title: The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes.
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 K(131)GKK 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.
authors.affiliation: Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
authors.forename: Mickey R
authors.initials: MR
authors.lastname: Miller
authors.forename: Zhu
authors.initials: Z
authors.lastname: Liu
authors.forename: Deanna J
authors.initials: DJ
authors.lastname: Cazier
authors.forename: Grant M
authors.initials: GM
authors.lastname: Gebhard
authors.forename: Steven R
authors.initials: SR
authors.lastname: Herron
authors.forename: Hani S
authors.initials: HS
authors.lastname: Zaher
authors.forename: Rachel
authors.initials: R
authors.lastname: Green
authors.forename: Allen R
authors.initials: AR
authors.lastname: Buskirk
mesh_terms: D000595:Amino Acid Sequence; D000926:Anticodon / Q000235:genetics; D002942:Circular Dichroism; D003062:Codon / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015151:Immunoblotting; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020653:Peptide Elongation Factor G / Q000235:genetics / Q000378:metabolism; D010444:Peptide Elongation Factor Tu / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism; D046249:Transfer RNA Aminoacylation
chemical_list: D000926:Anticodon; D003062:Codon; D020653:Peptide Elongation Factor G; D012329:RNA, Bacterial; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; C430328:small protein B; C096222:tmRNA; D012343:RNA, Transfer; D010444:Peptide Elongation Factor Tu