Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome

Sotaro Uemura, Magdalena Dorywalska, Tae-hee Lee, Harold D. Kim, Joseph D. Puglisi, Steven Chu

Research output: Contribution to journalArticle

77 Citations (Scopus)

Abstract

The ribosome is a molecular machine that translates the genetic code contained in the messenger RNA into an amino acid sequence through repetitive cycles of transfer RNA selection, peptide bond formation and translocation. Here we demonstrate an optical tweezer assay to measure the rupture force between a single ribosome complex and mRNA. The rupture force was compared between ribosome complexes assembled on an mRNA with and without a strong Shine-Dalgarno (SD) sequence - a sequence found just upstream of the coding region of bacterial mRNAs, involved in translation initiation. The removal of the SD sequence significantly reduced the rupture force in complexes carrying an aminoacyl tRNA, Phe-tRNAPhe, in the A site, indicating that the SD interactions contribute significantly to the stability of the ribosomal complex on the mRNA before peptide bond formation. In contrast, the presence of a peptidyl tRNA analogue, N-acetyl-Phe-tRNAPhe, in the A site, which mimicked the post-peptidyl transfer state, weakened the rupture force as compared to the complex with Phe-tRNAPhe, and the resultant force was the same for both the SD-containing and SD-deficient mRNAs. These results suggest that formation of the first peptide bond destabilizes the SD interaction, resulting in the weakening of the force with which the ribosome grips an mRNA. This might be an important requirement to facilitate movement of the ribosome along mRNA during the first translocation step.

Original languageEnglish (US)
Pages (from-to)454-457
Number of pages4
JournalNature
Volume446
Issue number7134
DOIs
StatePublished - Mar 22 2007

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Ribosomes
RNA, Transfer, Phe
Messenger RNA
Peptides
Rupture
Amino Acid Repetitive Sequences
Optical Tweezers
Genetic Code
Hand Strength
Transfer RNA

All Science Journal Classification (ASJC) codes

  • General

Cite this

Uemura, S., Dorywalska, M., Lee, T., Kim, H. D., Puglisi, J. D., & Chu, S. (2007). Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome. Nature, 446(7134), 454-457. https://doi.org/10.1038/nature05625
Uemura, Sotaro ; Dorywalska, Magdalena ; Lee, Tae-hee ; Kim, Harold D. ; Puglisi, Joseph D. ; Chu, Steven. / Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome. In: Nature. 2007 ; Vol. 446, No. 7134. pp. 454-457.
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Uemura, S, Dorywalska, M, Lee, T, Kim, HD, Puglisi, JD & Chu, S 2007, 'Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome', Nature, vol. 446, no. 7134, pp. 454-457. https://doi.org/10.1038/nature05625

Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome. / Uemura, Sotaro; Dorywalska, Magdalena; Lee, Tae-hee; Kim, Harold D.; Puglisi, Joseph D.; Chu, Steven.

In: Nature, Vol. 446, No. 7134, 22.03.2007, p. 454-457.

Research output: Contribution to journalArticle

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N2 - The ribosome is a molecular machine that translates the genetic code contained in the messenger RNA into an amino acid sequence through repetitive cycles of transfer RNA selection, peptide bond formation and translocation. Here we demonstrate an optical tweezer assay to measure the rupture force between a single ribosome complex and mRNA. The rupture force was compared between ribosome complexes assembled on an mRNA with and without a strong Shine-Dalgarno (SD) sequence - a sequence found just upstream of the coding region of bacterial mRNAs, involved in translation initiation. The removal of the SD sequence significantly reduced the rupture force in complexes carrying an aminoacyl tRNA, Phe-tRNAPhe, in the A site, indicating that the SD interactions contribute significantly to the stability of the ribosomal complex on the mRNA before peptide bond formation. In contrast, the presence of a peptidyl tRNA analogue, N-acetyl-Phe-tRNAPhe, in the A site, which mimicked the post-peptidyl transfer state, weakened the rupture force as compared to the complex with Phe-tRNAPhe, and the resultant force was the same for both the SD-containing and SD-deficient mRNAs. These results suggest that formation of the first peptide bond destabilizes the SD interaction, resulting in the weakening of the force with which the ribosome grips an mRNA. This might be an important requirement to facilitate movement of the ribosome along mRNA during the first translocation step.

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Uemura S, Dorywalska M, Lee T, Kim HD, Puglisi JD, Chu S. Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome. Nature. 2007 Mar 22;446(7134):454-457. https://doi.org/10.1038/nature05625