Systematic analysis of non programmed frameshift suppression in E. coli via translational tiling proteomics

Programmed ribosomal frameshifting is a process that augments the coding capacity of particular mRNA transcripts. Programmed ribosomal frameshifting may occur during the decoding of chromosomally encoded genes in both prokaryotes and eukaryotes. Although programmed ribosomal frameshifting has been intensively studied, less is known about the occurrence of translation errors that result in frameshifts. Detection of unexpectedly efficient frameshift suppression in E. coli (at levels ranging from 1% to 10% with two unrelated test proteins) led us to investigate the scope of events responsible for restoration of the native frame. To enable a comprehensive approach, we developed a targeted mass-spectrometry method–“translational tiling proteomics”–allowing interrogation of the full set of possible –1 slippage events that could lead to the observed instances of frameshift suppression in vitro and in cells. Our findings point to an unexpectedly high basal level of ribosomal frameshifting, suggest that frameshifted products may contribute more significantly to the proteome than generally assumed, and raise the possibility that particular pseudogenes may specify functional proteins.