Isolation of a site-specifically modified RNA from an unmodified transcript

Nucleic Acids Research

Volumn 34, Issue 3, 2006, Pages

  Hou, Ya Ming ^a   Li, Zhi ^a   Gamper, Howard ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RIBONUCLEASE H; TRANSFER RNA; OLIGONUCLEOTIDE;

ARTICLE; BIOCHEMISTRY; DNA CLEAVAGE; IN VITRO STUDY; METHANOCOCCUS JANNASCHII; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; RNA HYBRIDIZATION; RNA ISOLATION; CHEMISTRY; DNA METHYLATION; GENETICS; METABOLISM; METHANOCOCCUS; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; RNA PROCESSING;

BACTERIA (MICROORGANISMS); METHANOCALDOCOCCUS JANNASCHII;

BASE SEQUENCE; DNA METHYLATION; METHANOCOCCUS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; RIBONUCLEASE H, CALF THYMUS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, TRANSFER;

EID: 33644872214     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gnj018     Document Type: Article

References (34)

1. Decatur,W.A. and Fournier,M.J. (2002) rRNA modifications and ribosome function. Trends Biochem. Sci., 27, 344-351.
2. Agris,P.F. (2004) Decoding the genome: A modified view. Nucleic Acids Res., 32, 223-238.
3. Bjork,G. (1995) Biosynthesis and function of modified nucleotides. In Soll,D. and RajBhandary,U.L. (eds), tRNA: Structure, Biosynthesis, and Function. ASM, Washington, DC, pp. 165-206.
4. Motorin,Y. and Grosjean,H. (1998) Chemical structures and classification of posttranscriptionally modified nucleotides in RNA. In Grosjean,H. and Benne,R. (eds), Modification and Editing of RNA. American Society for Microbiology, Washington, DC, pp. 543-550.
5. Yarian,C., Marszalek,M., Sochacka,E., Malkiewicz,A., Guenther,R., Miskiewicz,A. and Agris,P.F. (2000) Modified nucleoside dependent Watson-Crick and wobble codon binding by tRNALysUUU species. Biochemistry, 39, 13390-13395.
6. Agris,P.F. (1996) The importance of being modified: Roles of modified nucleosides and Mg2+ in RNA structure and function. Prog. Nucleic Acid Res. Mol. Biol., 53, 79-129.
7. Nakanishi,K. and Nureki,O. (2005) Recent progress of structural biology of tRNA processing and modification. Mol. Cells, 19, 157-166.
8. Urbonavicius,J., Qian,Q., Durand,J.M., Hagervall,T.G. and Bjork,G.R. (2001) Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J., 20, 4863-4873.
9. Bjork,G.R. (1998) Modified nucleosides at positions 34 and 37 of tRNAs and their predicted coding capacities. In Grosjean,H. and Benne,R. (eds), Modification and Editing of RNA. American Society for Microbiology, Washington, DC, pp. 577-581.
10. Li,J., Esberg,B., Curran,J.F. and Bjork,G.R. (1997) Three modified nucleosides present in the anticodon stem and loop influence the in vivo aa-tRNA selection in a tRNA-dependent manner. J. Mol. Biol., 271, 209-221.
11. Bjork,G.R., Wikstrom,P.M. and Bystrom,A.S. (1989) Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. Science, 244, 986-989.
12. Hagervall,T.G., Ericson,J.U., Esberg,K.B., Li,J.N. and Bjork,G.R. (1990) Role of tRNA modification in translational fidelity. Biochim. Biophys. Acta., 1050, 263-266.
13. Bjork,G.R. and Kjellin-Straby,K. (1978) General screening procedure for RNA modificationless mutants: Isolation of Escherichia coli strains with specific defects in RNA methylation. J. Bacteriol., 133, 499-507.
14. Bjork,G.R., Jacobsson,K., Nilsson,K., Johansson,M.J., Bystrom,A.S. and Persson,O.P. (2001) A primordial tRNA modification required for the evolution of life? EMBO J., 20, 231-239.
15. Christian,T., Evilia,C., Williams,S. and Hou, Y.M. (2004) Distinct origins of tRNA(m1G37) methyltransferase. J. Mol. Biol., 339, 707-719.
16. Brule,H., Elliott,M., Redlak,, Zehner,Z.E. and Holmes,W.M. (2004) Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein. Biochemistry, 43, 9243-9255.
17. Redlak,M., Andraos-Selim,C., Giege,R., Florentz,C. and Holmes,W.M. (1997) Interaction of tRNA with tRNA (guanosine-1)methyltransferase: binding specificity determinants involve the dinucleotide G36pG37 and tertiary structure. Biochemistry, 36, 8699-8709.
18. Berkower,I., Leis,J. and Hurwitz,J. (1973) Isolation and characterization of an endonuclease from Escherichia coli specific for ribonucleic acid in ribonucleic acid-deoxyribonucleic acid hybrid structures. J. Biol. Chem., 248, 5914-5921.
19. Nowotny,M., Gaidamakov,S.A., Crouch,R.J. and Yang,W. (2005) Crystal structures of RNase H bound to an RNA/DNA hybrid: Substrate specificity and metal-dependent catalysis. Cell, 121, 1005-1016.
20. Yu,Y.T., Shu,M.D. and Steitz,J.A. (1997) A new method for detecting sites of 2′-O-methylation in RNA molecules. RNA, 3, 324-331.
21. Lipman,R.S., Wang,J., Sowers,K.R. and Hou,Y.M. (2002) Prevention of mis-aminoacylation of a dual-specificity aminoacyl-tRNA synthetase. J. Mol. Biol., 315, 943-949.
22. Jackman,J.E., Montange,R.K., Malik,H.S. and Phizicky,E.M. (2003) Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. RNA, 9, 574-585.
23. Droogmans,L., Roovers,M., Bujnicki,J.M., Tricot,C., Hartsch,T., Stalon,V. and Grosjean,H. (2003) Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucleic Acids Res., 31, 2148-2156.
24. Francis,T.A., Ehrenfeld,G.M., Gregory,M.R. and Hecht,S.M. (1983) Transfer RNA pyrophosphorolysis with CTP(ATP):tRNA nucleotidyltransferase. A direct route to tRNAs modified at the 3′ terminus. J. Biol. Chem., 258, 4279-4284.
25. Lapham,J. and Crothers,D.M. (1996) RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. RNA, 2, 289-296.
26. Lapham,J., Yu,Y.T., Shu,M.D., Steitz,J.A. and Crothers,D.M. (1997) The position of site-directed cleavage of RNA using RNase H and 2′-O-methyl oligonucleotides is dependent on the enzyme source. RNA, 3, 950-951.
27. Hou,Y.M. and Gamper,H.B. (1996) Inhibition of tRNA aminoacylation by 2′-O-methyl oligonucleotides. Biochemistry, 35, 15340-15348.
28. Wallace,R.B., Shaffer,J., Murphy,R.F., Bonner,J., Hirose,T. and Itakura,K. (1979) Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: The effect of single base pair mismatch. Nucleic Acids Res., 6, 3543-3557.
29. Zoller,M.J. and Smith,M. (1983) Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors. Methods Enzymol., 100, 468-500.
30. Stuart,J.W., Koshlap,K.M., Guenther,R. and Agris,P.F. (2003) Naturally-occurring modification restricts the anticodon domain conformational space of tRNA(Phe). J. Mol. Biol., 334, 901-918.
31. Steitz,T.A. and Steitz,J.A. (1993) A general two-metal-ion mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA, 90, 6498-6502.
32. 2+-dependent RNase HIII from Bacillus subtilis: Classification of RNases H into three families. Biochemistry, 38, 605-618.
33. Moore,M.J. and Query,C.C. (2000) Joining of RNAs by splinted ligation. Methods Enzymol., 317, 109-123.
34. Sherlin,L.D., Bullock,T.L., Nissan,T.A., Perona,J.J., Lariviere,F.J., Uhlenbeck,O.C. and Scaringe,S.A. (2001) Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization. RNA, 7, 1671-1678.