T box transcription antitermination riboswitch: Influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1789, Issue 3, 2009, Pages 185-191

  Fauzi, Hamid ^a   Agyeman, Akwasi ^a   Hines, Jennifer V ^a  

^a OHIO UNIVERSITY   (United States)

Author keywords

Binding; In vitro selection; Riboswitch; RNA; T box; Transcription antitermination

Indexed keywords

ADENOSINE TRIPHOSPHATE; COMPLEMENTARY DNA; DNA POLYMERASE; PHOSPHORUS 32; RNA POLYMERASE; SINGLE STRANDED DNA; T BOX TRANSCRIPTION FACTOR; TRANSFER RNA;

ANISOTROPY; ARTICLE; BINDING AFFINITY; FLUORESCENCE; GENETIC TRANSCRIPTION; IN VITRO SELECTION; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIBOSWITCH; RNA BINDING; RNA STRUCTURE; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION;

BASE PAIRING; BASE SEQUENCE; CONSERVED SEQUENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, BACTERIAL; RNA, MESSENGER; RNA, TRANSFER; TERMINATOR REGIONS, GENETIC; TRANSCRIPTION, GENETIC;

EID: 61449157240     PISSN: 18749399     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2008.12.004     Document Type: Article

References (45)

1. Grundy F.J., and Henkin T.M. Regulation of gene expression by effectors that bind to RNA. Curr. Opin. Microbiol. 7 (2004) 126-131
2. Tucker B.J., and Breaker R.R. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 15 (2005) 342-348
3. Henkin T.M., and Grundy F.J. Cold Spring Harbor Symp. Quant. Biol. Vol. 71 (2006), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 1-7
4. Grundy F.J., Rollins S.M., and Henkin T.M. Interaction between the acceptor end of transfer-RNA and the T box stimulates antitermination in the Bacillus-Subtilis tyrS gene-a new role for the discriminator base. J. Bacteriol. 176 (1994) 4518-4526
5. Grundy F.J., and Henkin T.M. The T box and S box transcription termination control systems. Front. Biosci. 8 (2003) D20-D31
6. Vitreschak A.G., Mironov A.A., Lyubetsky V.A., and Gelfand M.S. Comparative genomic analysis of T-box regulatory systems in bacteria. RNA 14 (2008) 717-735
7. Grundy F.J., Moir T.R., Haldeman M.T., and Henkin T.M. Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: disparity between conservation and functional requirements. Nucleic Acids Res. 30 (2002) 1646-1655
8. Grundy F.J., Hodil S.E., Rollins S.M., and Henkin T.M. Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination. J. Bacteriol. 179 (1997) 2587-2594
9. Grundy F.J., Collins J.A., Rollins S.M., and Henkin T.M. tRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene. RNA 6 (2000) 1131-1141
10. Nelson A.R., Henkin T.M., and Agris P.F. tRNA regulation of gene expression: interaction of an mRNA 5′-UTR with a regulatory tRNA. RNA 12 (2006) 1254-1261
11. Rollins S.M., Grundy F.J., and Henkin T.M. Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene. Molec. Microbiol. 25 (1997) 411-421
12. Grundy F.J., Winkler W.C., and Henkin T.M. tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 11121-11126
13. Putzer H., Condon C., Brechemier-Baey D., Brito R., and Grunberg-Manago M. Transfer RNA-mediated antitermination in vitro. Nucleic Acids Res. 30 (2002) 3026-3033
14. Gerdeman M.S., Henkin T.M., and Hines J.V. Solution structure of the Bacillus subtilis T box antiterminator RNA: seven nucleotide bulge characterized by stacking and flexibility. J. Mol. Biol. 326 (2003) 189-201
15. Gerdeman M.S., Henkin T.M., and Hines J.V. 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 (2002) 1065-1072
16. Fauzi H., Jack K.D., and Hines J.V. In vitro selection to identify determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding. Nucleic Acids Res. 33 (2005) 2595-2602
17. 2+ binding site in T box antiterminator RNA. Biochem. Biophys. Res. Commun. 370 (2008) 306-310
18. Wilson D.S., and Szostak J.W. In vitro selection of functional nucleic acids. Ann. Rev. Bioch. 68 (1999) 611-647
19. Garst A.D., Heroux A., Rambo R.P., and Batey R.T. Crystal structure of the lysine riboswitch regulatory mRNA element. J. Biol. Chem. 283 (2008) 22347-22351
20. Gilbert S.D., Rambo R.P., Van Tyne D., and Batey R.T. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat. Struct. Biol. 15 (2008) 177-182
21. Montange R.K., and Batey R.T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441 (2006) 1172-1175
22. Serganov A., Polonskaia A., Phan A.T., Breaker R.R., and Patel D.J. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441 (2006) 1167-1171
23. Thore S., Leibundgut M., and Ban N. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312 (2006) 1208-1211
24. Holbrook S.R. RNA structure: the long and the short of it. Curr. Opin. Struct. Biol. 15 (2005) 302-308
25. Batey R.T., Gilbert S.D., and Montange R.K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432 (2004) 411-415
26. Milligan J.F., and Uhlenbeck O.C. Synthesis of small RNAs using T7 RNA-polymerase. Methods Enzymol. 180 (1989) 51-62
27. Green M.R., Maniatis T., and Melton D.A. Human beta-globin pre-mRNA synthesized in vitro is accurately spliced in xenopus oocyte nuclei. Cell 32 (1983) 681-694
28. Means J.A., Wolf S., Agyeman A., Burton J.S., Simson C.M., and Hines J.V. T box riboswitch antiterminator affinity modulated by tRNA structural elements. Chem. Biol. Drug Design 69 (2007) 139-145
29. Uhlenbeck O.C. Less isn't always more. RNA 9 (2003) 1415-1417
30. Khvorova A., Lescoute A., Westhof E., and Jayasena S.D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol. 10 (2003)
31. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415
32. Doudna J.A., Szostak J.W., Rich A., and Usman N. Chemical synthesis of oligoribonucleotides containing 2-aminopurine-substrates for the investigation of ribozyme function. J. Org. Chem. 55 (1990) 5547-5549
33. Fujimoto J., Nuesca Z., Mazurek M., and Sowers L.C. Synthesis and hydrolysis of oligodeoxyribonucleotides containing 2-aminopurine. Nucleic Acids Res. 24 (1996) 754-759
34. Rist M.J., and Marino J.P. Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions. Curr. Org. Chem. 6 (2002) 775-793
35. Rist M.J., and Marino J.P. Association of an RNA kissing complex analyzed using 2-aminopurine fluorescence. Nucleic Acids Res. 29 (2001) 2401-2408
36. Lakowicz J. Principles of Fluorescence Spectrocopy. 2nd ed. (1999), Kluwer Academic/Plenum Publishers, New York, NY
37. Shchyolkina A.K., Borisova O.F., Chernov B.K., and Tchurikov N.A. Parallel-stranded DNA with mixed sequence. Evidence for conformational transition in solution at low water activity. J. Biomol. Struct. Dyn. 11 (1994) 1237-1249
38. Fortsch I., Fritzsche H., Birch-Hirschfeld E., Evertsz E., Klement R., Jovin T.M., and Zimmer C. Parallel-stranded duplex DNA containing dA.dU base pairs. Biopolymers 38 (1996) 209-220
39. Shchyolkina A.K., Borisova O.F., Livshits M.A., Pozmogova G.E., Chernov B.K., Klement R., and Jovin T.M. Parallel-stranded DNA with mixed AT/GC composition: role of trans G.C base pairs in sequence dependent helical stability. Biochemistry 39 (2000) 10034-10044
40. Germann M.W., Kalisch B.W., and van de Sande J.H. Relative stability of parallel- and antiparallel-stranded duplex DNA. Biochemistry 27 (1988) 8302-8306
41. Duconge F., and Toulme J.J. In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA 5 (1999) 1605-1614
42. Sekkal D., Dausse E., Di Primo C., Darfeuille F., Boiziau C., and Toulme J.J. In vitro selection of DNA aptamers against the HIV-1 TAR RNA hairpin. Antisense Nucleic Acid Drug Dev. 12 (2002) 265-274
43. Scarabino D., Crisari A., Lorenzini S., Williams K., and Tocchini-Valentini G.P. tRNA prefers to kiss. EMBO J. 18 (1999) 4571-4578
44. Grundy F.J., and Henkin T.M. Transfer-RNA as a positive regulator of transcription antitermination in Bacillus subtilis. Cell 74 (1993) 475-482
45. Yousef M.R., Grundy F.J., and Henkin T.M. tRNA requirements for glyQS antitermination: a new twist on tRNA. RNA 9 (2003) 1148-1156