Large-scale mass spectrometry-based analysis of Euplotes octocarinatus supports the high frequency of+1 programmed ribosomal frameshift

Programmed ribosomal frameshifting (PRF) is commonly used to express many viral and some cellular genes. We conducted a genome-wide investigation of + 1 PRF in ciliate Euplotes octocarinatus through genome and transcriptome sequencing and our results demonstrated that approximately 11.4% of genes require + 1 PRF to produce complete gene products. While nucleic acid-based evidence for candidate genes with + 1 PRF strong, only very limited information is available at protein levels to date. In this study, E. octocarinatus was subjected to large-scale mass spectrometry-based analysis to verify the high frequency of + 1 PRF and 226 + 1 PRF gene products were identified. Based on the amino acid sequences of the peptides spanning the frameshift sites, typical frameshift motif AAA-UAR for + 1 PRF in Euplotes was identified. Our data in this study provide very useful insight into the understanding of the molecular mechanism of + 1 PRF.