Human SRP targets secretory proteins to ER and protects their mRNAs.

SRP54 depletion globally downregulates secretory and membrane protein mRNAs.

SRP54 knockdown upregulates specific chaperone network and ubiquitination.

Loss of SRP54 leads to ribosomal stress and change in expression of RPS27 and RPS27L.

Data demonstrate complex nature of SRP function and dramatic consequences of defects.

Regulation of Aberrant Protein Production (RAPP) is a protein quality control in mammalian cells. RAPP degrades mRNAs of nascent proteins not able to associate with their natural interacting partners during synthesis at the ribosome. However, little is known about the molecular mechanism of the pathway, its substrates, or its specificity. The Signal Recognition Particle (SRP) is the first interacting partner for secretory proteins. It recognizes signal sequences of the nascent polypeptides when they are exposed from the ribosomal exit tunnel. Here, we reveal the generality of the RAPP pathway on the whole transcriptome level through depletion of human SRP54, an SRP subunit. This depletion triggers RAPP and leads to decreased expression of the mRNAs encoding a number of secretory and membrane proteins. The loss of SRP54 also leads to the dramatic upregulation of a specific network of HSP70/40/90 chaperones (HSPA1A, DNAJB1, HSP90AA1, and others), increased ribosome associated ubiquitination, and change in expression of RPS27 and RPS27L suggesting ribosome rearrangement. These results demonstrate the complex nature of defects in protein trafficking, mRNA and protein quality control, and provide better understanding of their mechanisms at the ribosome.

Signal sequence

Secretory proteins

Protein synthesis and transport

Translational control

Signal Recognition Particle

Deep RNA-seq data have been submitted to the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and available under accession number GSE182922.

© 2022 The Author(s). Published by Elsevier Ltd.