YebU is a m5C Methyltransferase Specific for 16 S rRNA Nucleotide 1407

Journal of Molecular Biology

Volumn 359, Issue 3, 2006, Pages 777-786

  Andersen, Niels Møller ^a   Douthwaite, Stephen ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

ribosomal subunit interface; RNA mass spectrometry; rRNA methylation; RsmF

Indexed keywords

DNA 16S; METHYLTRANSFERASE; NUCLEOTIDE; RECOMBINANT PROTEIN; SMALL SUBUNIT RIBOSOMAL RNA; ESCHERICHIA COLI PROTEIN; M(5)C RRNA METHYLTRANSFERASE; RNA 16S;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; COMPUTER MODEL; ESCHERICHIA COLI; IN VITRO STUDY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METHYLATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PURIFICATION; WILD TYPE; AMINO ACID SEQUENCE; BACTERIAL GENOME; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ENZYMOLOGY; GENETICS; GROWTH, DEVELOPMENT AND AGING; MASS SPECTROMETRY; METABOLISM; MOLECULAR GENETICS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

AMINO ACID SEQUENCE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENOME, BACTERIAL; METHYLATION; METHYLTRANSFERASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; RNA, RIBOSOMAL, 16S; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 33646806139     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.04.007     Document Type: Article

References (56)

1. Noller H.F. RNA structure: reading the ribosome. Science 309 (2005) 1508-1514
2. In: Grosjean H. (Ed). Fine-tuning of RNA Functions by Modification and Editing (2005), Springer Verlag, New York
3. Rozenski J., Crain P.F., and McCloskey J.A. The RNA Modification Database: 1999 update. Nucl. Acids Res. 27 (1999) 196-197
4. Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I., et al. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107 (2001) 679-688
5. 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
6. Wimberly B.T., Brodersen D.E., Clemons W.M.J., Morgan-Warren R.J., Carter A.P., et al. Structure of the 30 S ribosomal subunit. Nature 407 (2000) 327-339
7. Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H., and Noller H.F. Crystal structure of the ribosome at 5.5 Å resolution. Science 292 (2001) 883-896
8. 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
9. 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
10. Decatur W.A., and Fournier M.J. rRNA modifications and ribosome function. Trends Biochem. Sci. 27 (2002) 344-351
11. 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
12. Ofengand J., and Del Campo M. In: Curtiss R. (Ed). EcoSal-Escherichia coli and Salmonella: Cellular and Molecular Biology (2004), ASM Press, Washington, DC
13. Krzyzosiak W., Denman R., Nurse K., Hellmann W., Boubik M., Gehrke C.W., et al. In vitro synthesis of 16S ribosomal RNA containing single base changes and assembly into functional 30S ribosome. Biochemistry 26 (1987) 2353-2364
14. Green R., and Noller H.F. Reconstitution of functional 50S ribosomes from in vitro transcripts of Bacillus stearothermophilus 23 S rRNA. Biochemistry 38 (1999) 1772-1779
15. 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
16. Kiss T. Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109 (2002) 145-148
17. Decatur W.A., and Fournier M.J. RNA-guided nucleotide modification of ribosomal and other RNAs. J. Biol. Chem. 278 (2003) 695-698
18. Yu Y.-T., Terns R.M., and Terns M.P. In: Grosjean H. (Ed). Fine-tuning of RNA Functions by Modification and Editing vol. 12 (2005), Springer Verlag, New York 223-262
19. Ziesche S.M., Omer A.D., and Dennis P.P. RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea. Mol. Microbiol. 54 (2004) 980-993
20. Del Campo M., Kaya Y., and Ofengand J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615
21. Andersen T.E., Porse B.T., and Kirpekar F. A novel partial modification at C2501 in Escherichia coli 23 S ribosomal RNA. RNA 10 (2004) 907-913
22. 5C967 methyltransferase from Escherichia coli. Biochemistry 38 (1999) 4053-4057
23. 5C967 methyltransferase from Escherichia coli. Biochemistry 38 (1999) 1884-1892
24. Kagan R.M., and Clarke S. Widespread occurrence of three sequence motifs in diverse S-adenosylmethionine-dependent methyltransferases suggests a common structure for these enzymes. Arch. Biochem. Biophys. 310 (1994) 417-427
25. Malone T., Blumenthal R.M., and Cheng X. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Mol. Biol. 253 (1995) 618-632
26. Fauman E.B., Cheng X., and Blumenthal R.M. In: Cheng X., and Blumenthal R.M. (Eds). S-Adenosylmethionine Dependant Methyltransferases: Structures and Functions (1999), World Scientific, New Jersey 1-32
27. 5C methyltransferases from searching genomic and proteomic sequences. Nucl. Acids Res. 27 (1999) 3138-3145
28. 5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Structure (Camb) 11 (2003) 1609-1620
29. 5C methyltransferase from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. J. Mol. Biol. (2006) In the press.
30. 5C967 by their respective methyltransferases. Nucl. Acids Res. 19 (1991) 7089-7095
31. Schlünzen F., Tocilj A., Zarivach R., Harms J., Gluehmann M., Janell D., et al. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell 102 (2000) 615-623
32. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25 (1997) 3389-3402
33. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd edit. (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
34. Hamilton C.M., Aldea M., Washburn B.K., Babitzke P., and Kushner S.R. New method for generating deletions and gene replacements in Escherichia coli. J. Bacteriol. 171 (1989) 4617-4622
35. Gutgsell N., Englund N., Niu L., Kaya Y., Lane B.G., and Ofengand J. Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells. RNA 6 (2000) 1870-1881
36. Douthwaite S., Powers T., Lee J.Y., and Noller H.F. Defining the structural requirements for a helix in 23S ribosomal RNA that confers erythromycin resistance. J. Mol. Biol. 209 (1989) 655-665
37. Kirpekar F., Douthwaite S., and Roepstorff P. Mapping posttranscriptional modifications in 5 S ribosomal RNA by MALDI mass spectrometry. RNA 6 (2000) 296-306
38. Bujnicki J.M. Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases. FASEB J. 14 (2000) 2365-2368
39. Bujnicki J.M., and Rychlewski L. RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited-bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. BMC Bioinformatics 3 (2002) 10
40. Wrzesinski J., Bakin A., Nurse K., Lane B.G., and Ofengand J. Purification, cloning, and properties of the 16 S RNA pseudouridine 516 synthase from Escherichia coli. Biochemistry 34 (1995) 8904-8913
41. 2G1207 methyltransferase from Escherichia coli. J. Biol. Chem. 274 (1999) 924-929
42. Basturea G.N., Rudd K.E., and Deutscher M.P. Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family. RNA 12 (2006) 426-434
43. Helser T.L., Davies J.E., and Dahlberg J.E. Mechanism of kasugamycin resistance in Escherichia coli. Nature New Biol. 235 (1972) 6-9
44. 6-dimethyladenosines near the 3′ end of 16 S ribosomal RNA of Escherichia coli. III. Purification and properties of the methylating enzyme and methylase-30 S interactions. J. Biol. Chem. 254 (1979) 9094-9100
45. 1G745-deficient mutant. J. Bacteriol. 180 (1998) 359-365
46. Phe. RNA 1 (1995) 437-448
47. 5U1939 in 23S rRNA using MALDI mass spectrometry. Nucl. Acids Res. 31 (2003) 4738-4746
48. Conrad J., Sun D., Englund N., and Ofengand J. The rluC gene of Escherichia coli codes for a pseudouridine synthase that is solely responsible for synthesis of pseudouridine at positions 955, 2504, and 2580 in 23 S ribosomal RNA. J. Biol. Chem. 273 (1998) 18562-18566
49. Huang L., Ku J., Pookanjanatavip M., Gu X., Wang D., Greene P.J., and Santi D.V. Identification of two Escherichia coli pseudouridine synthases that show multisite specificity for 23 S RNA. Biochemistry 37 (1998) 15951-15957
50. Wrzesinski J., Bakin A., Ofengand J., and Lane B.G. Isolation and properties of Escherichia coli 23 SRNA pseudouridine 1911, 1915, 1917 synthase (RluD). IUBMB Life 50 (2000) 33-37
51. 5U1939 methyltransferase from Escherichia coli. J. Biol. Chem. 277 (2002) 8835-8840
52. Lovgren J.M., and Wikstrom P.M. The rlmB gene is essential for formation of Gm2251 in 23 S rRNA but not for ribosome maturation in Escherichia coli. J. Bacteriol. 183 (2001) 6957-6960
53. Caldas T., Binet E., Bouloc P., Costa A., Desgres J., and Richarme G. The FtsJ/RrmJ heat shock protein of Escherichia coli is a 23 S ribosomal RNA methyltransferase. J. Biol. Chem. 275 (2000) 16414-16419
54. Bugl H., Fauman E.B., Staker B.L., Zheng F., Kushner S.R., Saper M.A., et al. RNA methylation under heat shock control. Mol. Cell. 6 (2000) 349-360
55. Bjork G.R., and Isaksson L.A. Isolation of mutants of Escherichia coli lacking 5-methyluracil in transfer ribonucleic acid or 1-methylguanine in ribosomal RNA. J. Mol. Biol. 51 (1970) 83-100
56. Yanisch-Perron C., Vieira J., and Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33 (1985) 103-119