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. 2004 Jan;10(1):28-33.
doi: 10.1261/rna.5172104.

Genetic evidence against the 16S ribosomal RNA helix 27 conformational switch model

Affiliations

Genetic evidence against the 16S ribosomal RNA helix 27 conformational switch model

Daniel Rodriguez-Correa et al. RNA. 2004 Jan.

Abstract

A mechanistic understanding of ribosome function demands knowledge of the conformational changes that occur during protein synthesis. One current model proposes a conformational switch in Helix 27 (H27) of 16S rRNA involved in the decoding of mRNA. This model was based on the behavior of mutations in the 912 region of H27 of Escherichia coli 16S rRNA, which were predicted to stabilize the helix in either of two alternative conformations. This interpretation was supported by evidence from both genetics and structural biochemistry. However, recently published X-ray crystallographic structures of the Thermus thermophilus 30S subunit at different stages of tRNA selection have raised doubts regarding the validity of this model. We have therefore revisited the model genetically by constructing a H27 quadruple mutation (C912G, C910G, G885C, and G887C), which would create multiple mismatches in the proposed alternative conformation without perturbing the native H27 conformation seen in the crystal structures. Inconsistent with the H27 switch model, cells containing pure populations of quadruple mutant ribosomes grow at essentially wild-type rates. The mutants used to construct the H27 switch model all carried A2058G in 23S rRNA and C1192U in 16S rRNA as selectable markers. The quadruple mutant carrying these additional marker mutations is deleterious, and we conclude that they have a synergistic effect when combined with other mutations and are not phenotypically silent. Their presence confounded the interpretation of the original mutant phenotypes and, in light of the viability of the quadruple mutant, we conclude that the genetic evidence no longer supports the model.

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Figures

FIGURE 1.
FIGURE 1.
The H27 conformational switch model. (A) The two proposed conformations, 912–885 (left) and 912–888 (right), in H27 of wild-type 16S rRNA. (B) The quadruple mutation retains the Watson–Crick pairing configuration of the 912–885 conformation while preventing the formation of the alternative 912–888 pairing.
FIGURE 2.
FIGURE 2.
(A) Primer extension analysis of total RNA from the Δ7rrn strain carrying either wild-type (pKK3535) or the quadruple H27 mutant (pQuad) plasmid. The positions +14 (G903) of wild-type RNA and +5 (C912G) of mutant RNA are indicated, confirming that pQuad could displace pKK3535. (B) Growth and doubling times for the Δ7rrn strain containing wild-type plasmid (pKK3535), the quadruple mutant plasmid (pQuad) and plasmid pSTL102 with ribosomal selectable marker mutations C1192U and A2058G.
FIGURE 3.
FIGURE 3.
(A) Extensive packing of H27 with components of the decoding region, as viewed from the subunit interface. 16S rRNA helices 1, 24, 44 (blue) abut H27 (hot pink) with proteins S5 (cyan) and S12 (orange). H28 is omitted for clarity. (B) Residue 1192 within H34 in close proximity to ribosomal protein S5. C912–G885 base pair (red), 16S rRNA helices 1 and 27 (blue), proteins S5 (cyan) and S4 (green). Structures rendered using PyMOL molecular system software (DeLano 2002), and PDB file 1J5E (Wimberly et al. 2000).

References

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