Effect of SRP54 depletion on mRNA expression in cultured human cells

Regulation of Aberrant Protein Production (RAPP) is a recently discovered protein quality control pathway that monitors proteins during their synthesis at the ribosome and degrades their mRNA if the proteins are not able to interact with their natural partners. In this study we induced RAPP by knockdown of SRP54, a Signal Recognition Particle subunit, and studied its effect at the full transcriptome level. The mRNA expression levels of many secretory and membrane proteins were decreased demonstrating the generality of the pathway. The RAPP activation leads to dramatic upregulation of the specific network of ribosome-associated HSP70/40/90 chaperones (HSPA1A, DNAJB1, HSP90AA1, and others), increased ribosome associated ubiquitination, and change in expression of RPS27 and RPS27L suggesting ribosome rearrangement. The results demonstrate a complex nature of mRNA and protein quality control at the ribosome. Overall design: Two experimental condition (treated and control cells). Treatment: HeLa Tet-On cells were transfected with siRNA for SRP54 to knockdown SRP54. Control: HeLa Tet-On cells were transfected with control siRNA. Each experimental condition included three independent biological replicates.