Nucleic Acids Research Advance Access published online on March 15, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn100
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A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting
1School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, 2School of Medicine, Stanford University, Palo Alto CA, 3Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD and 4Chemical Engineering Department and Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
*To whom correspondence should be addressed. Tel: +1 302 831 0344; Fax: +1 302 831 4841; Email: KHL{at}udel.edu
Received January 10, 2008. Revised February 22, 2008. Accepted February 22, 2008.
Programmed ribosomal frameshifting (PRF) is a process by which ribosomes produce two different polypeptides from the same mRNA. In this study, we propose three different kinetic models of +1 PRF, incorporating the effects of the ribosomal E-, P- and A-sites toward promoting efficient +1 frameshifting in Escherichia coli. Specifically, the timing of E-site tRNA dissociation is discussed within the context of the kinetic proofreading mechanism of aminoacylated tRNA (aa-tRNA) selection. Mathematical modeling using previously determined kinetic rate constants reveals that destabilization of deacylated tRNA in the E-site, rearrangement of peptidyl-tRNA in the P-site, and availability of cognate aa-tRNA corresponding to the A-site act synergistically to promote efficient +1 PRF. The effect of E-site codon:anticodon interactions on +1 PRF was also experimentally examined with a dual fluorescence reporter construct. The combination of predictive modeling and empirical testing allowed the rate constant for P-site tRNA slippage (ks) to be estimated as ks 
1.9 s–1 for the release factor 2 (RF2) frameshifting sequence. These analyses suggest that P-site tRNA slippage is the driving force for +1 ribosomal frameshifting while the presence of a ‘hungry codon’ in the A-site and destabilization in the E-site further enhance +1 PRF in E. coli.