Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of proteins with alpha helical domains

Abstract

Increasingly many studies reveal how ribosome composition can be tuned to optimally translate the transcriptome of individual cell types. In this study, we investigated the expression pattern, structure within the ribosome and effect on protein synthesis of the ribosomal protein paralog 39L (RPL39L). With a novel mass spectrometric approach we have quantified the expression of RPL39L in human pluripotent cells, cancer cell lines and tissue samples, and in mouse germ cells. We generated RPL39L knock-out mouse embryonic stem cell (mESC) lines and demonstrated that RPL39L impacts the dynamics of translation, to support the pluripotency and differentiation, spontaneous and along the germ cell lineage. Most differences in protein abundance between WT and RPL39L KO lines were explained by widespread proteasomal activity. By CryoEM analysis of purified RPL39 and RPL39L-containing ribosomes we found that, unlike RPL39, RPL39L has two distinct conformations in the exposed segment of the nascent peptide exit tunnel, creating a distinct hydrophobic patch that has been predicted to support the efficient co-translational folding of alpha helices. Our study shows that ribosomal protein paralogs provide switchable modular components that can tune translation to the protein production needs of individual cell types.

Current limitations in predicting mRNA translation with deep learning models

“…Following [6], we downloaded the RNA-seq data from the SRA archive (SRR2986251), and ribosome-profiling data from an older archive (SRR1049521). The riboseq analysis was conducted as in [50], the RNA-seq was performed using zarp [51]. All nonsequential features (log ORF length, UTR length, G/C-content fraction of the UTR, number of exons, number of OOF uAUGs, number of IF uAUGs, normalized 5'UTR folding energy) were computed or extracted from the genome annotation.…”

“…Ribo-seq and mRNA-seq data were obtained from the European Nucleotide Archive, accession PRJNA591214. The riboseq analysis was conducted as in [50], the RNA-seq was performed as in [51]. For the calculation of the translation efficiency, we only took into account RNA-seq and ribo-seq reads in the CDS, not on the entire transcript.…”