Mass spectrometry-based detection of transfer RNAs by their signature endonuclease digestion products

RNA

Volumn 13, Issue 2, 2007, Pages 295-303

  Hossain, Mahmud ^a   Limbach, Patrick A ^a  

^a UNIVERSITY OF CINCINNATI   (United States)

Author keywords

E. Coli; Isoaccepting tRNA; Isoacceptors; MALDI MS; Mass spectrometry; RNase T1; Signature digestion product; TRNA

Indexed keywords

ENDONUCLEASE; RIBONUCLEASE T1; TRANSFER RNA;

ARTICLE; CELL LYSATE; CONTROLLED STUDY; ELECTROPHORESIS; ENZYME PURIFICATION; ESCHERICHIA COLI; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; RNA STRUCTURE;

ESCHERICHIA COLI; REPRODUCIBILITY OF RESULTS; RIBONUCLEASE T1; RNA, BACTERIAL; RNA, TRANSFER; RNA, TRANSFER, AMINO ACID-SPECIFIC; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

ESCHERICHIA COLI;

EID: 33846414324     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.272507     Document Type: Article

References (36)

1. Berhane, B.T. and Limbach, P.A. 2003a. Functional microfabricated sample targets for matrix-assisted laser desorption/ionization mass spectrometry analysis of ribonucleic acids. Anal. Chem. 75: 1997-2003.
2. Berhane, B.T. and Limbach, P.A. 2003b. Stable isotope labeling for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay analysis of ribonucleic acids. J. Mass Spectrom. 38: 872-878.
3. Bjork, G.R., Jacobsson, K., Nilsson, K., Johansson, M.J.O., Bystrom, A.S., and Persson, O.P. 2001. A primordial tRNA modification required for the evolution of life? EMBO J. 20: 231-239.
4. Cayama, E., Yepez, A., Rotondo, F., Bandeira, E., Ferreras, A.C., and Triana-Alonso, J.F. 2000. New chromatographic and biochemical strategies for quick preparative isolation of tRNA. Nucleic Acids Res. 28: e64.
5. Cherayil, J.D. 1990. Transfer RNAs and other soluble RNAs. CRC Press, Boca Raton, FL.
6. Cherayil, J.D. and Bock, R.M. 1965. A column chromatographic procedure for the fractionation of s-RNA. Biochemistry 4: 1174-1183.
7. Chinali, G. 1997. Isolation of tRNA isoacceptors by affinity chromatography with immobilized elongation factor Tu from Escherichia coli. J. Biochem. Biophys. Methods 34: 1-10.
8. Conrads, T., Anderson, G., Veenstra, T., Pasa-Tolic, L., and Smith, R. 2000. Utility of accurate mass tags for proteome-wide protein identification. Anal. Chem. 72: 3349-3354.
9. Dong, H., Nilsson, L., and Kurland, C.G. 1996. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol. 260: 649-663.
10. Garel, J., Garber, R.L., and Siddiqui, M.A. 1977. Transfer RNA in posterior silk gland of Bombyx mori: Polyacrylamide gel mapping of mature transfer RNA, identification and partial structural characterization of major isoacceptors species. Biochemistry 16: 3618-3624.
11. Hartmer, R., Strom, N., Boecker, S., Rodi, C.P., Hillenkamp, F., Jurinke, C., and Boom, D.V. 2003. RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis. Nucleic Acids Res. 31: e47.
12. Holley, R.W. and Merrill, S.H. 1959. Countercurrent distribution of an active ribonucleic acid. J. Am. Chem. Soc. 81: 753.
13. Holmes, W.M., Hurd, R.E., Reid, B.R., Rimerman, R.A., and Hatfield, G.W. 1975. Separation of transfer ribonucleic acids by sepharose chromatography using reverse salt gradients. Proc. Natl. Acad. Sci. 72: 1068-1071.
14. Ikemura, T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurance of the respective codons in its protein genes. J. Mol. Biol. 146: 1-21.
15. Ikemura, T. 1982. Correlation between codon usage and tRNA content in microorganisms. In Transfer RNA in protein synthesis (eds. L. Dolph et al.). CRC Press, Boca Raton, FL.
16. Ikemura, T. 1985. Codon usage, tRNA content, and rate of synonymous substitution. In Population genetics and molecular evolution (eds. T. Ohta and K. Aoki), pp. 385-406. Springer-Verlag, Berlin.
17. Ikemura, T. and Ozeki, H. 1983. Codon usage and transfer RNA contents: Organism-specific codon-choice patterns in reference to the isoacceptor contents. Cold Spring Harb. Symp. Quant. Biol. 47: 1087-1097.
18. Kanduc, D. 1994. Fractionation of rat liver tRNA by reversed-phase high performance liquid chromqtography: Isolation of iso-tRNAs. Prep. Biochem. 24: 167-174.
19. Kirpekar, F., Douthwaite, S., and Rosepstorff, P. 2000. Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry. RNA 6: 296-306.
20. Knochenmuss, R. 2003. A quantitative model of ultraviolet matrix-assisted laser desorption/ionization including analyte ion generation. Anal. Chem. 75: 2199-2207.
21. Kowalak, J., Bruenger, E., Crain, P.F., and McCloskey, J.A. 2000. Identities and phylogenic comparisons of posttranscriptional modifications in 16S ribosomal RNA from Haloferax volcanii. J. Biol. Chem. 275: 24484-24489.
22. Kowalak, J., Pomerantz, S., Crain, P.F., and McCloskey, J.A. 1993. A novel method for the determination of posttranscriptional modification in RNA by mass spectrometry. Nucleic Acids Res. 21: 4577-4583.
23. Limbach, P.A. 1996. Indirect mass spectrometric methods for the characterization and sequencing of oligoncleotides. Mass Spectrom. Rev. 15: 297-336.
24. McCloskey, J.A., Graham, D.A., Zhou, S.L., Crain, P.F., Ibba, M., Konisky, J., Söll, D., and Olsen, G.J. 2001. Posttranscriptional modification in archaeal tRNAs: Identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic methanococcales. Nucleic Acids Res. 29: 4699-4706.
25. 18O labeling. Int. J. Mass Spectrom. 234: 37-44.
26. 18O labeling and mass spectrometry. Anal. Chem. 77: 1891-1895.
27. Meng, Z. and Limbach, P.A. 2006. Mass spectrometry of RNA: Linking the genome to the proteome. Brief. Funct. Genomic. Proteomic. 5: 87-95.
28. Neidhardt, F.C., Bloch, P.L., and Smith, D.F. 1974. Culture medium for enterobacteria. J. Bacteriol. 119: 736-747.
29. Nordhoff, E., Kirpekar, F., and Roepstroff, P. 1996. Mass spectrometry of nucleic acids. Mass Spectrom. Rev. 15: 69-138.
30. Polo, L.M. and Limbach, P.A. 1998. Matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry for the analysis of RNase H cleavage products. J. Mass Spectrom. 33: 1226-1231.
31. Rajbhandary, U.L. and Ghosh, H.P. 1969. Studies on polynucleotides; XCI. Yeast methionine transfer ribonucleic acid: Purification, properties, and terminal nucleotides sequences. J. Biol. Chem. 244: 1104-1113.
32. Ribeiro, S., Nock, S., and Sprinzl, M. 1995. Purification of amino-acyl tRNA by affinity chromatography on immobilized Thermus thermophilus EF-TU-GTP. Anal. Biochem. 228: 330-335.
33. Rozenski, J. 2006. Nucleic acids toolbox. http://library.med.utah.edu/ masspec/.
34. Sprinzl, M. and Vassilenko, K.S. 2005. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 33: D139-D140.
35. Söll, D. and Rajbhandary, U.L. 1995. tRNA: Structure, biosynthesis and function. ASM Press, Washington, DC.
36. Weiss, J.F., Pearson, R.L., and Kelmers, A.D. 1968. Two additional reversed-phase chromatographic systems for the separations of transfer ribonucleic acids and their application to the preparation of two formylmethionine and a valine transfer ribonucleic acid from Escherichia coli B. Biochemistry 7: 3479-3487.