An experimentally-derived model for the secondary structure of the 16S ribosomal RNA from Escherichia coli

Abstract

Ribonucleoprotein fragments are isolated by mild ribonuclease digestion of E. coli 30S ribosomal subunits, and are deproteinized and subjected to a second partial digestion. Base-pairing between the resulting small RNA fragments is investigated using the two-dimensional gel electrophoresis procedure already reported (see Ref. 1). The interactions thus found are incorporated into a secondary structure model covering approximately 80% of the 16S RNA.

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

“…After denaturation by heat and urea, these are separated and sequenced. The strategy of cleavage and separation is similar to that used by Vigne and Jordan (25) with 5 S RNA and successfully employed by Brimacombe and his colleagues in deciphering the secondary structure of E. coli 16 S and 23 S rRNAs (11,(26)(27)(28). The major differences from our procedure were that the separation and denaturation were carried out in a single two-dimensional gel and, perhaps more significant, that the starting material was usually either purified RNA or ribosomes partly denatured by 2 M urea.…”

Structure of E. coli 16S RNA elucidated by psoralen crosslinking

“…On the basis of these data, Noller & Woese (1981) and Stiegler et al (1981) have proposed a general secondary structure model for all small subunit RNAs. Zwieb et al (1981) have also proposed a general model based on this evidence as well as UV crosslinking (Zwieb & Brimacombe, 1980), and denaturation studies (Ross & Brimacombe, 1979;Glotz & .Brimacombe, 1980). All three models are very similar.…”

Structure and function of ribosomal RNA

“…Specific conformational 'switches' (a switch being defined as the existence of two mutually exclusive secondary structural elements) have been proposed by various authors for 16S and 23S RNA (e.g. Glotz & Brimacombe, 1980;Glotz et al, 1981;Thompson & Hearst, 1983a;Atmadja et al, 1984) and also for 5S RNA (Trifonov & Bolshoi, 1983;De Wachter et al, 1984).…”

“…The most likely stage in the protein biosynthetic process where the rRNA might need to undergo radical conformational changes is during the translocation process (Glotz & Brimacombe, 1980;Thompson & Hearst, 1983b), since in this step the entire mRNA-tRNA-peptide complex must be physically shifted by one codon length across the ribosome, and this could be achieved by a cycle of switches in the ribosomal RNA. [In this context the reader is also referred to the work of Nierhaus & Rheinberger (1984), who have found strong evidence for the existence of a third tRNA binding site on the ribosome, in addition to the classical Aand P-sites.]…”