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. 1988 Nov 25;16(22):10529–10545. doi: 10.1093/nar/16.22.10529

Mutational analysis of the L1 binding site of 23S rRNA in Escherichia coli.

B Said 1, J R Cole 1, M Nomura 1
PMCID: PMC338922  PMID: 3060846

Abstract

The L11 ribosomal protein operon of Escherichia coli contains the genes for L11 and L1 and is feedback regulated by the translational repressor L1. Both the L1 binding site on 23S rRNA and the L1 repressor target site on L11 operon mRNA share similar proposed secondary structures and contain some primary sequence identity. Several site-directed mutations in the binding region of 23S rRNA were constructed and their effects on binding were examined. For in vitro analysis, a filter binding method was used. For in vivo analysis, a conditional expression system was used to overproduce a 23S rRNA fragment containing the L1 binding region, which leads to specific derepression of the synthesis of L11 and L1. Changes in the shared region of the 23S rRNA L1 binding site produced effects on L1 binding similar to those found previously in analysis of corresponding changes in the L11 operon mRNA target site. The results support the hypothesis that r-protein L1 interacts with both 23S rRNA and L11 operon mRNA by recognizing similar features on both RNAs.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Baughman G., Nomura M. Localization of the target site for translational regulation of the L11 operon and direct evidence for translational coupling in Escherichia coli. Cell. 1983 Oct;34(3):979–988. doi: 10.1016/0092-8674(83)90555-x. [DOI] [PubMed] [Google Scholar]
  2. Baughman G., Nomura M. Translational regulation of the L11 ribosomal protein operon of Escherichia coli: analysis of the mRNA target site using oligonucleotide-directed mutagenesis. Proc Natl Acad Sci U S A. 1984 Sep;81(17):5389–5393. doi: 10.1073/pnas.81.17.5389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Branlant C., Krol A., Machatt A., Ebel J. P. The secondary structure of the protein L1 binding region of ribosomal 23S RNA. Homologies with putative secondary structures of the L11 mRNA and of a region of mitochondrial 16S rRNA. Nucleic Acids Res. 1981 Jan 24;9(2):293–307. doi: 10.1093/nar/9.2.293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Cole J. R., Nomura M. Translational regulation is responsible for growth-rate-dependent and stringent control of the synthesis of ribosomal proteins L11 and L1 in Escherichia coli. Proc Natl Acad Sci U S A. 1986 Jun;83(12):4129–4133. doi: 10.1073/pnas.83.12.4129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dean D., Yates J. L., Nomura M. Escherichia coli ribosomal protein S8 feedback regulates part of spc operon. Nature. 1981 Jan 1;289(5793):89–91. doi: 10.1038/289089a0. [DOI] [PubMed] [Google Scholar]
  7. Gourse R. L., Thurlow D. L., Gerbi S. A., Zimmermann R. A. Specific binding of a prokaryotic ribosomal protein to a eukaryotic ribosomal RNA: implications for evolution and autoregulation. Proc Natl Acad Sci U S A. 1981 May;78(5):2722–2726. doi: 10.1073/pnas.78.5.2722. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gregory R. J., Zimmermann R. A. Site-directed mutagenesis of the binding site for ribosomal protein S8 within 16S ribosomal RNA from Escherichia coli. Nucleic Acids Res. 1986 Jul 25;14(14):5761–5776. doi: 10.1093/nar/14.14.5761. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Jinks-Robertson S., Nomura M. Regulation of ribosomal protein synthesis in an Escherichia coli mutant missing ribosomal protein L1. J Bacteriol. 1981 Mar;145(3):1445–1447. doi: 10.1128/jb.145.3.1445-1447.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Jinks-Robertson S., Nomura M. Ribosomal protein S4 acts in trans as a translational repressor to regulate expression of the alpha operon in Escherichia coli. J Bacteriol. 1982 Jul;151(1):193–202. doi: 10.1128/jb.151.1.193-202.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kearney K. R., Nomura M. Secondary structure of the autoregulatory mRNA binding site of ribosomal protein L1. Mol Gen Genet. 1987 Nov;210(1):60–68. doi: 10.1007/BF00337759. [DOI] [PubMed] [Google Scholar]
  12. Lindahl L., Zengel J. M. Ribosomal genes in Escherichia coli. Annu Rev Genet. 1986;20:297–326. doi: 10.1146/annurev.ge.20.120186.001501. [DOI] [PubMed] [Google Scholar]
  13. Maly P., Rinke J., Ulmer E., Zwieb C., Brimacombe R. Precise localization of the site of cross-linking between protein L4 and 23S ribonucleic acid induced by mild ultraviolet irradiation of Escherichia coli 50S ribosomal subunits. Biochemistry. 1980 Sep 2;19(18):4179–4188. doi: 10.1021/bi00559a007. [DOI] [PubMed] [Google Scholar]
  14. McEntee K., Weinstock G. M., Lehman I. R. recA protein-catalyzed strand assimilation: stimulation by Escherichia coli single-stranded DNA-binding protein. Proc Natl Acad Sci U S A. 1980 Feb;77(2):857–861. doi: 10.1073/pnas.77.2.857. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Nomura M., Gourse R., Baughman G. Regulation of the synthesis of ribosomes and ribosomal components. Annu Rev Biochem. 1984;53:75–117. doi: 10.1146/annurev.bi.53.070184.000451. [DOI] [PubMed] [Google Scholar]
  17. Peacock A. C., Dingman C. W. Molecular weight estimation and separation of ribonucleic acid by electrophoresis in agarose-acrylamide composite gels. Biochemistry. 1968 Feb;7(2):668–674. doi: 10.1021/bi00842a023. [DOI] [PubMed] [Google Scholar]
  18. Sor F., Nomura M. Cloning and DNA sequence determination of the L11 ribosomal protein operon of Serratia marcescens and Proteus vulgaris: translational feedback regulation of the Escherichia coli L11 operon by heterologous L1 proteins. Mol Gen Genet. 1987 Nov;210(1):52–59. doi: 10.1007/BF00337758. [DOI] [PubMed] [Google Scholar]
  19. Stark M. J., Gregory R. J., Gourse R. L., Thurlow D. L., Zwieb C., Zimmermann R. A., Dahlberg A. E. Effects of site-directed mutations in the central domain of 16 S ribosomal RNA upon ribosomal protein binding, RNA processing and 30 S subunit assembly. J Mol Biol. 1984 Sep 15;178(2):303–322. doi: 10.1016/0022-2836(84)90146-3. [DOI] [PubMed] [Google Scholar]
  20. Steen R., Dahlberg A. E., Lade B. N., Studier F. W., Dunn J. J. T7 RNA polymerase directed expression of the Escherichia coli rrnB operon. EMBO J. 1986 May;5(5):1099–1103. doi: 10.1002/j.1460-2075.1986.tb04328.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Studier F. W., Moffatt B. A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol. 1986 May 5;189(1):113–130. doi: 10.1016/0022-2836(86)90385-2. [DOI] [PubMed] [Google Scholar]
  22. Thomas M. S., Nomura M. Translational regulation of the L11 ribosomal protein operon of Escherichia coli: mutations that define the target site for repression by L1. Nucleic Acids Res. 1987 Apr 10;15(7):3085–3096. doi: 10.1093/nar/15.7.3085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Wower I., Wower J., Meinke M., Brimacombe R. The use of 2-iminothiolane as an RNA-protein cross-linking agent in Escherichia coli ribosomes, and the localisation on 23S RNA of sites cross-linked to proteins L4, L6, L21, L23, L27 and L29. Nucleic Acids Res. 1981 Sep 11;9(17):4285–4302. doi: 10.1093/nar/9.17.4285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Yates J. L., Nomura M. Feedback regulation of ribosomal protein synthesis in E. coli: localization of the mRNA target sites for repressor action of ribosomal protein L1. Cell. 1981 Apr;24(1):243–249. doi: 10.1016/0092-8674(81)90520-1. [DOI] [PubMed] [Google Scholar]
  25. Zoller M. J., Smith M. Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors. Methods Enzymol. 1983;100:468–500. doi: 10.1016/0076-6879(83)00074-9. [DOI] [PubMed] [Google Scholar]

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