Nucleic Acids Research Advance Access published online on September 26, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp796
RNA |
FSscan: a mechanism-based program to identify +1 ribosomal frameshift hotspots
1School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York and 2Chemical Engineering Department and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
*To whom correspondence should be addressed. Tel: +1 302 831 0344; Email: KHL{at}udel.edu
Received August 7, 2009. Revised September 8, 2009. Accepted September 9, 2009.
In +1 programmed ribosomal frameshifting (PRF), ribosomes skip one nucleotide toward the 3'-end during translation. Most of the genes known to demonstrate +1 PRF have been discovered by chance or by searching homologous genes. Here, a bioinformatic framework called FSscan is developed to perform a systematic search for potential +1 frameshift sites in the Escherichia coli genome. Based on a current state of the art understanding of the mechanism of +1 PRF, FSscan calculates scores for a 16-nt window along a gene sequence according to different effects of the stimulatory signals, and ribosome E-, P- and A-site interactions. FSscan successfully identified the +1 PRF site in prfB and predicted yehP, pepP, nuoE and cheA as +1 frameshift candidates in the E. coli genome. Empirical results demonstrated that potential +1 frameshift sequences identified promoted significant levels of +1 frameshifting in vivo. Mass spectrometry analysis confirmed the presence of the frameshifted proteins expressed from a yehP-egfp fusion construct. FSscan allows a genome-wide and systematic search for +1 frameshift sites in E. coli. The results have implications for bioinformatic identification of novel frameshift proteins, ribosomal frameshifting, coding sequence detection and the application of mass spectrometry on studying frameshift proteins.