A conformational switch involving the 915 region of Escherichia coli 16 S ribosomal RNA

Abstract

A novel alternative conformation, which involves an interaction between the 5′ terminal and 915 regions (E. coli numbering), is proposed after a screening of compiled sequences of small subunit ribosomal RNAs. This conformation contains a pseudoknot helix between residues 12–16 and 911–915, and its formation requires the partial melting of the 5′ terminal helix and the disruption of the 17–19/916–918 pseudoknot helix of the classical 16 S rRNA secondary structure. The alternate pseudoknot helix is proximal to the binding site of streptomycin and various mutations in rRNA which confer resistance to streptomycin have been located in each strund of the proposed helix. It is suggested that the presence of streptomycin favours the shift towards the alternate conformation, thereby stabilizing drug binding. Mutations which destabilize the novel pseudoknot helix would restrict the response to streptomycin.

A Ribosomal Gene Mutation in Streptomycin-ResistantMycobacterium tuberculosis Isolates

“…These results have recently been confirmed by Meier et al, (1994). Pinard et al, (1993) investigated the idea that the 5' proximal helix of the ribosome is involved in streptomycin binding by a conformational change to stabilize the binding of the drug (Leclerc & Gingras, 1991 ). Four mutations (13 u-A, 13U-c, 914 A-U and 914 A-G) were introduced, either individually or as double mutations ( 13 u-A and 914 A-U or 13U-C and 914 A-+G) into E. coli.…”

A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. fitting the RNA to a 3D electron microscopic map at 20 Å 1 1Edited by D. E. Drapper

“…With regard to helices 2 and 27, we have already noted above that the potential base-pairs (Lodmell et al, 1995) between nucleotides 885 to 887 and 910 to 912 (the latter being part of the connecting strand between the two helices; Figure 1), can be formed only if the pseudoknot helix 2 becomes unpaired; a number of dynamic models have been proposed (e.g. see Leclerc & Brakier-Gingras, 1991) suggesting just such a process.…”

Spectinomycin interacts specifically with the residues G1064and C1192in 16S rRNA, thereby potentially freezing this molecule into an inactive conformation

“…streptomycin and neomycin-like aminoglycosides, have also been suggested to bind to specific helices in 16S rRNA. For example, streptomycin may interact with nucleotides in the helix formed by the regions 12-16 and 911-915 (18). Footprinting experiments had already shown that streptomycin protects the residues 911-915 (8).…”