The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes

Mickey R. Miller, Zhu Liu, Deanna J. Cazier, Grant M. Gebhard, Steven R. Herron, Hani S. Zaher, Rachel Green, Allen Buskirk

Research output: Contribution to journalArticle

Abstract

In bacteria, stalled ribosomes are recycled by a hybrid transfer-messenger RNA (tmRNA). Like tRNA, tmRNA is aminoacylated with alanine and is delivered to the ribosome by EF-Tu, where it reacts with the growing polypeptide chain. tmRNA entry into stalled ribosomes poses a challenge to our understanding of ribosome function because it occurs in the absence of a codon- anticodon interaction. Instead, tmRNA entry is licensed by the binding of its protein partner, SmpB, to the ribosomal decoding center. We analyzed a series of SmpB mutants and found that its C-terminal tail is essential for tmRNA accommodation but not for EF-Tu activation. We obtained evidence that the tail likely functions as a helix on the ribosome to promote accommodation and identified key residues in the tail essential for this step. In addition, our mutational analysis points to a role for the conserved K131GKK tail residues in trans-translation after peptidyl transfer to tmRNA, presumably EF-G-mediated translocation or translation of the tmRNA template. Surprisingly, analysis of A1492, A1493, and G530 mutants reveals that while these ribosomal nucleotides are essential for normal tRNA selection, they play little to no role in peptidyl transfer to tmRNA. These studies clarify how SmpB interacts with the ribosomal decoding center to license tmRNA entry into stalled ribosomes. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish (US)
Pages (from-to)1727-1736
Number of pages10
JournalRNA
Volume17
Issue number9
DOIs
StatePublished - Sep 2011

Fingerprint

Licensure
Transfer RNA
Ribosomes
Messenger RNA
Peptide Elongation Factor Tu
Peptide Elongation Factor G
Anticodon
Codon
Alanine
Carrier Proteins
Nucleotides
Bacteria
Peptides

Keywords

  • Decoding
  • EF-Tu
  • Ribosome
  • SmpB
  • tmRNA

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Miller, M. R., Liu, Z., Cazier, D. J., Gebhard, G. M., Herron, S. R., Zaher, H. S., ... Buskirk, A. (2011). The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes. RNA, 17(9), 1727-1736. https://doi.org/10.1261/rna.2821711

The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes. / Miller, Mickey R.; Liu, Zhu; Cazier, Deanna J.; Gebhard, Grant M.; Herron, Steven R.; Zaher, Hani S.; Green, Rachel; Buskirk, Allen.

In: RNA, Vol. 17, No. 9, 09.2011, p. 1727-1736.

Research output: Contribution to journalArticle

Miller, MR, Liu, Z, Cazier, DJ, Gebhard, GM, Herron, SR, Zaher, HS, Green, R & Buskirk, A 2011, 'The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes', RNA, vol. 17, no. 9, pp. 1727-1736. https://doi.org/10.1261/rna.2821711
Miller MR, Liu Z, Cazier DJ, Gebhard GM, Herron SR, Zaher HS et al. The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes. RNA. 2011 Sep;17(9):1727-1736. https://doi.org/10.1261/rna.2821711
Miller, Mickey R. ; Liu, Zhu ; Cazier, Deanna J. ; Gebhard, Grant M. ; Herron, Steven R. ; Zaher, Hani S. ; Green, Rachel ; Buskirk, Allen. / The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes. In: RNA. 2011 ; Vol. 17, No. 9. pp. 1727-1736.
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