title: Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.
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.
authors.affiliation: 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.
authors.forename: Jin
authors.initials: J
authors.lastname: Chen
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Western Gateway Building, Western Road, Cork, Ireland.
authors.forename: Arthur
authors.initials: A
authors.lastname: Coakley
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Western Gateway Building, Western Road, Cork, Ireland.
authors.forename: Michelle
authors.initials: M
authors.lastname: O'Connor
authors.affiliation: Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
authors.forename: Alexey
authors.initials: A
authors.lastname: Petrov
authors.affiliation: Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
authors.forename: Seán E
authors.initials: SE
authors.lastname: O'Leary
authors.affiliation: 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.
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
authors.affiliation: Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA. Electronic address: puglisi@stanford.edu.
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Puglisi
mesh_terms: D024506:5' Flanking Region; D000926:Anticodon; D001483:Base Sequence; D003062:Codon; D004926:Escherichia coli / Q000378:metabolism*; D031541:Fluorescence Resonance Energy Transfer; D055029:Inverted Repeat Sequences; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020653:Peptide Elongation Factor G / Q000378:metabolism; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism*
chemical_list: D000926:Anticodon; D003062:Codon; D020653:Peptide Elongation Factor G; D012333:RNA, Messenger