title: The many paths to frameshifting: kinetic modelling and analysis of the effects of different elongation steps on programmed -1 ribosomal frameshifting.
abstract: Several important viruses including the human immunodeficiency virus type 1 (HIV-1) and the SARS-associated Coronavirus (SARS-CoV) employ programmed -1 ribosomal frameshifting (PRF) for their protein expression. Here, a kinetic framework is developed to describe -1 PRF. The model reveals three kinetic pathways to -1 PRF that yield two possible frameshift products: those incorporating zero frame encoded A-site tRNAs in the recoding site, and products incorporating -1 frame encoded A-site tRNAs. Using known kinetic rate constants, the individual contributions of different steps of the translation elongation cycle to -1 PRF and the ratio between two types of frameshift products were evaluated. A dual fluorescence reporter was employed in Escherichia coli to empirically test the model. Additionally, the study applied a novel mass spectrometry approach to quantify the ratios of the two frameshift products. A more detailed understanding of the mechanisms underlying -1 PRF may provide insight into developing antiviral therapeutics.
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Pei-Yu
authors.initials: PY
authors.lastname: Liao
authors.forename: Yong Seok
authors.initials: YS
authors.lastname: Choi
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Dinman
authors.forename: Kelvin H
authors.initials: KH
authors.lastname: Lee
mesh_terms: D018965:Frameshifting, Ribosomal; D015497:HIV-1 / Q000235:genetics; D015368:Human T-lymphotropic virus 1 / Q000235:genetics; D007700:Kinetics; D013058:Mass Spectrometry; D008957:Models, Genetic; D010441:Peptide Chain Elongation, Translational; D012343:RNA, Transfer / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism
chemical_list: D012343:RNA, Transfer
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