Local RNA Structure, not Primary Sequence, Governs the Binding Specificity of PCID2 in Drosophila melanogaster

Nuclear export of mRNA is one of the key stages of gene expression in eukaryotes. A wide range of mRNAs is exported by the TREX-2 complex, which includes the PCID2 RNA-binding protein. Previously, we showed that PCID2 is responsible for specific recognition of transcripts, and we identified its binding site on the Drosophila ras2 gene mRNA within the 3'-non-coding region. However, the interaction was not localized for other mRNAs, which makes it impossible to identify the general patterns of PCID2 interaction with mRNA. In this work, we investigated the interaction of PCID2 with the mRNA of the kruppel gene of Drosophila melanogaster. In the EMSA experiments, we showed that PCID2 binds to two fragments of kruppel mRNA, from the 5' non-coding and coding mRNA regions. Thus, the PCID2 binding site can be located not only in the 3'-non-coding region, as in the case of the ras2 mRNA, but also in other mRNA regions. PCID2 has a lower affinity for binding sites in the kruppel mRNA than in the ras2 mRNA. Our analysis of the mRNA structure at three binding sites led to a general interaction model, in which a hairpin-type conformation emerges as the most probable structural motif at these sites.