Identifying Modifications in RNA by MALDI Mass Spectrometry

Methods in Enzymology

Volumn 425, Issue , 2007, Pages

  Douthwaite, Stephen ^a   Kirpekar, Finn ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; RIBOSOME RNA; TRINUCLEOTIDE; RNA;

ACCURACY; ANALYTIC METHOD; ANTIBIOTIC RESISTANCE; CELL FREE SYSTEM; ENZYME MECHANISM; GENE SEQUENCE; IN VITRO STUDY; MASS; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION MASS SPECTROMETRY; METHYLATION; PRIORITY JOURNAL; PROTEIN SYNTHESIS; REVIEW; RNA ANALYSIS; ANIMAL; CHEMISTRY; HUMAN; METABOLISM; METHODOLOGY; PHYSIOLOGY; RNA PROCESSING;

ANIMALS; HUMANS; RNA; RNA PROCESSING, POST-TRANSCRIPTIONAL; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 34548722786     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)25001-3     Document Type: Review

References (56)

1. 5U1939 methyltransferase from Escherichia coli. J. Biol. Chem. 277 (2002) 8835-8840
2. 5C methyltransferase specific for 16S rRNA nucleotide 1407. J. Mol. Biol. 359 (2006) 777-786
3. Andersen T.E., Kirpekar F., and Haselmann K.F. RNA fragmentation in MALDI mass spectrometry studied by H/D-exchange: Mechanisms of general applicability to nucleic acids. J. Am. Soc. Mass Spectrom. 17 (2006) 1353-1368
4. Andersen T.E., Porse B.T., and Kirpekar F. A novel partial modification at 2501 in Escherichia coli 23S ribosomal RNA. RNA 10 (2004) 907-913
5. Asara J.M., and Allison J. Enhanced detection of oligonucleotides in UV-MALDI-MS using the tetraamine spermine as a matrix additive. Anal. Chem. 71 (1999) 2866-2870
6. Bakin A., and Ofengand J. Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: Analysis by the application of a new sequencing technique. Biochemistry 32 (1993) 9754-9762
7. Ban N., Nissen P., Hansen J., Moore P.B., and Steitz T.A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289 (2000) 905-920
8. Brimacombe R., Mitchell P., Osswald M., Stade K., and Bochkariov D. Clustering of modified nucleotides at the functional center of bacterial ribosomal RNA. FASEB J. 7 (1993) 161-167
9. Cundliffe E. How antibiotic-producing organisms avoid suicide. Annu. Rev. Microbiol. 43 (1989) 207-233
10. Decatur W.A., and Fournier M.J. rRNA modifications and ribosome function. Trends Biochem. Sci. 27 (2002) 344-351
11. Dennis P.P., and Omer A. Small non-coding RNAs in Archaea. Curr. Opin. Microbiol. 8 (2005) 685-694
12. Felden B., Hanawa K., Atkins J.F., Himeno H., Muto A., Gesteland R.F., McCloskey J.A., and Crain P.F. Presence and location of modified nucleotides in Escherichia coli tmRNA: Structural mimicry with tRNA acceptor branches. EMBO J. 17 (1998) 3188-3196
13. Gale E.F., Cundliffe E., Reynolds P.E., Richmond M.H., and Waring M.J. "The Molecular Basis of Antibiotic Action." (1981), John Wiley and Sons, London
14. Green R., and Noller H.F. Reconstitution of functional 50S ribosomes from in vitro transcripts of Bacillus stearothermophilus 23S rRNA. Biochemistry 38 (1999) 1772-1779
15. Grosjean H., Keith G., and Droogmans L. Detection and quantification of modified nucleotides in RNA using thin-layer chromatography. Methods Mol. Biol. 265 (2004) 357-391
16. Gutgsell N.S., Campo M.D., Raychaudhuri S., and Ofengand J. A second function for pseudouridine synthetases: A point mutant of RluD unable to form pseudouridines 1911, 1915 and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to a RluD-minus strain. RNA 7 (2001) 990-998
17. Guymon R., Pomerantz S.C., Crain P.F., and McCloskey J.A. Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: The complete modification map of 16S rRNA of Thermus thermophilus. Biochemistry 45 (2006) 4888-4899
18. Hansen L.H., Kirpekar F., and Douthwaite S. Recognition of nucleotide G745 in 23S ribosomal RNA by the rrmA methyltransferase. J. Mol. Biol. 310 (2001) 1001-1010
19. Hansen L.H., Mauvais P., and Douthwaite S. The macrolide-ketolide antibiotic binding site is formed by structures in domains II and V of 23S ribosomal RNA. Mol. Microbiol. 31 (1999) 623-631
20. Hansen M.A., Kirpekar F., Ritterbusch W., and Vester B. Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria. RNA 8 (2002) 202-213
21. Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I., Bartels H., Franceschi F., and Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107 (2001) 679-688
22. Johansen S.K., Maus C.E., Plikaytis B.B., and Douthwaite S. Capreomycin binds across the ribosomal subunit interface using tlyA-encoded 2′-O-methylations in 16S and 23S rRNAs. Mol. Cell 23 (2006) 173-182
23. Karas M., and Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60 (1988) 2299-2301
24. Kehrenberg C., Schwarz S., Jacobsen L., Hansen L.H., and Vester B. A new mechanism for chloramphenicol, florfenicol and clindamycin resistance: Methylation of 23S ribosomal RNA at A2503. Mol. Microbiol. 57 (2005) 1064-1073
25. Khaitovich P., Tenson T., Kloss P., and Mankin A.S. Reconstitution of functionally active Thermus aquaticus large ribosomal subunits with in vitro-transcribed rRNA. Biochemistry 38 (1999) 1780-1788
26. Kirpekar F., Douthwaite S., and Roepstorff P. Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry. RNA 6 (2000) 296-306
27. Kirpekar F., Hansen L.H., Rasmussen A., Poehlsgaard J., and Vester B. The archaeon Haloarcula marismortui has few modifications in the central parts of its 23S ribosomal RNA. J. Mol. Biol. 348 (2005) 563-573
28. Kirpekar F., and Krogh T.N. RNA fragmentation studied in a matrix-assisted laser desorption/ionisation tandem quadropole/orthogonal time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 15 (2001) 8-14
29. Kirpekar F., Nordhoff E., Larsen L.K., Kristiansen K., Roepstorff P., and Hillenkamp F. DNA sequence analysis by MALDI mass spectrometry. Nucleic Acids Res. 26 (1998) 2554-2559
30. Kiss T. Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions. Cell 109 (2002) 145-148
31. Korostelev A., Trakhanov S., Laurberg M., and Noller H.F. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126 (2006) 1065-1077
32. Kowalak J.A., Bruenger E., and McCloskey J.A. Posttranscriptional modification of the central loop of domain V in Escherichia coli 23S ribosomal RNA. J. Biol. Chem. 270 (1995) 17758-17764
33. Kowalak J.A., Pomerantz S.C., Crain P.F., and McCloskey J.A. A novel method for the determination of post-transcriptional modification in RNA by mass spectrometry. Nucleic Acids Res. 21 (1993) 4577-4585
34. Krupp G., and Soll D. Simplified in vitro synthesis of mutated RNA molecules. An oligonucleotide promoter determines the initiation site of T7RNA polymerase on ss M13 phage DNA. FEBS Lett. 212 (1987) 271-275
35. Krzyzosiak W., Denman R., Nurse K., Hellmann W., Boubik M., Gehrke C.W., Agris P.F., and Ofengand J. In vitro synthesis of 16S ribosomal RNA containing single base changes and assembly into functional 30S ribosome. Biochemistry 26 (1987) 2353-2364
36. Lesnyak D.V., Osipiuk J., Skarina T., Sergiev P.V., Bogdanov A.A., Edwards A., Savchenko A., Joachimiak A., and Dontsova O.A. Methyltransferase that modifies guanine 966 of the 16S rRNA: Functional identification and tertiary structure. J. Biol. Chem. 282 (2007) 5880-5887
37. Maden B.E., Corbett M.E., Heeney P.A., Pugh K., and Ajuh P.M. Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie 77 (1995) 22-29
38. Madsen C.T., Jakobsen L., Buriankova K., Doucet-Populaire F., Pernodet J.L., and Douthwaite S. Methyltransferase Erm(37) slips on rRNA to confer atypical resistance in Mycobacterium tuberculosis. J. Biol. Chem. 280 (2005) 38942-38947
39. 5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 31 (2003) 4738-4746
40. McCloskey J.A., and Rozenski J. The small subunit rRNA modification database. Nucleic Acids Res. 33 (2005) D135-D138
41. McLuckey S.A., Van Berkel G.J., and Glish G.L. Tandem mass spectrometry of small multiply charged oligonucleotides. J. Am. Soc. Mass Spectrom. 3 (1992) 60-70
42. Mengel-Jorgensen J., and Kirpekar F. Detection of pseudouridine and other modifications in tRNA by cyanoethylation and MALDI mass spectrometry. Nucleic Acids Res. 30 (2002) e135
43. Mengel-Jorgensen J., Jensen S.S., Rasmussen A., Poehlsgaard J., Iversen J.J., and Kirpekar F. Modifications in Thermus thermophilus 23S ribosomal RNA are centered in regions of RNA-RNA contact. J. Biol. Chem. 281 (2006) 22108-22117
44. Nordhoff E., Cramer R., Karas M., Hillenkamp F., Kirpekar F., Kristiansen K., and Roepstorff P. Ion stability of nucleic acids in infrared matrix-assisted laser desorption/ionization mass spectrometry. Nucleic Acids Res. 21 (1993) 3347-3357
45. Ofengand J., and Del Campo M. Modified nucleotides of Escherichia coli ribosomal RNA. In: Curtiss R. (Ed). "EcoSal - Escherichia coli and Salmonella: Cellular and Molecular Biology" (2004), ASM Press, Washington, DC. http://www.ecosal.org
46. Okamoto S., Tamaru A., Nakajima C., Nishimura K., Tanaka Y., Tokuyama S., Suzuki Y., and Ochi K. Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteria. Mol. Microbiol. 63 (2007) 1096-1106
47. 6-dimethyladenosines near the 3′-end of 16S ribosomal RNA of Escherichia coli. III. Purification and properties of the methylating enzyme and methylase-30S interactions. J. Biol. Chem. 254 (1979) 9094-9100
48. Rozenski J., Crain P.F., and McCloskey J.A. The RNA Modification Database: 1999 update. Nucl. Acids Res. 27 (1999) 196-197
49. Schlünzen F., Tocilj A., Zarivach R., Harms J., Gluehmann M., Janell D., Bashan A., Bartels H., Agmon I., Franceschi F., and Yonath A. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell 102 (2000) 615-623
50. Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., and Cate J.H. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310 (2005) 827-834
51. Selmer M., Dunham C.M., Murphy F.V.T., Weixlbaumer A., Petry S., Kelley A.C., Weir J.R., and Ramakrishnan V. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006) 1935-1942
52. Stern S., Moazed D., and Noller H.F. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 164 (1988) 481-489
53. Treede I., Jakobsen L., Kirpekar F., Vester B., Weitnauer G., Bechthold A., and Douthwaite S. The avilamycin resistance determinants AviRa and AviRb methylate 23S rRNA at the guanosine 2535 base and the uridine 2479 ribose. Mol. Microbiol. 49 (2003) 309-318
54. Wu K.J., Shaler T.A., and Becker C.H. Time-of-flight mass spectrometry of underivatized single-stranded DNA oligomers by matrix-assisted laser desorption. Anal. Chem. 66 (1994) 1637-1645
55. Zhang Z., Jackson G.W., Fox G.E., and Willson R.C. Microbial identification by mass cataloging. BMC Bioinformatics 7 (2006) 117
56. Zhu Y.F., Chung C.N., Taranenko N.I., Allman S.L., Martin S.A., Haff L., and Chen C.H. The study of 2,3,4-trihydroxyacetophenone and 2,4,6-trihydroxyacetophenone as matrices for DNA detection in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 10 (1996) 383-388