Genome-wide Translational Changes Induced by the Prion [PSI+]

Abstract

Prions are infectious proteins that can adopt a structural conformation that is then propagated among other molecules of the same protein. [PSI(+)] is an aggregated conformation of the translational release factor eRF3. [PSI(+)] modifies cellular fitness, inducing various phenotypes depending on genetic background. However, the genes displaying [PSI(+)]-controlled expression remain unknown. We used ribosome profiling in isogenic [PSI(+)] and [psi(-)] strains to identify the changes induced by [PSI(+)]. We found 100 genes with stop codon readthrough events and showed that many stress-response genes were repressed in the presence of [PSI(+)]. Surprisingly, [PSI(+)] was also found to affect reading frame selection independently of its effect on translation termination efficiency. These results indicate that [PSI(+)] has a broader impact than initially anticipated, providing explanations for the phenotypic differences between [psi(-)] and [PSI(+)] strains.

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

“…As would be expected, both eRF1 and eRF3 are essential for yeast viability; however, the N terminus of eRF3 can be deleted. This N-terminal prion domain of eRF3 is the basis of the [PSI + ] aggregation of eRF3 (reviewed in Liebman and Chernoff 2012), resulting in impaired translation termination (Baudin-Baillieu et al 2014). Following release of the completed polypeptide, an 80S ribosome is bound to the mRNA with a deacylated tRNA in the P site base paired to the penultimate codon.…”

Mapping the non-standardized biases of ribosome profiling

“…DESeq tool) have been applied in a few ribosome profiling studies (Baudin-Baillieu et al, 2014;Sidrauski et al, 2015). Still, they require a test that the ribosome profiling read counts follow the underlying distributions required by many tools designed for DE analysis of RNA-Seq, for example DESeq (Anders and Huber, 2010), EdgeR , and baySeq (Hardcastle and Kelly, 2010).…”

“…Thereby, the mismatches in the seed count stronger than those in the extensions. Mostly, default Bowtie parameters (parameter n for the seed-based approach) are used (Guo et al, 2010;Li et al, 2012;Baudin-Baillieu et al, 2014;Subramaniam et al, 2014). Some studies apply the mismatch approach (Ingolia et al, 2011;Gerashchenko et al, 2012) which scores every base of each read equally.…”

“…In the ribosome profiling datasets a large fraction of the reads map at multiple positions to the genome (in the range of 30% and more), however there is no uniform strategy on how to handle them. Strategies range from considering only reads uniquely mapping to the genome (Guo et al, 2010;Baudin-Baillieu et al, 2014), to allowing more than 200 or unlimited number of positions (Ingolia et al, 2011). One strategy to estimate the true location of reads that map to many (multimappable) locations involves proportional assignment of reads based on the read density of the neighboring positions (Trapnell et al, 2010).…”

“…In the majority of ribosome profiling experiments (Ingolia et al, 2009(Ingolia et al, , 2011Guo et al, 2010;Gerashchenko et al, 2012;Li et al, 2012;Chew et al, 2013;Guttman et al, 2013;Aspden et al, 2014;Baudin-Baillieu et al, 2014;Bazzini et al, 2014;Subramaniam et al, 2014), Bowtie (Langmead et al, 2009) is used as a BWT-based mapping program. Bowtie offers two ways of mapping a read to a reference sequence: seed-(parameter n) and mismatchbased approach (parameter v, Table 1).…”