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Cell. 2015 Nov 19;163(5):1267-1280. doi: 10.1016/j.cell.2015.10.064.

Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.

Author information

1
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA.
2
School of Biochemistry and Cell Biology, University College Cork, Western Gateway Building, Western Road, Cork, Ireland.
3
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
4
School of Biochemistry and Cell Biology, University College Cork, Western Gateway Building, Western Road, Cork, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA. Electronic address: j.atkins@ucc.ie.
5
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA. Electronic address: puglisi@stanford.edu.

Abstract

Nearly half of the ribosomes translating a particular bacteriophage T4 mRNA bypass a region of 50 nt, resuming translation 3' of this gap. How this large-scale, specific hop occurs and what determines whether a ribosome bypasses remain unclear. We apply single-molecule fluorescence with zero-mode waveguides to track individual Escherichia coli ribosomes during translation of T4's gene 60 mRNA. Ribosomes that bypass are characterized by a 10- to 20-fold longer pause in a non-canonical rotated state at the take-off codon. During the pause, mRNA secondary structure rearrangements are coupled to ribosome forward movement, facilitated by nascent peptide interactions that disengage the ribosome anticodon-codon interactions for slippage. Close to the landing site, the ribosome then scans mRNA in search of optimal base-pairing interactions. Our results provide a mechanistic and conformational framework for bypassing, highlighting a non-canonical ribosomal state to allow for mRNA structure refolding to drive large-scale ribosome movements.

PMID:
26590426
PMCID:
PMC4813330
DOI:
10.1016/j.cell.2015.10.064
[Indexed for MEDLINE]
Free PMC Article

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