Kraut-Cohen, J., Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Afanasieva, E., Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Haim-Vilmovsky, L., Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Slobodin, B., Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Yosef, I., Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
Bibi, E., Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
Gerst, J.E., Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel

mRNAs encoding secreted/membrane proteins (mSMPs) are believed to reach the endoplasmic reticulum (ER) in a translation-dependent manner to confer protein translocation. Evidence exists, however, for translation- and signal recognition particle (SRP)-inde-pendent mRNA localization to the ER, suggesting that there are alternate paths for RNA delivery. We localized endogenously expressed mSMPs in yeast using an aptamer-based RNA-tagging procedure and fluorescence microscopy. Unlike mRNAs encoding polarity and secretion factors that colocalize with cortical ER at the bud tip, mSMPs and mRNAs encoding soluble, nonsecreted, nonpolarized proteins localized mainly to ER peripheral to the nucleus (nER). Synthetic nontranslatable uracil-rich mRNAs were also demonstrated to colocalize with nER in yeast. This mRNA-ER association was verified by subcellular fractionation and reverse transcription-PCR, single-molecule fluorescence in situ hybridization, and was not inhibited upon SRP inactivation. To better understand mSMP targeting, we examined aptamer-tagged USE1, which encodes a tail-anchored membrane protein, and SUC2, which encodes a soluble secreted enzyme. USE1 and SUC2 mRNA targeting was not abolished by the inhibition of translation or removal of elements involved in translational control. Overall we show that mSMP targeting to the ER is both translation- and SRP-independent, and regulated by cis elements contained within the message and trans-acting RNA-binding proteins (e.g., She2, Puf2). © 2013 Kraut-Cohen et al.