Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1978 Mar;5(3):805–823. doi: 10.1093/nar/5.3.805

Studies on ribosome structure and interactions near the m62Am62A sequence.

P Thammana, C R Cantor
PMCID: PMC342025  PMID: 347402

Abstract

Antibodies raised against N6, N6-dimethyl adenosine were used to study the environment and role of the m62Am62A sequences in the E. coli ribosome. It is observed that this sequence is exposed on the surface of isolated 30S subunits, but becomes inaccessible for IgG interaction upon heat activation. The m62Am62A sequence is also inaccessible for IgG interaction in 70S ribosomes or 30S subunits immediately after dissociation of 70S particles. The presence of IgGs results in a significant inhibition of IF3 binding to unactivated 30S particles. IF3 binding to activated 30S subunits is unaffected by the IgGs. Crosslinking of 30S proteins S18 and S21 with the bifunctional phenylene dimaleimide reagents results in a reduction in the extent of 30S-IgG interaction. From what is already known about the location of S18, S21 and the IF3 binding site, it is suggested that the m62Am62A sequence is located close to the initiator tRNA binding site of the 30S subunit during initiation of protein synthesis.

Full text

PDF
805

Selected References

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

  1. Baan R. A., Duijfjes J. J., van Leerdam E., van Knippenberg P. H., Bosch L. Specific in situ cleavage of 16S ribosomal RNA of Escherichia coli interferes with the function of initiation factor IF-1. Proc Natl Acad Sci U S A. 1976 Mar;73(3):702–706. doi: 10.1073/pnas.73.3.702. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Branlant C., Widada J. S., Krol A., Ebel J. P. Extensions of the known sequences at the 3' and 5' ends of 23S ribosomal RNA from Escherichia coli, possible base pairing between these 23S RNA regions and 16S ribosomal RNA. Nucleic Acids Res. 1976 Jul;3(7):1671–1687. doi: 10.1093/nar/3.7.1671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chang F. N., Flaks J. G. The specific cross-linking of two proteins from the Escherichia coli 30 s ribosomal subunit. J Mol Biol. 1972 Jul 14;68(1):177–180. doi: 10.1016/0022-2836(72)90272-0. [DOI] [PubMed] [Google Scholar]
  4. Chapman N. M., Noller H. F. Protection of specific sites in 16 S RNA from chemical modification by association of 30 S and 50 S ribosomes. J Mol Biol. 1977 Jan 5;109(1):131–149. doi: 10.1016/s0022-2836(77)80049-1. [DOI] [PubMed] [Google Scholar]
  5. Cooperman B. S., Dondon J., Finelli J., Grunberg-Manago M., Michelson A. M. Photosensitized cross-linking of IF-3 to Escherichia coli 30 S subunits. FEBS Lett. 1977 Apr 1;76(1):59–63. doi: 10.1016/0014-5793(77)80120-8. [DOI] [PubMed] [Google Scholar]
  6. Czernilofsky A. P., Kurland C. G., Stöffler G. 30S ribosomal proteins associated with the 3'-terminus of 16S RNA. FEBS Lett. 1975 Oct 15;58(1):281–284. doi: 10.1016/0014-5793(75)80279-1. [DOI] [PubMed] [Google Scholar]
  7. Dahlberg A. E., Dahlberg J. E. Binding of ribosomal protein S1 of Escherichia coli to the 3' end of 16S rRNA. Proc Natl Acad Sci U S A. 1975 Aug;72(8):2940–2944. doi: 10.1073/pnas.72.8.2940. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Englander S. W., Crowe D. Rapid microdialysis and hydrogen exchange. Anal Biochem. 1965 Sep;12(3):579–584. doi: 10.1016/0003-2697(65)90225-3. [DOI] [PubMed] [Google Scholar]
  9. Fiser I., Scheit K. H., Stöffler G., Kuechler E. Proteins at the mRNA binding site of the Escherichia coli ribosome. FEBS Lett. 1975 Aug 15;56(2):226–229. doi: 10.1016/0014-5793(75)81097-0. [DOI] [PubMed] [Google Scholar]
  10. Ginzburg I., Miskin R., Zamir A. N-ethyl maleimide as a probe for the study of functional sites and conformations of 30 S ribosomal subunits. J Mol Biol. 1973 Sep 25;79(3):481–494. doi: 10.1016/0022-2836(73)90400-2. [DOI] [PubMed] [Google Scholar]
  11. Ginzburg I., Zamir A. Characterization of different conformational forms of 30 S ribosomal subunits in isolated and associated states: possible correlations between structure and function. J Mol Biol. 1975 Apr 25;93(4):465–476. doi: 10.1016/0022-2836(75)90240-5. [DOI] [PubMed] [Google Scholar]
  12. Hardy S. J., Kurland C. G., Voynow P., Mora G. The ribosomal proteins of Escherichia coli. I. Purification of the 30S ribosomal proteins. Biochemistry. 1969 Jul;8(7):2897–2905. doi: 10.1021/bi00835a031. [DOI] [PubMed] [Google Scholar]
  13. Helser T. L., Davies J. E., Dahlberg J. E. Change in methylation of 16S ribosomal RNA associated with mutation to kasugamycin resistance in Escherichia coli. Nat New Biol. 1971 Sep 1;233(35):12–14. doi: 10.1038/newbio233012a0. [DOI] [PubMed] [Google Scholar]
  14. Helser T. L., Davies J. E., Dahlberg J. E. Mechanism of kasugamycin resistance in Escherichia coli. Nat New Biol. 1972 Jan 5;235(53):6–9. doi: 10.1038/newbio235006a0. [DOI] [PubMed] [Google Scholar]
  15. LOWRY O. H., ROSEBROUGH N. J., FARR A. L., RANDALL R. J. Protein measurement with the Folin phenol reagent. J Biol Chem. 1951 Nov;193(1):265–275. [PubMed] [Google Scholar]
  16. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  17. Langlois R., Lee C. C., Cantor C. R., Vince R., Pestka S. The distance between two functionally significant regions of the 50 S Escherichia coli ribosome: the erythromycin binding site and proteins L7/L12. J Mol Biol. 1976 Sep 15;106(2):297–313. doi: 10.1016/0022-2836(76)90087-5. [DOI] [PubMed] [Google Scholar]
  18. Lee-Huang S., Ochoa S. Preparation and properties of crystalline initiation factor 1 (IF1) from Escherichia coli. Methods Enzymol. 1974;30:31–39. doi: 10.1016/0076-6879(74)30006-7. [DOI] [PubMed] [Google Scholar]
  19. Lutter L. C., Zeichhardt H., Kurland C. G. Ribosomal protein neighborhoods. I. S18 and S21 as well as S5 and S8 are neighbors. Mol Gen Genet. 1972;119(4):357–366. [PubMed] [Google Scholar]
  20. Moore P. B. Reaction of N-ethyl maleimide with the ribosomes of Escherichia coli. J Mol Biol. 1971 Aug 28;60(1):169–184. doi: 10.1016/0022-2836(71)90456-6. [DOI] [PubMed] [Google Scholar]
  21. Nashimoto H., Held W., Kaltschmidt E., Nomura M. Structure and function of bacterial ribosomes. XII. Accumulation of 21 s particles by some cold-sensitive mutants of Escherichia coli. J Mol Biol. 1971 Nov 28;62(1):121–138. doi: 10.1016/0022-2836(71)90135-5. [DOI] [PubMed] [Google Scholar]
  22. Noll M., Hapke B., Schreier M. H., Noll H. Structural dynamics of bacterial ribosomes. I. Characterization of vacant couples and their relation to complexed ribosomes. J Mol Biol. 1973 Apr 5;75(2):281–294. doi: 10.1016/0022-2836(73)90021-1. [DOI] [PubMed] [Google Scholar]
  23. Noll M., Stöffler G., Highland J. H. Dissociation of Escherichia coli ribosomes into active subunits. J Mol Biol. 1976 Nov;108(1):259–264. doi: 10.1016/s0022-2836(76)80107-6. [DOI] [PubMed] [Google Scholar]
  24. Okuyama A., Watanabe T., Tanaka N. Effects of aminoglycoside antibiotics on initiation of viral RNA-directed protein synthesis. J Antibiot (Tokyo) 1972 Apr;25(4):212–218. doi: 10.7164/antibiotics.25.212. [DOI] [PubMed] [Google Scholar]
  25. Politz S. M., Glitz D. G. Ribosome structure: localization of N6,N6-dimethyladenosine by electron microscopy of a ribosome-antibody complex. Proc Natl Acad Sci U S A. 1977 Apr;74(4):1468–1472. doi: 10.1073/pnas.74.4.1468. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pon C. L., Friedman S. M., Gualerzi C. Studies on the interaction between ribosomes and 14 CH 3 -F 3 initation factor. Mol Gen Genet. 1972;116(2):192–198. doi: 10.1007/BF00582228. [DOI] [PubMed] [Google Scholar]
  27. Pongs O., Stöffler G., Lanka E. The codon binding site of the Escherichia coli ribosome as studied with a chemically reactive A-U-G analog. J Mol Biol. 1975 Dec 5;99(2):301–315. doi: 10.1016/s0022-2836(75)80148-3. [DOI] [PubMed] [Google Scholar]
  28. Shine J., Dalgarno L. Determinant of cistron specificity in bacterial ribosomes. Nature. 1975 Mar 6;254(5495):34–38. doi: 10.1038/254034a0. [DOI] [PubMed] [Google Scholar]
  29. Sommer A., Traut R. R. Identification of neighboring protein pairs in the Escherichia coli 30 S ribosomal subunit by crosslinking with methyl-4-mercaptobutyrimidate. J Mol Biol. 1976 Oct 5;106(4):995–1015. doi: 10.1016/0022-2836(76)90348-x. [DOI] [PubMed] [Google Scholar]
  30. Steitz J. A., Jakes K. How ribosomes select initiator regions in mRNA: base pair formation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4734–4738. doi: 10.1073/pnas.72.12.4734. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Tai P. C., Wallace B. J., Davis B. D. Actions of aurintricarboxylate, kasugamycin, and pactamycin on Escherichia coli polysomes. Biochemistry. 1973 Feb;12(4):616–620. doi: 10.1021/bi00728a008. [DOI] [PubMed] [Google Scholar]
  32. Thammana P., Held W. A. Methylation of 16S RNA during ribosome assembly in vitro. Nature. 1974 Oct 25;251(5477):682–686. doi: 10.1038/251682a0. [DOI] [PubMed] [Google Scholar]
  33. Tischendorf G. W., Zeichhardt H., Stöffler G. Architecture of the Escherichia coli ribosome as determined by immune electron microscopy. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4820–4824. doi: 10.1073/pnas.72.12.4820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Turnowsky F., Högenauer G. Colicin E 3, an inactivating agent of the ribosomal A-site. Biochem Biophys Res Commun. 1973 Dec 19;55(4):1246–1254. doi: 10.1016/s0006-291x(73)80028-2. [DOI] [PubMed] [Google Scholar]
  35. Van Duin J., Kurland C. G., Dondon J., Grunberg-Mangago M., Branlant C., Ebel J. P. New aspects of the IF3-ribosome interaction. FEBS Lett. 1976 Feb 15;62(2):111–114. doi: 10.1016/0014-5793(76)80030-0. [DOI] [PubMed] [Google Scholar]
  36. Weber K., Pringle J. R., Osborn M. Measurement of molecular weights by electrophoresis on SDS-acrylamide gel. Methods Enzymol. 1972;26:3–27. doi: 10.1016/s0076-6879(72)26003-7. [DOI] [PubMed] [Google Scholar]
  37. Wishnia A., Boussert A., Graffe M., Dessen P. H., Grunberg-Manago M. Kinetics of the reversible association of ribosomal subunits: stopped-flow studies of the rate law and of the effect of Mg2+. J Mol Biol. 1975 Apr 25;93(4):499–415. doi: 10.1016/0022-2836(75)90242-9. [DOI] [PubMed] [Google Scholar]
  38. Zamir A., Miskin R., Vogel Z., Elson D. The inactivation and reactivation of Escherichia coli ribosomes. Methods Enzymol. 1974;30:406–426. doi: 10.1016/0076-6879(74)30042-0. [DOI] [PubMed] [Google Scholar]
  39. Zimmermann R. A., Mackie G. A., Muto A., Garrett R. A., Ungewickell E., Ehresmann C., Stiegler P., Ebel J. P., Fellner P. Location and characteristics of ribosomal protein binding sites in the 16S RNA of Escherichia coli. Nucleic Acids Res. 1975 Feb;2(2):279–302. doi: 10.1093/nar/2.2.279. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES