING; CELL SPECIFICITY; CONFORMATIONAL TRANSITION; GENE CONTROL; GENE EXPRESSION; HYDROGEN BOND; LIGAND BINDING; METABOLITE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROCESSING; PROTEIN STRUCTURE; RIBOSWITCH; RNA BINDING;

5' UNTRANSLATED REGIONS; ALLOSTERIC REGULATION; APTAMERS, NUCLEOTIDE; BACILLUS SUBTILIS; BASE SEQUENCE; GUANINE; HYPOXANTHINE; LIGANDS; MAGNESIUM; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RNA, BACTERIAL;

EID: 33846898497     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1094     Document Type: Article

References (39)

1. Hermann,T. and Patel,D.J. (2000) Adaptive recognition by nucleic acid aptamers. Science, 287, 820-825.
2. Nonin,S., Jiang,F. and Patel,D.J. (1997) Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex. J. Mol. Biol., 268, 359-374.
3. Jucker,F.M., Phillips,R.M., McCallum,S.A. and Pardi,A. (2003) Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex. Biochemistry, 42, 2560-2567.
4. Patel,D.J., Suri,A.K., Jiang,F., Jiang,L., Fan,P., Kumar,R.A. and Nonin,S. (1997) Structure, recognition and adaptive binding in RNA aptamer complexes. J. Mol. Biol., 272, 645-664.
5. Mandal,M., Boese,B., Barrick,J.E., Winkler,W.C. and Breaker,R.R. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell, 113, 577-586.
6. Sudarsan,N., Barrick,J.E. and Breaker,R.R. (2003) Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA, 9, 644-647.
7. Kubodera,T., Watanabe,M., Yoshiuchi,K., Yamashita,N., Nishimura,A., Nakai,S., Gomi,K. and Hanamoto,H. (2003) Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR. FEBS Lett., 555, 516-520.
8. Batey,R.T., Gilbert,S.D. and Montange,R.K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411-415.
9. Serganov,A., Yuan,Y.R., Pikovskaya,O., Polonskaia,A., Malinina,L., Phan,A.T., Hobartner,C., Micura,R., Breaker,R.R. and Patel,D.J. (2004) Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol., 11, 1729-1741.
10. Thore,S., Leibundgut,M. and Ban,N. (2006) Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science, 312, 1208-1211.
11. Serganov,A., Polonskaia,A., Phan,A.T., Breaker,R.R. and Patel,D.J. (2006) Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature, 441, 1167-1171.
12. Edwards,T.E. and Ferre-D'Amare,A.R. (2006) Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure, 14, 1459-1468.
13. Montange,R.K. and Batey,R.T. (2006) Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature, 441, 1172-1175.
14. Noeske,J., Richter,C., Grundl,M.A., Nasiri,H.R., Schwalbe,H. and Wohnert,J. (2005) An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. Proc. Natl Acad. Sci. USA, 102, 1372-1377.
15. Gilbert,S.D., Stoddard,C.D., Wise,S.J. and Batey,R.T. (2006) Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J. Mol. Biol., 359, 754-768.
16. Furtig,B., Richter,C., Wohnert,J. and Schwalbe,H. (2003) NMR spectroscopy of RNA. Chembiochem, 4, 936-962.
17. Chworos,A., Severcan,I., Koyfman,A.Y., Weinkam,P., Oroudjev,E., Hansma,H.G. and Jaeger,L. (2004) Building programmable jigsaw puzzles with RNA. Science, 306, 2068-2072.
18. Stoldt,M., Wohnert,J., Ohlenschlager,O., Gorlach,M. and Brown,L.R. (1999) The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition. EMBO J., 18, 6508-6521.
19. Bartels,C., Xia,T.-H., Billeter,M., Güntert,P. and Wüthrich,K. (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR, 6, 1-10.
20. Piotto,M., Saudek,V. and Sklenar,V. (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR, 2, 661-665.
21. Grzesiek,S. and Bax,A. (1993) The importance of not saturating water in protein NMR. Application to sensitivity enhancement and NOE measurements. J. Am. Chem. Soc., 115, 12593-12594.
22. 15N HSQC experiments. J. Biomol. NMR, 4, 117-122.
23. Wijmenga,S.S. and van Buuren,B.N.M. (1998) The use of NMR methods for conformational studies of nucleic acids. Prog. NMR Spectroscopy, 32, 287-387.
24. NN couplings. J. Am. Chem. Soc., 120, 8293-8297.
25. Ohlenschlager,O., Wohnert,J., Bucci,E., Seitz,S., Hafner,S., Ramachandran,R., Zell,R. and Gorlach,M. (2004) The structure of the stem-loop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C. Structure, 12, 237-248.
26. Jansen,J.A., McCarthy,T.J., Soukup,G.A. and Soukup,J.K. (2006) Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS ribozyme. Nature Struct. Mol. Biol., 13, 517-523.
27. Hampel,K.J. and Tinsley,M.M. (2006) Evidence for preorganization of the glmS ribozyme ligand binding pocket. Biochemistry, 45, 7861-7871.
28. McDaniel,B.A., Grundy,F.J. and Henkin,T.M. (2005) A tertiary structural element in S box leader RNAs is required for S-adenosylmethionine-directed transcription termination. Mol. Microbiol., 57, 1008-1021.
29. Khvorova,A., Lescoute,A., Westhof,E. and Jayasena,S.D. (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nature Struct. Biol., 10, 708-712.
30. De la Pena,M., Gago,S. and Flores,R. (2003) Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J., 22, 5561-5570.
31. Murchie,A.I., Thomson,J.B., Walter,F. and Lilley,D.M. (1998) Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol. Cell, 1, 873-881.
32. Corbino,K.A., Barrick,J.E., Lim,J., Welz,R., Tucker,B.J., Puskarz,I., Mandal,M., Rudnick,N.D. and Breaker,R.R. (2005) Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol., 6, R70.
33. Roth,A., Nahvi,A., Lee,M., Jona,I. and Breaker,R.R. (2006) Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA, 12, 607-619.
34. Wilkinson,S.R. and Been,M.D. (2005) A pseudoknot in the 3′ non-core region of the glmS ribozyme enhances self-cleavage activity. RNA, 11, 1788-1794.
35. Soukup,G.A. (2006) Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure. Nucleic Acids Res., 34, 968-975.
36. Grundy,F.J., Lehman,S.C. and Henkin,T.M. (2003) The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc. Natl Acad. Sci. USA, 100, 12057-12062.
37. LeMay,J.F., Penedo,J.C., Tremblay,R., Lilley,D.M. and Lafontaine,D.A. (2006) Folding of the adenine riboswitch. Chem. Biol., 13, 857-868.
38. Cate,J.H., Gooding,A.R., Podell,E., Zhou,K., Golden,B.L., Kundrot,C.E., Cech,T.R. and Doudna,J.A. (1996) Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science, 273, 1678-1685.
39. Nissen,P., Ippolito,J.A., Ban,N., Moore,P.B. and Steitz,T.A. (2001) RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc. Natl Acad. Sci. USA, 98, 4899-4903.