Extending the Spacing between the Shine–Dalgarno Sequence and P-Site Codon Reduces the Rate of mRNA Translocation. Issue 16 (24th July 2020)

• Record Type: Journal Article
• Authors: Wakabayashi, Hironao; Warnasooriya, Chandani; Ermolenko, Dmitri N.
• Is Part Of: Journal of molecular biology. Volume 432:Issue 16(2020)
• Page Start: 4612
• Page End: 4622
• Publication Date: 2020-07-24
• Subjects: SD Shine–Dalgarno -- aSD anti-Shine–Dalgarno -- ORFs open reading frames -- PRF programmed ribosome frameshifting -- RF2 release factor 2 -- FRET Förster resonance energy transfer -- EF-G elongation factor G; translation pausing -- frameshifting -- toeprinting assay -- translocation kinetics -- Förster resonance energy transfer; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2020.06.008
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract : By forming base-pairing interactions with the 3′ end of 16S rRNA, mRNA Shine–Dalgarno (SD) sequences positioned upstream of open reading frames facilitate translation initiation. During the elongation phase of protein synthesis, intragenic SD-like sequences stimulate ribosome frameshifting and may also slow down ribosome movement along mRNA. Here, we show that the length of the spacer between the SD sequence and P-site codon strongly affects the rate of ribosome translocation. Increasing the spacer length beyond 6 nt destabilizes mRNA–tRNA–ribosome interactions and results in a 5- to 10-fold reduction of the translocation rate. These observations suggest that during translation, the spacer between the SD sequence and P-site codon undergoes structural rearrangements, which slow down mRNA translocation and promote mRNA frameshifting. Graphical abstract: Unlabelled Image Highlights: mRNA Shine–Dalgarno (SD) sequences regulate translation elongation. Extending the spacer between the SD sequence and P-site codon destabilizes mRNA–tRNA–ribosome interactions. Extending the spacer between the SD sequence and P-site codon inhibits mRNA translocation.