Chapter 11 Identification and Analysis of tRNAs That Are Degraded in Saccharomyces cerevisiae Due To Lack of Modifications

Methods in Enzymology

Volumn 449, Issue C, 2008, Pages 221-237

  Chernyakov, Irina ^a   Baker, Melanie A ^a   Grayhack, Elizabeth J ^a   Phizicky, Eric M ^a  

^a UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

AMINOACYLATION; MICROARRAY ANALYSIS; NONHUMAN; NORTHERN BLOTTING; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; RNA ANALYSIS; RNA DEGRADATION; RNA ISOLATION; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 59649123170     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(08)02411-7     Document Type: Chapter

References (25)

1. Alexandrov A., Chernyakov I., Gu W., Hiley S.L., Hughes T.R., Grayhack E.J., and Phizicky E.M. Rapid tRNA decay can result from lack of nonessential modifications. Mol. Cell 21 (2006) 87-96
2. Anderson J., Phan L., Cuesta R., Carlson B.A., Pak M., Asano K., Bjork G.R., Tamame M., and Hinnebusch A.G. The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. Genes Dev. 12 (1998) 3650-3662
3. Copela L.A., Chakshusmathi G., Sherrer R.L., and Wolin S.L. The La protein functions redundantly with tRNA modification enzymes to ensure tRNA structural stability. RNA 12 (2006) 644-654
4. Derrick W.B., and Horowitz J. Probing structural differences between native and in vitro transcribed Escherichia coli valine transfer RNA: Evidence for stable base modification-dependent conformers. Nucleic Acids Res. 21 (1993) 4948-4953
5. Dittmar K.A., Sorensen M.A., Elf J., Ehrenberg M., and Pan T. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 6 (2005) 151-157
6. Gu W., Hurto R.L., Hopper A.K., Grayhack E.J., and Phizicky E.M. Depletion of Saccharomyces cerevisiae tRNA(His) guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m(5)C. Mol. Cell. Biol. 25 (2005) 8191-8201
7. Hall K.B., Sampson J.R., Uhlenbeck O.C., and Redfield A.G. Structure of an unmodified tRNA molecule. Biochem. 28 (1989) 5794-5801
8. Hiley S.L., Jackman J., Babak T., Trochesset M., Morris Q.D., Phizicky E., and Hughes T.R. Detection and discovery of RNA modifications using microarrays. Nucleic Acids Res. 33 (2005) e2
9. Hughes T.R., Hiley S.L., Saltzman A.L., Babak T., and Blencowe B.J. Microarray analysis of RNA processing and modification. Methods Enzymol. 410 (2006) 300-316
10. Jimenez A., Tipper D.J., and Davies J. Mode of action of thiolutin, an inhibitor of macromolecular synthesis in Saccharomyces cerevisiae. Antimicrob. Agents Chemother. 3 (1973) 729-738
11. Johansson M.J., and Bystrom A.S. Dual function of the tRNA(m(5)U54)methyltransferase in tRNA maturation. RNA 8 (2002) 324-335
12. Jones G.M., Stalker J., Humphray S., West A., Cox T., Rogers J., Dunham I., and Prelich G. A systematic library for comprehensive overexpression screens in Saccharomyces cerevisiae. Nature Methods (2008)
13. Met in S. cerevisiae. Genes Dev. 18 (2004) 1227-1240
14. Kadaba S., Wang X., and Anderson J.T. Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. RNA 12 (2006) 508-521
15. Kohrer C., and Rajbhandary U.L. The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases. Methods 44 (2008) 129-138
16. Kotelawala L., Grayhack E.J., and Phizicky E.M. Identification of yeast tRNA Um44 2′-O-methyltransferase (Trm44) and demonstration of a Trm44 role in sustaining levels of specific tRNASer species. RNA 14 (2008) 158-169
17. Kruger M.K., and Sorensen M.A. Aminoacylation of hypomodified tRNAGlu in vivo. J. Mol. Biol. 284 (1998) 609-620
18. Maglott E.J., Deo S.S., Przykorska A., and Glick G.D. Conformational transitions of an unmodified tRNA: Implications for RNA folding. Biochem. 37 (1998) 16349-16359
19. 2+-dependent tRNA folding. Nucleic Acids Res. 30 (2002) 4751-4760
20. Perret V., Garcia A., Puglisi J., Grosjean H., Ebel J.P., Florentz C., and Giege R. Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides. Biochimie 72 (1990) 735-743
21. Rubin G.M. Preparation of RNA and ribosomes from yeast. Methods Cell Biol. 12 (1975) 45-64
22. Sampson J.R., and Uhlenbeck O.C. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc. Natl. Acad. Sci. USA 85 (1988) 1033-1037
23. Sprinzl M., Vassilenko K.S., Emmerich J., and Bauer F. Compilation of tRNA sequences and sequences of tRNA genes (1999). http://www.uni-bayreuth.de/departments/biochemie/trna/
24. Varshney U., Lee C., and RajBhandary U. Direct analysis of aminoacylation levels of tRNAs in vivo: Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase. J. Biol. Chem. 266 (1991) 24712-24718
25. Xing F., Hiley S.L., Hughes T.R., and Phizicky E.M. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J. Biol. Chem. 279 (2004) 17850-17860