title: Factors that influence selection of coding resumption sites in translational bypassing: minimal conventional peptidyl-tRNA:mRNA pairing can suffice.
abstract: This study investigates bypassing initiated from codons immediately 5' of a stop codon. The mRNA slips and is scanned by the peptidyl-tRNA for a suitable landing site, and standard decoding resumes at the next 3' codon. This work shows that landing sites with potentially strong base pairing between the peptidyl-tRNA anticodon and mRNA are preferred, but sites with little or no potential for Watson-Crick or wobble base pairing can also be utilized. These results have implications for re-pairing in ribosomal frameshifting. Shine-Dalgarno sequences in the mRNA can alter the distribution of landing sites observed. The bacteriophage T4 gene 60 nascent peptide, known to influence take-off in its native context, imposes stringent P-site pairing requirements, thereby limiting the number of suitable landing sites.
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330.
authors.forename: Alan J
authors.initials: AJ
authors.lastname: Herr
authors.forename: Norma M
authors.initials: NM
authors.lastname: Wills
authors.forename: Chad C
authors.initials: CC
authors.lastname: Nelson
authors.forename: Raymond F
authors.initials: RF
authors.lastname: Gesteland
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
mesh_terms: D001483:Base Sequence; D018965:Frameshifting, Ribosomal; D013058:Mass Spectrometry; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger; D012346:RNA, Transfer, Amino Acyl; C019037:tRNA, peptidyl-