ErmE methyltransferase recognition elements in RNA substrates

Journal of Molecular Biology

Volumn 282, Issue 2, 1998, Pages 255-264

  Vester, Birte ^a   Nielsen, Allan K ^b   Hansen, Lykke Haastrup ^b   Douthwaite, Stephen ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Base modification; Erm methyltransferase; MLS antibiotic resistance; RNA structure; RNA protein interaction

Indexed keywords

MACROLIDE; MAGNESIUM; METHYLTRANSFERASE; RIBOSOME RNA;

ANTIBIOTIC RESISTANCE; ARTICLE; ESCHERICHIA; IONIC STRENGTH; METHYLATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN RNA BINDING; RNA STRUCTURE; RNA TRANSCRIPTION; SACCHAROPOLYSPORA;

ESCHERICHIA COLI;

EID: 0032544482     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2024     Document Type: Article

References (35)

1. Allain, F. H.-T. & Varani, G. (1997). How accurately and precisely can RNA structure be determined by NMR? J. Mol. Biol. 267, 338-351.
2. Brimacombe, R., Greuer, B., Mitchell, P., Osswald, M., Rinke-Appel, J., Schüler, D. & Stade, K. (1990). Three dimensional structure and function of Escherichia coli 16S and 23 S rRNA as studied by cross-linking techniques. In The Structure, Function, and Evolution of Ribosomes (Hill, W., Dahlberg, A., Garrett, R. A., Moore, P. B., Schlessinger, D. & Warner, J., eds), pp. 93-106, American Society for Microbiology, Washington DC.
3. Bujard, H., Gentz, R., Lanzer, M., Stueber, D., Mueller, M., Ibrahimi, I., Haeuptle, M. & Dobberstein, B. (1987). A T5 promoter-based transcription-translation system for the analysis of proteins in vitro and in vivo. Methods Enzymol. 155, 416-433.
4. Douthwaite, S., Voldborg, B., Hansen, L. H., Rosendahl, G. & Vester, B. (1995). Recognition determinants for proteins and antibiotics within 23 S rRNA. Biochem. Cell. Biol. 73, 1179-1185.
5. Egebjerg, J., Larsen, N. & Garrett, R. A. (1990). Structural map of 23 S rRNA. In The Structure, Function, and Evolution of Ribosomes (Hill, W., Dahlberg, A., Garrett, R. A., Moore, P. B., Schlessinger, D. & Warner, J., eds), pp. 168-179, American Society for Microbiology, Washington DC.
6. Ehresmann, C., Baudin, F., Mougel, M., Romby, P., Ebel, J.-P. & Ehresmann, B. (1987). Probing the structure of RNA in solution. Nucl. Acids Res. 15, 9109-9128.
7. Gutell, R. R., Gray, M. W. & Schnare, M. N. (1993). A compilation of large subunit (23 S and 23 S-like) ribosomal RNA structures. Nucl. Acids Res. 21, 3055-3074.
8. Gutell, R. R., Larsen, N. & Woese, C. R. (1994). Lessons from an evolving rRNA: 16 S and 23 S rRNA structures from a comparative perspective. Microbiol. Rev. 58, 10-26.
9. Hanahan, D. (1985). Techniques for transformation of E. coli. In DNA Cloning: A Practical Approach (Glover, D. M., ed.), vol. 1, pp. 109-135, IRL Press, Oxford.
10. Jaeger, J. A., Turner, D. H. & Zuker, M. (1989). Predicting optimal and suboptimal secondary structures for RNA. Methods Enzymol. 183, 281-306.
11. Katz, L., Brown, D., Boris, K. & Tuan, J. (1987). Expression of the macrolide-lincosamide-streptogramin-B-resistance methylase gene, ermE, from Streptomyces erythraeus in Escherichia coli results in N-6-monomethylation and N-6,N-6-dimethyation of ribosomal RNA. Gene, 55, 319-325.
12. Kovalic, D., Giannattasio, R. B., Hyung-Jong, J. & Weisblum, B. (1994). 23 S rRNA domain V, a fragment that can be specifically methylated in vitro by the ErmSF (TlrA) methyltransferase. J. Bacteriol. 176, 6992-6998.
13. Kovalic, D., Giannattasio, R. B. & Weisblum, B. (1995). Methylation of minimalist 23 S rRNA sequences in vitro by ErmSF (TrlA) N-methyltransferase. Biochemistry, 34, 15838-15844.
14. Kunkel, T. A., Roberts, J. D. & Zakour, R. (1987). Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154, 367-382.
15. Labeda, D. P. (1987). Transfer of the type strain of Streptomyces erythraeus (Waksman 1923) Waksman and Henrici 1948 to the genus Saccharopolyspora Lacy and Goodfellow 1979 as Saccharopolyspora erythraea sp. nov., and designation of a neotype strain for Streptomyces erythraeus. Int. J. System. Bacteriol. 37, 19-22.
16. 6A dimethylation in the 3′-terminal loop of 18 S rRNA is essential in yeast. J. Mol. Biol. 241, 492-497.
17. Lai, C. & Weisblum, B. (1971). Altered methylation of ribosomal RNA in an erythromycin-resistant strain of Staphylococcus aureus. Proc. Natl Acad. Sci. USA, 68, 856-60.
18. 2+ ions. Specific and non-specific effects. J. Mol. Biol. 237, 577-587.
19. Leffers, H., Egebjerg, J., Andersen, A., Christensen, T. & Garrett, R. A. (1988). Domain VI of Escherichia coli 23 S ribosomal RNA: structure, assembly and function. J. Mol. Biol. 204, 507-522.
20. McGuire, J. M., Bunch, R. L., Anderson, R. C., Boaz, H. E., Flynn, E. H., Powell, H. M. & Smith, J. W. (1952). "Ilotycin", a new antibiotic. Antibiot. Chemother. 2, 281-283.
21. Moazed, D., Stern, S. & Noller, H. F. (1986). Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension. J. Mol. Biol. 187, 399-416.
22. Noller, H. F. (1984). Structure of ribosomal RNA. Annu. Rev. Biochem. 53, 119-162.
23. Peattie, D. A. & Gilbert, W. (1980). Chemical probes for higher order structures in RNA. Proc. Natl Acad. Sci. USA, 77, 4679-4682.
24. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, 2nd edit., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
25. Shivakumar, A. G. & Dubnau, D. (1981). Characterization of a plasmid-specified ribosome methylase associated with macrolide resistance. Nucl. Acids Res. 9, 2549-2562.
26. Sigmund, C. D., Ettayebi, M., Borden, A. & Morgan, E. A. (1988). Antibiotic resistance mutations in ribosomal RNA genes of Escherichia coli. Methods Enzymol. 164, 673-690.
27. Skinner, R. H. & Cundliffe, E. (1982). Dimethylation of adenine and the resistance of Streptomyces erythraeus to erythromycin. J. Gen. Microbiol. 128, 2411-2416.
28. Skinner, R., Cundliffe, E. & Schmidt, F. J. (1983). Site of action of a ribosomal RNA methylase responsible for resistance to erythromycin and other antibiotics. J. Biol. Chem. 258, 12702-12706.
29. Thisted, T., Sørensen, N. S., Wagner, E. G. H. & Gerdes, K. (1994). Mechanism of post-segregational killing: Sok antisense RNA interacts with Hok mRNA via its 5′-end single-stranded leader and competes with the 3′-end of Hok mRNA for binding to the mok translational initiation region. EMBO J. 13, 1960-1968.
30. Vester, B. & Douthwaite, S. (1994). Domain V of 23 S rRNA contains all the structural elements necessary for recognition by the ErmE methyltransferase. J. Bacteriol. 176, 6999-7004.
31. Vester, B., Hansen, L. H & Douthwaite, S. (1995). The conformation of 23 S rRNA nucleotide A2058 determines its recognition by the ErmE methyltransferase. RNA, 1, 501-509.
32. Weisblum, B. (1995). Erythromycin resistance by ribosome modification. Antimicrob. Agents. Chemother. 39, 577-585.
33. Yanisch-Perron, C., Vieira, J. & Messing, J. (1985). Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene, 33, 103-119.
34. Zalacain, M. & Cundliffe, E. (1990). Methylation of 23 S ribosomal RNA due to carB, and antibiotic-resistance determinant from the carbomycin producer, Streptomyces thermotolerans. Eur. J. Biochem. 189, 67-72.
35. Zhong, P., Pratt, S. D., Edalji, R. P., Walter, K. A., Holzman, T. F., Shivakumar, A. G. & Katz, L. (1995). Substrate requirements for ErmC′ methyltransferase activity. J. Bacteriol. 177, 4327-4332.