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

Abstract

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 is 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.

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

“…Lobanov et al . used ribosome profiling to explore global translation in the ciliate Euplotes where numerous instances of ribosomal frameshifting have been reported ( 149 , 150 ). It appears that, like C. magnum , termination of translation takes place only on stop codons in close proximity to polyA tails, while internal stop codons trigger either +1 or +2 ribosomal frameshifting depending on the preceding codon ( 151 ).…”

The Sub‐Chromosomic Macronuclear Pheromone Genes of the Ciliate Euplotes raikovi: Comparative Structural Analysis and Insights into the Mechanism of Expression

“…; Wang et al. ,b). An even more convincing reason is the recent demonstration in Condylostoma , Parduczia, and Blastocrithidia , that all three UAA, UAG, and UGA stop codons may act as sense codons, depending on the relative position that they take in the transcript sequence (Alkalaeva and Mikhailova ; Heaphy et al.…”

Phenotypic mutations contribute to protein diversity and shape protein evolution

“…58 An exceptional case are the ciliates of the Euplotes genus, which use +1 or +2 frameshifting in more than 10% of their genes. 59,60 Invariably, frameshifting happens at in-frame stop codons, and it is suspected that Euplotes evolved to use additional signals for genuine termination, while the default behavior at a stop codon is frameshifting and continued translation. 59 Unlike single amino acid misincorporations, frameshifting can generate an entirely new protein sequence and can occur at orders of magnitude higher frequencies.…”