Dissecting the binding behaviour of the multi-RRM protein Rrm4 during endosomal mRNA transport in Ustilago maydis

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The transport of mRNAs is crucial to determine where and when proteins are expressed in the cell. A well-studied translocation mechanism is endosomal mRNA transport along microtubules in infectious hyphae of the corn pathogen Ustilago maydis. The key factor is Rrm4, containing three RNA recognition motif (RRM) domains for RNA binding. Recently, we identified the small glycine-rich RNA-binding protein (RBP) Grp1 as a novel interaction partner and component of shuttling endosomal mRNPs. Using a comparative study of the two co-localising RBPs, we cast the first transcriptome-wide view of endosomal mRNA transport. This revealed that both proteins share a large set of about 2,000 common target mRNAs. Both RBPs bind preferentially in the 3´ UTR in close vicinity, suggesting a conjoint function. In case of Rrm4, the sequence UAUG was identified as a defined binding motif that occurs mostly in binding sites in open reading frames and is bound by Rrm4’s third RRM. Interestingly, Rrm4 specifically recognises translational landmark sites such as start and stop codons, suggesting a close link between transport and translational regulation of target mRNAs. Thus, the endosomal transport machinery appears to use tailor-made transport strategies for distinct sets of its cargo mRNAs.In the second funding period, we will address (i) how the different transport strategies are achieved by Rrm4 via its three RRM domains, and (ii) what are the molecular consequences of binding to translational landmark sites for the spatio-temporal expression of the encoded proteins. To this end, we will team up with partners of the FOR2333 and combine global approaches, such as iCLIP and ribosome profiling. Thus, this work will lay the foundation to understand how RBPs with multiple RNA-binding domains and various interaction partners orchestrate their function during cellular processes such as mRNA transport.