A consensus motif in ASH1 and further transcripts unifies several RNA motifs required for interaction with the She2p/She3p transport machinery and mRNA localization in yeast

Asymmetric localization of the ASH1 transcript is a central step in the regulation of mating type switching in Saccharomyces cerevisae and a paradigm for localized mRNAs specifically recognized by the She2p/3p transport machinery. Four RNA elements in ASH1 are known to mediate bud localization, but it remained unclear what a consensus motif of all four She2p/3p recognition sites (SRS) might look like. In this study, we derive the SRS consensus motif, which is characterized by an L-shaped, double-stranded RNA conformation with two cytosine-containing sequence motifs at conserved positions and a central asymmetric bulge. It is noteworthy that the spatial arrangement of these features can be retained, despite their altered order within the nucleotide sequence. We termed these variations "configurations" and confirmed in biochemical studies that SRS function in ASH1 elements is preserved when changing configurations. We tested other known and predicted SRS elements in target transcripts of She2p/3p by biochemical and biophysical studies and confirmed the conserved SRS function even in switched configuration. Consistently, we present the SRS instance collection, which includes further predictions of SRS instances of transcript targets of the She2p/3p translocation pathway.