A stochastic model of translation with -1 programmed ribosomal frameshifting

Brenae L. Bailey, Koen Visscher, Joseph C Watkins

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Many viruses produce multiple proteins from a single mRNA sequence by encoding overlapping genes. One mechanism to decode both genes, which reside in alternate reading frames, is -1 programmed ribosomal frameshifting. Although recognized for over 25 years, the molecular and physical mechanism of -1 frameshifting remains poorly understood. We have developed a mathematical model that treats mRNA translation and associated -1 frameshifting as a stochastic process in which the transition probabilities are based on the energetics of local molecular interactions. The model predicts both the location and efficiency of -1 frameshift events in HIV-1. Moreover, we compute -1 frameshift efficiencies upon mutations in the viral mRNA sequence and variations in relative tRNA abundances, predictions that are directly testable in experiment.

Original languageEnglish (US)
Article number016009
JournalPhysical Biology
Volume11
Issue number1
DOIs
StatePublished - Feb 2014

Fingerprint

Ribosomal Frameshifting
Overlapping Genes
Stochastic Processes
Reading Frames
Messenger RNA
Protein Biosynthesis
Transfer RNA
HIV-1
Theoretical Models
Viruses
Mutation
Genes
Proteins

Keywords

  • elongation
  • ribosomal frameshift
  • stochastic models
  • translation

ASJC Scopus subject areas

  • Biophysics
  • Molecular Biology
  • Cell Biology
  • Structural Biology
  • Medicine(all)

Cite this

A stochastic model of translation with -1 programmed ribosomal frameshifting. / Bailey, Brenae L.; Visscher, Koen; Watkins, Joseph C.

In: Physical Biology, Vol. 11, No. 1, 016009, 02.2014.

Research output: Contribution to journalArticle

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