Long range RNA-RNA interactions in the 30 S ribosomal subunit ofE. coli

Abstract

We have attempted to identify long-range interactions in the tertiary structure of RNA in the E. coli 30 S ribosome. Native subunits were cleaved with ribonuclease and separated into nucleoprotein fragments which were deproteinized and fractionated into multi-oligonucleotide complexes under conditions intended to preserve RNA-RNA interactions. The final products were denatured by urea and heat and their constituent oligonucleotides resolved and sequenced. Many complexes contained complementary sequences known to be bound together in the RNA secondary structure, attesting to the validity of the technique. Other co-migrating oligonucleotides, not joined in the secondary structure, contained mutually complementary sequences in locations that allow base-pairing interaction without disrupting pre-existing secondary structure. In seven instances the complementary relationship was found to have been preserved during phylogenetic diversification.

Alternative base pairing between 5′- and 3′-terminal sequences of small subunit RNA may provide the basis of a conformational switch of the small ribosomal subunit

“…This extended type of mRNA recognition with 3' and 5'-terminal sequences of 16S rRNA pairing on adjacent regions of mRNA would imply neighbourhood of the two termini, but in contrast to our model would also imply melting of helices 1 (positions 9-13) and 2 (positions [18][19][20] during mRNA recognition.…”

“…Proposal of a functional two state model of the small ribosomal subunit Alternative base pairings for certain parts of small subunit rRNAs or base pairings for tertiary interactions have been proposed earlier (20,21,22,23), for review see also ref. (16), but none of the proposals include sequences from the two termini or the 'pseudo-knot' helix.…”

Higher order structure in ribosomal RNA.

“…The few properly compensated bp replacements that do result are within chance expectation. Similarly seven or more of the tertiary interactions proposed by Spitnik-Elson et al (1985) show a relatively high level of mispairs when tested on a properly aligned and extensive set of eubacterial sequences (unpublished data).…”

“…A number of higher order interactions have already been proposed that do not withstand rigorous comparative test. Thompson and Hearst (1983) have suggested three of them for the 16S rRNA, while Spitnik-Elson et al (1985) have proposed 17. Comparing the first group of proposed structures in a set of 22 eubacterial sequences that has been properly aligned shows the vast majority of the nucleotide replacements to result in mispairs.…”

Computer modeling 16 S ribosomal RNA

“…It was possible to identify within one or two residues which bases are crosslinked for these seven but that is not possible for the rare crosslink between the 5' and 3' domains (0354 X U1330). Other research confirms the existence of this interaction (Spitnik-Elson et al, 1985) so it is retained. Bases from the middle of the crosslinked fragments were chosen and a van der Waals contact lower bound was used.…”