The ybiN Gene of Escherichia coli Encodes Adenine-N6 Methyltransferase Specific for Modification of A1618 of 23 S Ribosomal RNA, a Methylated Residue Located Close to the Ribosomal Exit Tunnel

Journal of Molecular Biology

Volumn 375, Issue 1, 2008, Pages 291-300

  Sergiev, Petr V ^a   Serebryakova, Marina V ^b   Bogdanov, Alexey A ^a   Dontsova, Olga A ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

Author keywords

methylation; modification; ribosome; rlmF; ybiN

Indexed keywords

ADENINE NUCLEOTIDE; ESCHERICHIA COLI PROTEIN; LITHIUM CHLORIDE; METHYLTRANSFERASE; PROTEIN A1618; PROTEIN YBIN; RECOMBINANT PROTEIN; RIBOSOME PROTEIN; RIBOSOME RNA; UNCLASSIFIED DRUG;

ARTICLE; ESCHERICHIA COLI; GENE EXPRESSION; GENE IDENTIFICATION; GENE OVEREXPRESSION; IN VITRO STUDY; METHYLATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION;

ESCHERICHIA COLI;

EID: 36348929415     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.10.051     Document Type: Article

References (37)

1. Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., et al. The comparative RNA Web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BioMed. Central Bioinformatics 3 (2002) 15
2. Mueller F., and Brimacombe R. A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 Å. J. Mol. Biol. 271 (1997) 524-544
3. Voss N.R., Gerstein M., Steitz T.A., and Moore P.B. The geometry of the ribosomal polypeptide exit tunnel. J. Mol. Biol. 360 (2006) 893-906
4. Nakatogawa H., and Ito K. The ribosomal exit tunnel functions as a discriminating gate. Cell 108 (2002) 629-636
5. Gong F., and Yanofsky C. Instruction of translating ribosome by nascent peptide. Science 297 (2002) 1864-1867
6. Tenson T., and Ehreneberg M. Regulatory nascent peptides in the ribosomal tunnel. Cell 108 (2002) 591-594
7. Schlunzen F., Zarivach R., Harms J., Bashan A., Tocilj A., Albrecht R., et al. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413 (2001) 814-821
8. Tenson T., and Mankin A. Antibiotics and the ribosome. Mol. Microbiol. 59 (2006) 1664-1677
9. Branlant C., Krol A., Machatt M.A., Pouyet J., Ebel J.P., Edwards K., and Kossel H. Primary and secondary structures of Escherichia coli MRE600 23 S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23 S rRNA and for large portions of mouse and human 16 S mitochondrial rRNAs. Nucl. Acids Res. 9 (1981) 4303-4324
10. 1G745-deficient mutant. J. Bacteriol. 180 (1998) 359-365
11. Wrzesinski J., Nurse K., Bakin A., Lane B.G., and Ofengand J. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi746 in 23 S RNA is also specific for psi32 in tRNA(phe). RNA 1 (1995) 437-448
12. 5U1939 in 23 S rRNA using MALDI mass spectrometry. Nucl. Acids Res. 31 (2003) 4738-4746
13. 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
14. Sergiev P.V., Bogdanov A.A., and Dontsova O.A. Ribosomal RNA guanine-(N2)-methyltransferases and their targets. Nucl. Acids Res. 35 (2007) 2295-2301
15. 5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359 (2006) 777-786
16. Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., et al. Construction of Escherichia coli K-12 in-frame, single-gene knock-out mutants the Keio collection. Mol. Systems Biol. 2 (2006) 2006.0008
17. Datsenko K.A., and Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97 (2000) 6640-6645
18. 2G methyltransferases: II. The ygjO gene encodes a methyltransferase specific for G1835 of the 23 S rRNA. J. Mol. Biol. 364 (2006) 26-31
19. 2G methyltransferases: I. The ycbY gene encodes a methyltr.ansferase specific for G2445 of the 23 S rRNA. J. Mol. Biol 364 (2006) 20-25
20. Lesnyak D.V., Osipiuk J., Skarina T., Sergiev P.V., Bogdanov A.A., Edwards A., et al. Methyltransferase that modifies guanine 966 of the 16 S rRNA: Functional identification and tertiary structure. J. Biol. Chem. 282 (2006) 5880-5887
21. Helser T.L., Davies J.E., and Dahlberg J.E. Change in methylation of 16 S ribosomal RNA associated with mutation to kasugamycin resistance in Escherichia coli. Nature New. Biol. 233 (1971) 12-14
22. Kitagawa M., Ara T., Arifuzzaman M., Ioka-Nakamichi T., Inamoto E., Toyonaga H., and Mori H. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF Archive): unique resources for biological research. DNA Res. 12 (2005) 291-299
23. Nierhaus K.H. Reconstitution of ribosomes. In: Spedding G. (Ed). Ribosomes and Protein Synthesis: A Practical Approach (1990), Oxford University Press, Oxford 161-189
24. Dammel C.S., and Noller H.F. A cold-sensitive mutation in 16 S rRNA provides evidence for helical switching in ribosome assembly. Genes Dev. 7 (1993) 660-670
25. Jeltsch A. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. ChemBiochem. 3 (2002) 274-293
26. Kelley L.A., MacCallum R.M., and Sternberg M.J. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299 (2000) 499-520
27. Schluckebier G., Zhong P., Stewart K.D., Kavanaugh T.J., and Abad-Zapatero C. The 2.2 Å structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J. Mol. Biol. 289 (1999) 277-291
28. Choi K.M., and Brimacombe R. The path of the growing peptide chain through the 23 S rRNA in the 50 S ribosomal subunit; a comparative crosslinking study with three different peptide families. Nucl. Acids Res. 26 (1998) 887-895
29. 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
30. 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
31. 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
32. Selmer M., Dunham C.M., Murphy IV F.V., Weixlbaumer A., Petry S., Kelley A.C., et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006) 1935-1942
33. Chittum H.S., and Champney W.S. Ribosomal protein gene sequence changes in erythromycin-resistant mutants of Escherichia coli. J. Bacteriol. 176 (1994) 6192-6198
34. Mankin A.S. Nascent peptide in the "birth canal" of the ribosome. Trends Biochem. Sci. (2005)
35. Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4 (2003) 41
36. Goringer H.U., Hijazi K.A., Murgola E.J., and Dahlberg A.E. Mutations in 16S rRNA that affect UGA(stop-codon)-directed translation termination. Proc. Natl. Acad. Sci. USA 88 (1991) 6603-6607
37. Sergiev P., Dokudovskaya S., Romanova E., Topin A., Bogdanov A., Brimacombe R., and Dontsova O. The environment of 5S rRNA in the ribosome: cross-links to the GTPase-associated area of 23 S rRNA. Nucl. Acids Res. 26 (1998) 2519-2525