Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch

RNA

Volumn 17, Issue 1, 2011, Pages 74-84

  Erion, Thanh V ^a   Strobel, Scott A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Aptamers; Cooperativity; Glycine; Riboswit

Indexed keywords

APTAMER; GLYCINE;

ARTICLE; LIGAND BINDING; MACROMOLECULE; MOLECULAR DYNAMICS; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN RNA BINDING; RIBOSWITCH; RNA STRUCTURE;

APTAMERS, NUCLEOTIDE; BASE PAIRING; BASE SEQUENCE; BINDING SITES; DNA FOOTPRINTING; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GLYCINE; HYDROXYL RADICAL; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RIBOSWITCH; RNA, BACTERIAL; VIBRIO CHOLERAE;

EID: 78650424317     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2271511     Document Type: Article

References (44)

1. Bohr C, Hasselbach KA, Krogh A. 1904. Uber einen in biologischen beziehung wichtigen einfluss, den die kohlen-suer-spannung des blutes auf dessen sauerstoffbindung ubt. Skand Arch Physiol 15: 401-412.
2. Cilley CD, Williamson JR. 1999. PACE analysis of RNA-peptide interactions. Methods Mol Biol 118: 129-141.
3. Copeland RA. 2000. Cooperativity in enyzme catalysis. Enzymes: A practical introduction to structure, mechanisms, and data analysis. Wiley-VCH, Inc., Berlin, Germany.
4. Cromie MJ, Shi Y, Latifi T, Groisman EA. 2006. An RNA sensor for intracellular Mg(2+). Cell 125: 71-84.
5. Forsen S, Linse S. 1995. Cooperativity: Over the Hill. Trends Biochem Sci 20: 495-497.
6. Fuchs RT, Grundy FJ, Henkin TM. 2006. The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat Struct Mol Biol 13: 226-233.
7. Gagnon MG, Steinberg SV. 2002. GU receptors of double helices mediate tRNA movement in the ribosome. RNA 8: 873-877.
8. Gagnon MG, Mukhopadhyay A, Steinberg SV. 2006. Close packing of helices 3 and 12 of 16S rRNA is required for normal ribosome function. J Biol Chem 281: 39349-39357.
9. Gilbert SD, Rambo RP, Van Tyne D, Batey RT. 2008. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol 2: 177-182.
10. Grundy FJ, Lehman SC, Henkin TM. 2003. The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc Natl Acad Sci 100: 12057-12062.
11. Hill AV. 1910. The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40: iv-vii.
12. Jose AM, Soukup GA, Breaker RR. 2001. Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res 29: 1631-1637.
13. Koizumi M, Soukup GA, Kerr JN, Breaker RR. 1999. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nat Struct Biol 6: 1062-1071.
14. Koshland DE Jr, Hamadani K. 2002. Proteomics and models for enzyme cooperativity. J Biol Chem 277: 46841-46844.
15. Kwon M, Strobel SA. 2008. Chemical basis of glycine riboswitch cooperativity. RNA 14: 25-34.
16. Laing C, Jung S, Iqbal A, Schlick T. 2009. Tertiary motifs revealed in analyses of higher-order RNA junctions. J Mol Biol 393: 67-82.
17. Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. 2007. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol 365: 1393-1406.
18. Mandal M, Breaker RR. 2004. Gene regulation by riboswitches. Nat Rev Mol Cell Biol 5: 451-463.
19. Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. 2003. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113: 577-586.
20. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279.
21. Montange RK, Batey RT. 2006. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441: 1172-1175.
22. Ortoleva-Donnelly L, Kronman M, Strobel SA. 1998. Identifying RNA minor groove tertiary contacts by nucleotide analogue interference mapping with N2-methylguanosine. Biochemistry 37: 12933-12942.
23. Perutz MF. 1989. Mechanisms of cooperativity and allosteric regulation in proteins. Q Rev Biophys 22: 139-237.
24. Pogozelski WK, McNeese TJ, Tullius TD. 1995. What species is responsible for strand scission in the reaction of [Fe(EDTA)]2-and H2O2 with DNA? J Am Chem Soc 117: 6428-6433.
25. Regulski EE, Breaker RR. 2008. In-line probing analysis of riboswitches. Methods Mol Biol 419: 53-67.
26. Rife JP, Cheng CS, Moore PB, Strobel SA. 1998. N 2-methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops. Nucleic Acids Res 26: 3640-3644.
27. Roth A, Breaker RR. 2009. The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78: 305-334.
28. Royer WE Jr, Knapp JE, Strand K, Heaslet HA. 2001. Cooperative hemoglobins: Conserved fold, diverse quaternary assemblies and allosteric mechanisms. Trends Biochem Sci 26: 297-304.
29. Ryder SP, Strobel SA. 1999. Nucleotide analog interference mapping. Methods 18: 38-50.
30. Serganov A, Patel DJ. 2009. Amino acid recognition and gene regulation by riboswitches. Biochim Biophys Acta 1789: 592-611.
31. Serganov A, Huang L, Patel DJ. 2008. Structure insights into aminoacid binding and gene control by a lysine riboswitch. Nature 455: 1263-1267.
32. Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA. 2009. Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol 16: 1218-1223.
33. Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR. 2003. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev 17: 2688-2697. (Pubitemid 37363073)
34. Sudarsan N, Hammond MC, Block KF, Welz R, Barrick JE, Roth A, Breaker RR. 2006. Tandem riboswitch architectures exhibit complex gene control functions. Science 314: 300-304.
35. Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR. 2008. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321: 411-413.
36. Tripp HJ, Schwalbach MS, Meyer MM, Kitner JB, Breaker RR, Giovannoni SJ. 2009. Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. Environ Microbiol 11: 230-238.
37. Tullius TD, Greenbaum JA. 2005. Mapping nucleic acid structure by hydroxyl radical cleavage. Curr Opin Chem Biol 9: 127-134.
38. Turner GJ, Galacteros F, Doyle ML, Hedlund B, Pettigrew DW, Turner BW, Smith FR, Moo-Penn W, Rucknagel DL, Ackers GK. 1992. Mutagenic dissection of hemoglobin cooperativity: Effects of amino acid alteration on subunit assembly of oxy and deoxy tetramers. Proteins 14: 333-350.
39. Welz R, Breaker RR. 2007. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA 13: 573-582.
40. Whitty A. 2008. Cooperativity and biological complexity. Nat Chem Biol 4: 435-439.
41. Winkler WC, Breaker RR. 2005. Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol 59: 487-517.
42. Winkler WC, Cohen-Chalamish S, Breaker RR. 2002. An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci 99: 15908-15913.
43. Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR. 2003. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol 10: 701-707. (Pubitemid 37052407)
44. Yarnell WS, Roberts JW. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284: 611-615.