An rRNA fragment and its antisense can alter decoding of genetic information

Journal of Bacteriology

Volumn 180, Issue 10, 1998, Pages 2744-2748

  Arkov, Alexey L ^a   Mankin, Alexander ^b   Murgola, Emanuel J ^a,c  

^a UNIVERSITY OF TEXAS   (United States)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RIBOSOME RNA;

ARTICLE; BACTERIAL GENE; ESCHERICHIA COLI; GENE EXPRESSION; NONHUMAN; NONSENSE MUTATION; PRIORITY JOURNAL; PROMOTER REGION; TRANSLATION REGULATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0031923139     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.180.10.2744-2748.1998     Document Type: Article

References (40)

1. Arkov, A. L., D. V. Freislrofler, M. Ehrenberg, and E. J. Murgola. 1998. Mutations in RNAs of both ribosomal subunits cause defects in translation termination. EMBO J. 17:1507-1514.
2. Atkins, J. F., B. P. Nichols, and S. Thompson. 1983. The nucleotide sequence of the first externally suppressible -1 frameshift mutant, and of some nearby leaky frameshift mutants. EMBO J. 2:1345-1350.
3. Bronson, M. J., and C. Yanofsky. 1974. Characterization of mutations in the tryptophan operon of Escherichia coli by RNA nucleotide sequencing. J. Mol. Biol. 88:913-916.
4. Brown, C. M., K. K. McCaughan, and W. P. Tate. 1993. Two regions of the Escherichia coli 16S ribosomal RNA are important for decoding stop signals in polypeptide chain termination. Nucleic Acids Res. 21:2109-2115.
5. Buckingham, R. H. 1990. Codon context. Experientia 46:1126-1133.
6. Buckingham, R. H., P. Sörensen, F. T. Pagel, K. A. Hijazi, B. H. Mims, D. Brechemier-Baey, and E. J. Murgola. 1990. Third position base changes in codons 5′ and 3′ adjacent UGA codons affect UGA suppression in vivo. Biochim. Biophys. Acta 1050:259-262.
7. Bullard, J. M., M. A. van Waes, D. J. Bucklin, and W. E. Hill. 1995. Regions of 23 S ribosomal RNA proximal to transfer RNA bound at the P and E sites. J. Mol. Biol. 252:572-582.
8. Caskey, C. T., L. Bosch, and D. S. Konecki. 1977. Release factor binding to ribosome requires an intact 16S rRNA3′ terminus. J. Biol. Chem. 252:4435-4437.
9. de Peer, Y. V., S. Chapelle, and R. De Wachter. 1996. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res. 24:3381-3391.
10. Egebjerg, J., H. Leffers, A. Christensen, H. Andersen, and R. A. Garrett. 1987. Structure and accessibility of domain I of Escherichia coli 23S RNA in free RNA, in the L24-RNA complex and in 50S subunits. J. Mol. Biol. 196:125-136.
11. Elela, S. A., L. Good, Y. F. Melekhovets, and R. N. Nazar. 1994. Inhibition of protein synthesis by an efficiently expressed mutation in the yeast 5.8S ribosomal RNA. Nucleic Acids Res. 22:686-693.
12. Elela, S. A., and R. N. Nazar. 1997. Role of the 5.8S rRNA in ribosome translocation. Nucleic Acids Res. 25:1788-1794.
13. Emory, S. A., P. Bouvet, and J. G. Belasco. 1992. A 5′-terminal stem-loop structure can stabilize mRNA in Escherichia coli. Genes Dev. 6:135-148.
14. Founny, D., M. I. Recht, S. C. Blanchard, and J. D. Puglisi. 1996. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 274:1367-1371.
15. Fredericq, P. 1969. The recombination of colicinogenic factors with other episomes and plasmids, p. 163-174. In G. E. Wolstenholme and M. O'Connor (ed.), Bacterial plasmids and episomes. Little, Brown & Co., Boston, Mass.
16. Gualerzi, C. O., and C. L. Pon. 1996. mRNA-ribosome interaction during initiation of protein synthesis, p. 259-276. In R. A. Zimmermann and A. E. Dahlberg (ed.), Ribosomal RNA: structure, evolution, processing, and function in protein biosynthesis. CRC Press, Inc., Boca Raton, Fia.
17. Gudkov, A. V., A. R. Kazarov, R. Thimmapaya, S. A. Axenovich, I. A. Mazo, and I. B. Roninson. 1994. Cloning mammalian genes by expression selection of genetic suppressor elements: association of kinesin with drug resistance and cell immortalization. Proc. Natl. Acad. Sci. USA 91:3744-3748.
18. Gutell, R. R., N. Larsen, and C. R. Woese. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58:10-26.
19. Gutell, R. R., and C. R. Woese. 1990. Higher order structural elements in ribosomal RNAs: pseudo-knots and the use of noncanonical pairs. Proc. Natl. Acad. Sci. USA 87:663-667.
20. Holzmayer, T. A., D. G. Pestov, and I. B. Roninson. 1992. Isolation of dominant negative mutants and inhibitory antisense RNA sequences by expression selection of random DNA fragments. Nucleic Acids Res. 20:711-717.
21. Howard, B., G. Thom, I. Jeffrey, D. Colthurst, D. Knowles, and C. Prescott. 1995. Fragmentation of the ribosome to investigate RNA-ligand interactions. Biochem. Cell Biol. 73:1161-1166.
22. Jemiolo, D. K., F. T. Pagel, and E. J. Murgola. 1995. UGA suppression by a mutant RNA of the large ribosomal subunit. Proc. Natl. Acad. Sci. USA 92:12309-12313.
23. Leffers, H., J. Kjems, L. Østergaard, N. Larsen, and R. A. Garrett. 1987. Evolutionary relationships amongst archaebacteria. A comparative study of 23S ribosomal RNAs of a sulphur-dependent extreme thermophile, an extreme halophile and a thermophilic methanogen. J. Mol. Biol. 195:43-61.
24. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-110.
25. McLaren, R. S., S. F. Newbury, G. S. C. Dance, H. C. Causton, and C. F. Higgins. 1991. mRNA degradation by processive 3′ -5′ exoribonucleases in vitro and implications for prokaryotic mRNA decay in vivo. J. Mol. Biol. 221:81-95.
26. Munishkin, A., and I. G. Wool. 1997. The ribosome-in-pieces: binding of elongation factor EF-G to oligoribonucleotides that mimic the sarcin/ricin and thiostrepton domains of 23S ribosomal RNA. Proc. Natl. Acad. Sci. USA 94:12280-12284.
27. Murgola, E. J., F. T. Pagel, K. A. Hijazi, A. L. Arkov, W. Xu, and S. Q. Zhao. 1995. Variety of nonsense suppressor phenotypes associated with mutational changes at conserved sites in Escherichia coli ribosomal RNA. Biochem. Cell Biol. 73:925-931.
28. Nichols, B. P., and C. Yanofsky. 1979. Nucleotide sequences of trpA of Salmonella typhimurium and Escherichia coli: an evolutionary comparison. Proc. Natl. Acad. Sci. USA 76:5244-5248.
29. Noller, H. F., V. Hoffarth, and L. Zimniak. 1992. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256:1416-1419.
30. Noller, H. F., T. Powers, P. N. Allen, D. Moazed, and S. Stern. 1996. rRNA and translation: tRNA selection and movement in the ribosome, p. 259-276. In R. A. Zimmermann and A. E. Dahlberg (ed.), Ribosomal RNA: structure, evolution, processing, and function in protein biosynthesis. CRC Press, Inc., Boca Raton, Fla.
31. Osswald, M., B. Greuer, and R. Brimacombe. 1990. Localization of a series of RNA-protein cross-link sites in the 23S and 5S ribosomal RNA from Escherichia coli, induced by treatment of 50S subunits with three different bifunctional reagents. Nucleic Acids Res. 18:6755-6760.
32. Pagel, F. T., and E. J. Murgola. Unpublished data.
33. Pagel, F. T., S. Q. Zhao, K. A. Hijazi, and E. J. Murgola. 1997. Phenotypic heterogeneity of mutational changes at a conserved nucleotide in 16S ribosomal RNA. J. Mol. Biol. 267:1113-1123.
34. Purohit, P., and S. Stern. 1994. Interaction of a small RNA with antibiotic and RNA ligands of the 30S subunit. Nature 370:659-662.
35. Tate, W. P., E. S. Poole, and S. A. Mannering. 1996. Hidden infidelities of the translational stop signal. Prog. Nucleic Acid Res. Mol. Biol. 52:293-335.
36. Tate, W. P., and S. A. Mannering. 1996. Three, four or more: the translational stop signal at length. Mol. Microbiol. 21:213-219.
37. Tenson, T., A. DeBlasio, and A. Mankin. 1996. A functional peptide encoded in the Escherichia coli 23S rRNA. Proc. Natl. Acad. Sci. USA 93:5641-5646.
38. Tucker, S. D., E. J. Murgola, and F. T. Pagel. 1989. Missense and nonsense suppressors can correct frameshift mutations. Biochimie 71:729-739.
39. Walker, K., S. A. Elela, and R. N. Nazar. 1990. Inhibition of protein synthesis by anti-5.8S rRNA oligodeoxyribonucleotides. J. Biol. Chem. 265:2428-2430.
40. Yanofsky, C., D. R. Helinski, and B. D. Maling. 1961. The effects of mutation on the composition and properties of the A protein of Escherichia coli tryptophan synthetase. Cold Spring Harbor Symp. Quant. Biol. 26:11-23.