Abstract
A series of base substitution and deletion mutations were constructed in the highly conserved 530 stem and loop region of E. coli 16S rRNA involved in binding of tRNA to the ribosomal A site. Base substitution and deletion of G517 produced significant effects on cell growth rate and translational fidelity, permitting readthrough of UGA, UAG and UAA stop codons as well as stimulating +1 and -1 frameshifting in vivo. By contrast, mutations at position 534 had little or no effect on growth rate or translational fidelity. The results demonstrate the importance of G517 in maintaining translational fidelity but do not support a base pairing interaction between G517 and U534.
Full text
PDF![4221](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9d7/334129/f15e3c9e5ce2/nar00227-0104.png)
![4222](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9d7/334129/37d05e3d3ab6/nar00227-0105.png)
![4223](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9d7/334129/5075d59e4aff/nar00227-0106.png)
![4224](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9d7/334129/0ae357efd6ed/nar00227-0107.png)
![4225](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9d7/334129/352a8afa05c3/nar00227-0108.png)
![4226](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9d7/334129/00e86fe5d424/nar00227-0109.png)
![4227](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9d7/334129/b41a77efe6e9/nar00227-0110.png)
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Allen P. N., Noller H. F. A single base substitution in 16S ribosomal RNA suppresses streptomycin dependence and increases the frequency of translational errors. Cell. 1991 Jul 12;66(1):141–148. doi: 10.1016/0092-8674(91)90146-p. [DOI] [PubMed] [Google Scholar]
- Andersson D. I., Bohman K., Isaksson L. A., Kurland C. G. Translation rates and misreading characteristics of rpsD mutants in Escherichia coli. Mol Gen Genet. 1982;187(3):467–472. doi: 10.1007/BF00332630. [DOI] [PubMed] [Google Scholar]
- Andersson D. I., Kurland C. G. Ram ribosomes are defective proofreaders. Mol Gen Genet. 1983;191(3):378–381. doi: 10.1007/BF00425749. [DOI] [PubMed] [Google Scholar]
- Atkins J. F., Elseviers D., Gorini L. Low activity of -galactosidase in frameshift mutants of Escherichia coli. Proc Natl Acad Sci U S A. 1972 May;69(5):1192–1195. doi: 10.1073/pnas.69.5.1192. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Atkins J. F., Weiss R. B., Gesteland R. F. Ribosome gymnastics--degree of difficulty 9.5, style 10.0. Cell. 1990 Aug 10;62(3):413–423. doi: 10.1016/0092-8674(90)90007-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Aulin M. R., Hughes D. Overproduction of release factor reduces spontaneous frameshifting and frameshift suppression by mutant elongation factor Tu. J Bacteriol. 1990 Dec;172(12):6721–6726. doi: 10.1128/jb.172.12.6721-6726.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brimacombe R. RNA-protein interactions in the Escherichia coli ribosome. Biochimie. 1991 Jul-Aug;73(7-8):927–936. doi: 10.1016/0300-9084(91)90134-m. [DOI] [PubMed] [Google Scholar]
- Brosius J., Dull T. J., Sleeter D. D., Noller H. F. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol. 1981 May 15;148(2):107–127. doi: 10.1016/0022-2836(81)90508-8. [DOI] [PubMed] [Google Scholar]
- Davies J., Jones D. S., Khorana H. G. A further study of misreading of codons induced by streptomycin and neomycin using ribopolynucleotides containing two nucleotides in alternating sequence as templates. J Mol Biol. 1966 Jun;18(1):48–57. doi: 10.1016/s0022-2836(66)80075-x. [DOI] [PubMed] [Google Scholar]
- Dayhuff T. J., Atkins J. F., Gesteland R. F. Characterization of ribosomal frameshift events by protein sequence analysis. J Biol Chem. 1986 Jun 5;261(16):7491–7500. [PubMed] [Google Scholar]
- Gauthier A., Turmel M., Lemieux C. Mapping of chloroplast mutations conferring resistance to antibiotics in Chlamydomonas: evidence for a novel site of streptomycin resistance in the small subunit rRNA. Mol Gen Genet. 1988 Oct;214(2):192–197. doi: 10.1007/BF00337710. [DOI] [PubMed] [Google Scholar]
- Girshovich A. S., Bochkareva E. S., Vasiliev V. D. Localization of elongation factor Tu on the ribosome. FEBS Lett. 1986 Mar 3;197(1-2):192–198. doi: 10.1016/0014-5793(86)80325-8. [DOI] [PubMed] [Google Scholar]
- Gourse R. L., Takebe Y., Sharrock R. A., Nomura M. Feedback regulation of rRNA and tRNA synthesis and accumulation of free ribosomes after conditional expression of rRNA genes. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1069–1073. doi: 10.1073/pnas.82.4.1069. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gutell R. R., Weiser B., Woese C. R., Noller H. F. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. doi: 10.1016/s0079-6603(08)60348-7. [DOI] [PubMed] [Google Scholar]
- Göringer H. U., Hijazi K. A., Murgola E. J., Dahlberg A. E. Mutations in 16S rRNA that affect UGA (stop codon)-directed translation termination. Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6603–6607. doi: 10.1073/pnas.88.15.6603. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hirsh D., Gold L. Translation of the UGA triplet in vitro by tryptophan transfer RNA's. J Mol Biol. 1971 Jun 14;58(2):459–468. doi: 10.1016/0022-2836(71)90363-9. [DOI] [PubMed] [Google Scholar]
- Kirsebom L. A., Isaksson L. A. Involvement of ribosomal protein L7/L12 in control of translational accuracy. Proc Natl Acad Sci U S A. 1985 Feb;82(3):717–721. doi: 10.1073/pnas.82.3.717. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Langer J. A., Lake J. A. Elongation factor Tu localized on the exterior surface of the small ribosomal subunit. J Mol Biol. 1986 Feb 20;187(4):617–621. doi: 10.1016/0022-2836(86)90339-6. [DOI] [PubMed] [Google Scholar]
- Liu J. D., Parkinson J. S. Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control. J Bacteriol. 1989 Mar;171(3):1254–1261. doi: 10.1128/jb.171.3.1254-1261.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lopilato J., Bortner S., Beckwith J. Mutations in a new chromosomal gene of Escherichia coli K-12, pcnB, reduce plasmid copy number of pBR322 and its derivatives. Mol Gen Genet. 1986 Nov;205(2):285–290. doi: 10.1007/BF00430440. [DOI] [PubMed] [Google Scholar]
- Melançon P., Lemieux C., Brakier-Gingras L. A mutation in the 530 loop of Escherichia coli 16S ribosomal RNA causes resistance to streptomycin. Nucleic Acids Res. 1988 Oct 25;16(20):9631–9639. doi: 10.1093/nar/16.20.9631. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Menninger J. R. Peptidyl transfer RNA dissociates during protein synthesis from ribosomes of Escherichia coli. J Biol Chem. 1976 Jun 10;251(11):3392–3398. [PubMed] [Google Scholar]
- Moazed D., Noller H. F. Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature. 1987 Jun 4;327(6121):389–394. doi: 10.1038/327389a0. [DOI] [PubMed] [Google Scholar]
- Moazed D., Noller H. F. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell. 1986 Dec 26;47(6):985–994. doi: 10.1016/0092-8674(86)90813-5. [DOI] [PubMed] [Google Scholar]
- Murgola E. J., Hijazi K. A., Göringer H. U., Dahlberg A. E. Mutant 16S ribosomal RNA: a codon-specific translational suppressor. Proc Natl Acad Sci U S A. 1988 Jun;85(12):4162–4165. doi: 10.1073/pnas.85.12.4162. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Neefs J. M., Van de Peer Y., Hendriks L., De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 1990 Apr 25;18 (Suppl):2237–2317. doi: 10.1093/nar/18.suppl.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Noller H. F. Ribosomal RNA and translation. Annu Rev Biochem. 1991;60:191–227. doi: 10.1146/annurev.bi.60.070191.001203. [DOI] [PubMed] [Google Scholar]
- O'Connor M., Gesteland R. F., Atkins J. F. tRNA hopping: enhancement by an expanded anticodon. EMBO J. 1989 Dec 20;8(13):4315–4323. doi: 10.1002/j.1460-2075.1989.tb08618.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Parker J. Errors and alternatives in reading the universal genetic code. Microbiol Rev. 1989 Sep;53(3):273–298. doi: 10.1128/mr.53.3.273-298.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Powers T., Noller H. F. A functional pseudoknot in 16S ribosomal RNA. EMBO J. 1991 Aug;10(8):2203–2214. doi: 10.1002/j.1460-2075.1991.tb07756.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Remaut E., Tsao H., Fiers W. Improved plasmid vectors with a thermoinducible expression and temperature-regulated runaway replication. Gene. 1983 Apr;22(1):103–113. doi: 10.1016/0378-1119(83)90069-0. [DOI] [PubMed] [Google Scholar]
- Rinke-Appel J., Jünke N., Stade K., Brimacombe R. The path of mRNA through the Escherichia coli ribosome; site-directed cross-linking of mRNA analogues carrying a photo-reactive label at various points 3' to the decoding site. EMBO J. 1991 Aug;10(8):2195–2202. doi: 10.1002/j.1460-2075.1991.tb07755.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shen Z. H., Fox T. D. Substitution of an invariant nucleotide at the base of the highly conserved '530-loop' of 15S rRNA causes suppression of yeast mitochondrial ochre mutations. Nucleic Acids Res. 1989 Jun 26;17(12):4535–4539. doi: 10.1093/nar/17.12.4535. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sigmund C. D., Ettayebi M., Borden A., Morgan E. A. Antibiotic resistance mutations in ribosomal RNA genes of Escherichia coli. Methods Enzymol. 1988;164:673–690. doi: 10.1016/s0076-6879(88)64077-8. [DOI] [PubMed] [Google Scholar]
- Stern S., Powers T., Changchien L. M., Noller H. F. RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA. Science. 1989 May 19;244(4906):783–790. doi: 10.1126/science.2658053. [DOI] [PubMed] [Google Scholar]
- Stern S., Weiser B., Noller H. F. Model for the three-dimensional folding of 16 S ribosomal RNA. J Mol Biol. 1988 Nov 20;204(2):447–481. doi: 10.1016/0022-2836(88)90588-8. [DOI] [PubMed] [Google Scholar]
- Stoker N. G., Fairweather N. F., Spratt B. G. Versatile low-copy-number plasmid vectors for cloning in Escherichia coli. Gene. 1982 Jun;18(3):335–341. doi: 10.1016/0378-1119(82)90172-x. [DOI] [PubMed] [Google Scholar]
- Tapio S., Kurland C. G. Mutant EF-Tu increases missense error in vitro. Mol Gen Genet. 1986 Oct;205(1):186–188. doi: 10.1007/BF02428051. [DOI] [PubMed] [Google Scholar]
- Tapprich W. E., Goss D. J., Dahlberg A. E. Mutation at position 791 in Escherichia coli 16S ribosomal RNA affects processes involved in the initiation of protein synthesis. Proc Natl Acad Sci U S A. 1989 Jul;86(13):4927–4931. doi: 10.1073/pnas.86.13.4927. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Triman K., Becker E., Dammel C., Katz J., Mori H., Douthwaite S., Yapijakis C., Yoast S., Noller H. F. Isolation of temperature-sensitive mutants of 16 S rRNA in Escherichia coli. J Mol Biol. 1989 Oct 20;209(4):645–653. doi: 10.1016/0022-2836(89)92000-7. [DOI] [PubMed] [Google Scholar]
- Weiss R. B., Dunn D. M., Atkins J. F., Gesteland R. F. Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting. Cold Spring Harb Symp Quant Biol. 1987;52:687–693. doi: 10.1101/sqb.1987.052.01.078. [DOI] [PubMed] [Google Scholar]
- Weiss W. A., Edelman I., Culbertson M. R., Friedberg E. C. Physiological levels of normal tRNA(CAGGln) can effect partial suppression of amber mutations in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1987 Nov;84(22):8031–8034. doi: 10.1073/pnas.84.22.8031. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zoller M. J., Smith M. Oligonucleotide-directed mutagenesis using M13-derived vectors: an efficient and general procedure for the production of point mutations in any fragment of DNA. Nucleic Acids Res. 1982 Oct 25;10(20):6487–6500. doi: 10.1093/nar/10.20.6487. [DOI] [PMC free article] [PubMed] [Google Scholar]