T box riboswitch antiterminator affinity modulated by tRNA structural elements

Chemical Biology and Drug Design

Volumn 69, Issue 2, 2007, Pages 139-145

  Means, John A ^a   Wolf, Steffen ^b   Agyeman, Akwasi ^a   Burton, Jeremy S ^a   Simson, Crystal M ^a   Hines, Jennifer V ^a  

^a OHIO UNIVERSITY   (United States)

^b UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

Antiterminator; Fluorescence; Ligand screening; Riboswitch; tRNA

Indexed keywords

T BOX TRANSCRIPTION FACTOR; TETRAMER; TRANSFER RNA;

ARTICLE; BASE PAIRING; BINDING AFFINITY; DISSOCIATION CONSTANT; FLUORESCENCE; GENE INTERACTION; MOLECULAR MODEL; MOLECULE; PRIORITY JOURNAL; RIBOSWITCH; RNA BINDING; STEADY STATE; STRUCTURE ANALYSIS;

BASE PAIRING; GRAM-POSITIVE BACTERIA; MODELS, MOLECULAR; RNA, BACTERIAL; RNA, MESSENGER; RNA, TRANSFER; TERMINATOR REGIONS (GENETICS);

BACTERIA (MICROORGANISMS);

EID: 33947412770     PISSN: 17470277     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2007.00476.x     Document Type: Article

References (38)

1. Grundy F.J., Henkin T.M. (1993) tRNA as a positive regulator of transcription antitermination in Bacillus subtilis. Cell;74:475-482.
2. Grundy F.J., Moir T.R., Haldeman M.T., Henkin T.M. (2002) Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: disparity between conservation and functional requirements. Nucleic Acids Res;30:646-1655.
3. Grundy F.J., Collins J.A., Rollins S.M., Henkin T.M. (2000) tRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene. RNA;6:1131-1141.
4. Grundy F.J., Winkler W.C., Henkin T.M. (2002) tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome. Proc Natl Acad Sci U S A; 99:11121-11126.
5. Grundy F.J., Yousef M.R., Henkin T.M. (2005) Monitoring uncharged tRNA during transcription of the Bacillus subtilis glyQS gene. J Mol Biol;346:73-81.
6. Grundy F.J., Rollins S.M., Henkin T.M. (1994) Interaction between the acceptor end of tRNA and the T-box stimulates antitermination in the Bacillus subtilis tyrS gene - a new role for the discriminator base. J Bacteriol;176:4518-4526.
7. Henkin T.M. (1994) tRNA-directed transcription antitermination. Mol Microbiol;13:381-387.
8. Grundy F.J., Henkin T.M. (2004) Regulation of gene expression by effectors that bind to RNA. Curr Opin Microbiol;7:126-131.
9. Tucker B.J., Breaker R.R. (2005) Riboswitches as versatile gene control elements. Curr Opin Struct Biol;15:342-348.
10. Henkin T.M., Grundy F.J. (2006) Sensing Metabolic Signals with Nascent RNA Transcripts: the T Box and S Box Riboswitches as Paradigms. Cold Spring Harbor Symposia on Quantitative Biology 2006. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press;p. 1-7.
11. Gerdeman M.S., Henkin T.M., Hines J.V. (2003) Solution structure of the Bacillus subtilis T box antiterminator RNA: seven nucleotide bulge characterized by stacking and flexibility. J Mol Biol;326:189-201.
12. Rollins S.M., Grundy F.J., Henkin T.M. (1997) Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene. Mol Microbiol;25:411-421.
13. Gerdeman M.S., Henkin T.M., Hines J.V. (2002) In vitro structure-function studies of the Bacillus subtilis tyrS mRNA antiterminator: evidence for factor-independent tRNA acceptor stem binding specificity. Nucleic Acids Res;30:1065-1072.
14. Means J.A., Hines J.V. (2005) Fluorescence resonance energy transfer studies of aminoglycoside binding to a T box antiterminator RNA. Bioorg Med Chem Lett;15:2169-2172.
15. Means J.A., Katz S.J., Nayek A., Anupam R., Hines J.V., Bergmeier S.C. (2006) Structure activity studies of oxazolidinone analogs as RNA-binding agents. Bioorg Med Chem Lett;16:3600-3604.
16. Milligan J.F., Groebe D.R., Witherell G.W., Uhlenbeck O.C. (1987) Oligoribonucleotide synthesis using T7 RNA-polymerase and synthetic DNA templates. Nucleic Acids Res;15:8783-8798.
17. Milligan J.F., Uhlenbeck O.C. (1989) Synthesis of small RNAs using T7 RNA-polymerase. Methods Enzymol;180:51-62.
18. Sanbrook J., Fritsch E.F., Maniatis T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor: Cold Spring Harbor Lab. Press.
19. Kirk S.R., Luedtke N.W., Tor Y. (2001) 2-aminopurine as a real-time probe of enzymatic cleavage and inhibition of hammerhead ribozymes. Bioorg Med Chem;9:2295-2301.
20. Rist M.J., Marino J.P. (2001) Association of an RNA kissing complex analyzed using 2-aminopurine fluorescence. Nucleic Acids Res;29:2401-2408.
21. O'Neill M.A., Barton J.K. (2002) 2-Aminopurine: a probe of structural dynamics and charge transfer in DNA and DNA:RNA hybrids. J Am Chem Soc;124:13053-13066.
22. Shi J.P., Francklyn C., Hill K., Schimmel P. (1990) A nucleotide that enhances the charging of RNA minihelix sequence variants with alanine. Biochemistry;29:3621-3626.
23. Nashimoto M., Tamura M., Kaspar R.L. (1999) Minimum requirements for substrates of mammalian tRNA 3′ processing endoribonuclease. Biochemistry;38:12089-12096.
24. Mathews D.H., Sabina J., Zuker M., Turner D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol;288:911-940.
25. Zuker M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res;31:3406-3415.
26. Bradrick T.D., Marino J.P. (2004) Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA. RNA;10:1459-1468.
27. Grundy F.J., Hodil S.E., Rollins S.M., Henkin T.M. (1997) Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination. J Bacteriol;179:2587-2594.
28. Lakowicz J.R. (1999) Principles of Fluorescence Spectroscopy, 2nd edn. New York, NY: Kluwer Academic/Plenum Publishers.
29. Khvorova A., Lescoute A., Westhof E., Jayasena S.D. (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol;10:708-712.
30. Uhlenbeck O.C. (2003) Less isn't always more. RNA;9:1415-1417.
31. Gly and the Bacillus subtilis glyQS T box leader RNA. J Mol Biol;349:273-287.
32. Fauzi H., Jack K.D., Hines J.V. (2005) In vitro selection to identity determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding. Nucleic Acids Res;33:2595-2602.
33. Yousef M.R., Grundy F.J., Henkin T.M. (2003) tRNA requirements for glyQS antitermination: a new twist on tRNA. RNA;9:1148-1156.
34. Smagowicz J., Wierzchowski K.L. (1974) Lowest excited states of 2-aminopurine. J Luminesc;8:210-232.
35. Evans K.O., Xu D., Kim Y., Nordlund T.M. (1992) 2-Aminopurine optical spectra: solvent, pentose ring and DNA helix melting dependence. J Fluoresc;2:209-216.
36. Ward D.C., Reich E., Stryer L. (1969) Fluorescence studies of nucleotides and polynucleotides: I. Formycin, 2-aminopurine riboside, 2, 6-diaminopurine riboside, and their derivatives. J Biol Chem;244:1228-1237.
37. Scheit K.H., Rackwitz H.R. (1982) Synthesis and physicochemical properties of 2 analogs of poly(da)-poly(2-aminopurine-9-beta-D- deoxyribonucleotide) and poly 2-amino-deoxyadenylic acid. Nucleic Acids Res;10:4059-4069.
38. Guest C.R., Hochstrasser R.A., Sowers L.C., Millar D.P. (1991) Dynamics of mismatched base-pairs in DNA. Biochemistry;30:3271-3279.