Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry

RNA

Volumn 6, Issue 2, 2000, Pages 296-306

  Kirpekar, Finn ^a   Douthwaite, Stephen ^a   Roepstorff, Peter ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Archaea; Bacillus; Halobacteriacae; rRNA; Sequence; Sulfolobus

Indexed keywords

RIBONUCLEASE; RIBOSOME RNA; RNA 5S;

ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; GEOBACILLUS STEAROTHERMOPHILUS; HALOARCULA MARISMORTUI; HALOBACTERIUM SALINARUM; MASS SPECTROMETRY; PRIORITY JOURNAL; RNA ANALYSIS; RNA PROCESSING; RNA SEQUENCE; SULFOLOBUS ACIDOCALDARIUS;

BACILLUS STEAROTHERMOPHILUS; BASE SEQUENCE; HALOARCULA MARISMORTUI; HALOBACTERIUM SALINARUM; METHYLATION; PHOSPHORYLATION; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 5S; SPECIES SPECIFICITY; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SULFOLOBUS ACIDOCALDARIUS;

ARCHAEA; BACTERIA (MICROORGANISMS); GEOBACILLUS STEAROTHERMOPHILUS; HALOARCULA MARISMORTUI; HALOBACTERIUM SALINARUM; SULFOLOBUS; SULFOLOBUS ACIDOCALDARIUS;

EID: 0033950924     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838200992148     Document Type: Article

References (38)

1. Bakin A, Ofengand J. 1993. 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 32:9754-9762.
2. Brock TD, Brock KM, Belly RT, Weiss RL. 1972. Sulfolobus: A new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Microbiol 84:54-68.
3. Bruenger E, Kowalak JA, Kuchino Y, McCloskey JA, Mizushima H, Stetter KO, Crain PF. 1993. 5S rRNA modification in the hyperthermophilic archaea Sulfolobus solfataricus and Pyrodictium occultum. FASEB J 7:196-200.
4. Cundliffe E. 1987. On the nature of antibiotic binding sites in ribosomes. Biochimie 69:863-869.
5. Cunningham PR, Richard RB, Weitzmann CJ, Nurse K, Ofengand J. 1991. The absence of modified nucleotides affects both in vitro assembly and in vivo function of the 30S ribosomal subunit of Escherichia coli. Biochimie 73:789-796.
6. Dennis PP, Ziesche S, Mylvaganam S. 1998. Transcriptional analysis of two disparate rRNA operons in the halphilic archaeon Haloarcula marismortui. J Bacteriol 180:4804-4813.
7. Donis-Keller H. 1980. Phy M: An RNase activity specific for U and A residues useful in RNA sequence analysis. Nucleic Acids Res 8:3133-3142.
8. Donis-Keller H, Maxam AM, Gilbert W. 1977. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res 4:2527-2538.
9. Douthwaite S, Christensen A, Garrett RA. 1982. Binding site of ribosomal proteins on prokaryotic 5S ribonucleic acids: A study with ribonucleases. Biochemistry 27:2313-2320.
10. Durovic P, Kutay U, Schleper C, Dennis PP. 1994. Strain identification and 5S rRNA gene characterization of the hyperthermophilic archaebacterium Sulfolobus acidocaldarius. J Bacteriol 176:514-517.
11. Felden B, Hanawa K, Atkins JF, Himeno H, Muto A, Gesteland RF, McCloskey JA, Crain PF. 1998. Presence and location of modified nucleotides in Escherichia coli tmRNA: Structural mimicry with tRNA acceptor branches. EMBO J 17:3188-3196.
12. Green R, Noller HF. 1996. In vitro complementation analysis localizes 23S rRNA posttranscriptional modifications that are required for Escherichia coli 50S ribosomal subunit assembly and function. RNA 2:1011-1021.
13. Green R, Noller HF. 1999. Reconstitution of functional 50S ribosomes from in vitro transcripts of Bacillus stearothermophilus 23S rRNA. Biochemistry 30:1772-1779.
14. Karas M, Hillenkamp F. 1988. Laserdesorption ionisation of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60:2299-2301.
15. Khaitovich P, Tenson T, Mankin AS, Green R. 1999a. Peptidyl transferase activity catalyzed by protein-free 23S ribosomal RNA remains elusive. RNA 5:605-608.
16. Khaitovich P, Tenson T, Kloss P, Mankin AS. 1999b. Reconstitution of functionally active Thermus aquaticus large ribosomal subunits with in vitro-transcribed RNA. Biochemistry 30:1780-1788.
17. Kirpekar F, Nordhoff E, Kristiansen K, Roepstorff P, Lezius A, Hahner S, Karas M, Hillenkamp F. 1994. Matrix assisted laser desorption/ ionization mass spectrometry of enzymatically synthesized RNA up to 150 kDa. Nucleic Acids Res 22:3866-3870.
18. Kowalak JA, Bruenger E, McCloskey JA. 1995. Posttranscriptional modification of the central loop of domain V in Escherichia coli 23 S ribosomal RNA. J Biol Chem 270:17758-17764.
19. Kowalak JA, Pomerantz SC, Crain PF, McCloskey JA. 1993. A novel method for the determination of posttranscriptional modification in RNA by mass spectrometry. Nucleic Acids Res 27:4577-4585.
20. Mankin AS, Kagramanova VK. 1986. Complete nucleotide sequence of the single RNA operon of Halobacterium halobium: Secondary structure of the archaebacterial 23 S rRNA. Mol Gen Genet 202: 152-161.
21. McLuckey SA, Van Berkel GJ, Glish GL. 1992. Tandem mass spectrometry of small multiply charged oligonucleotides. J Am Soc Mass Spectrom 3:60-70.
22. Noller HF, Hoffarth, Zimniak L. 1992. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256:1416-1419.
23. Noon KR, Bruenger E, McCloskey JA. 1998. Posttranscriptional modifications in 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfataricus. J Bacteriol 180:2883-2888.
24. Nordhoff E, Ingendoh A, Cramer R, Overberg A, Stahl B, Karas M, Hillenkamp F, Crain PF. 1992. Matrix-assisted laser desorption/ ionization mass spectrometry of nucleic acids with wavelengths in the ultraviolet and infrared. Rapid Commun Mass Spectrom 6:771-776.
25. Nordhoff E, Kirpekar F, Roepstorff P. 1996. Mass spectrometry of nucleic acids. Mass Spectrom Rev 15:67-138.
26. Peattie DA. 1979. Direct chemical method for sequencing RNA. Proc Natl Acad Sci USA 76:1760-1764.
27. Raychaudhuri S, Conrad J, Hall BG, Ofengand J. 1998. A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli. RNA 4:1407-1417.
28. Rodriguez-Valera F. 1995. Cultivation of halophile archaea. In: DasSarma S, Fleischmann EM, eds. Archaea: A laboratory manual. Halophiles. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. pp 13-16.
29. Rozenski J, Crain PF, McCloskey JA. 1999. The RNA modification database: 1999 update. Nucleic Acids Res 27:196-197.
30. Sirum-Connolly K, Manson TL. 1993. Functional requirement of a site-specific ribose methylation in ribosomal RNA. Science 262: 1886-1889.
31. Skinner R, Cundliffe E, Schmidt FJ. 1983. Site of action of a ribosomal RNA methylase responsible for resistance to erythromycin and other antibiotics. J Biol Chem 258:12702-12706.
32. Spengler B, Kirsch D, Kaufmann R, Jaeger E. 1992. Peptide sequencing by matrix-assisted laser-desorption mass spectrometry. Rapid Commun Mass Spectrom 6:105-108.
33. Stern S, Moazed D, Noller HF. 1988. Structural analysis of RNA using chemical and enzymatic probing by primer extension. Methods Enzymol 164:481-489.
34. Thompson J, Schmidt F, Cundliffe E. 1982. Site of action of a ribosomal RNA methylase conferring resistance to thiostrepton. J Biol Chem 257:7915-7917.
35. Weisblum B. 1995. Erythromycin resistance by ribosome modification. Antimicrob Agents Chemother 39:577-585.
36. Wolter MA, Engels JW. 1995. Nanospray mass spectrometry/mass spectrometry for the analysis of modified oligoribonucleotides. Eur Mass Spectrom 1:583-590.
37. Wolter MA, Engels JW, Montanarella L, Tilio R, Facchetti S. 1995. Influence of the matrix on the analysis of small oligoribonucleotides by fast atom bombardment mass spectrometry. J Mass Spectrom 30:485-491.
38. Zimmermann J, Erdmann VA. 1978. Binding sites of E. coli and B. stearothermophilus ribosomal proteins on B. stearothermophilus 5S RNA. Nucleic Acids Res 5:2267-2288.