Examining SRP pathway function in mRNA localization to the endoplasmic reticulum

• Published in: RNA (Cambridge) 2023-11, Vol.29 (11), p.1703-1724
• Main Authors: Child, Jessica R, Hofler, Alex C, Chen, Qiang, Yang, Brenda H, Kristofich, JohnCarlo, Zheng, Tianli, Hannigan, Molly M, Elles, Andrew L, Reid, David W, Nicchitta, Christopher V
• Format: Article
• Language: English
• Subjects: Animals; Cell lines; CRISPR; Cytosol; Cytosol - metabolism; Endoplasmic reticulum; Endoplasmic Reticulum - genetics; Endoplasmic Reticulum - metabolism; Localization; Mammals - genetics; Membrane proteins; Membrane Proteins - genetics; mRNA; Protein transport; Ribosomes; Ribosomes - genetics; Ribosomes - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Signal recognition particle; Signal Recognition Particle - genetics; Signal Recognition Particle - metabolism; siRNA; Translation initiation
• ISSN: 1355-8382; 1469-9001; 1469-9001
• DOI: 10.1261/rna.079643.123

Signal recognition particle (SRP) pathway function in protein translocation across the endoplasmic reticulum (ER) is well established; its role in RNA localization to the ER remains, however, unclear. In current models, mRNAs undergo translation- and SRP-dependent trafficking to the ER, with ER localization mediated via interactions between SRP-bound translating ribosomes and the ER-resident SRP receptor (SR), a heterodimeric complex comprising SRA, the SRP-binding subunit, and SRB, an integral membrane ER protein. To study SRP pathway function in RNA localization, SR knockout (KO) mammalian cell lines were generated and the consequences of SR KO on steady-state and dynamic mRNA localization examined. CRISPR/Cas9-mediated KO resulted in profound destabilization of SRA. Pairing siRNA silencing of in KO cells yielded viable SR KO cells. Steady-state mRNA compositions and ER-localization patterns in parental and SR KO cells were determined by cell fractionation and deep sequencing. Notably, steady-state cytosol and ER mRNA compositions and partitioning patterns were largely unaltered by loss of SR expression. To examine SRP pathway function in RNA localization dynamics, the subcellular trafficking itineraries of newly exported mRNAs were determined by 4-thiouridine (4SU) pulse-labeling/4SU-seq/cell fractionation. Newly exported mRNAs were distinguished by high ER enrichment, with ER localization being SR-independent. Intriguingly, under conditions of translation initiation inhibition, the ER was the default localization site for all newly exported mRNAs. These data demonstrate that mRNA localization to the ER can be uncoupled from the SRP pathway function and reopen questions regarding the mechanism of RNA localization to the ER.