RNA-binding landscape of Rrm4, a key RNA-binding protein mediating mRNA transport in Ustilago maydis
Final Report Abstract
Ustilago maydis is a phytopathogenic fungus that switches form yeast to hyphal growth during infection. Important for efficient hyphal growth is long-distance transport along microtubules. Key carriers are early endosomes that shuttle bidirectionally along microtubules by the action of molecular motors such as kinesin and cytoplasmic dynein. Important cargo includes mRNAs and associated ribosomes. The key RNA-binding protein for RNA transport is Rrm4, containing three RNA recognition motifs for RNA binding. Rrm4 is connected to endosome via Upa1, which carries a FYVE domain for specific interaction with endosomal lipids. Important cargo mRNAs encode septins that form heteromeric complexes on the cytoplasmic surface of endosomes. Septin complexes are transported towards the growing tip, where they form septin filaments. Thus, research over the last years has identified crucial components of the endosomal transport machinery. However, similar to other systems a transcriptome-wide view on mRNA transport was missing. To address this gap of knowledge, we applied the powerful iCLIP technique to study fungal RNA-binding proteins. Thereby numerous target mRNAs were identified including the cognate binding sites of the RNA-binding proteins at single nucleotide resolution. Performing a comparative iCLIP approach studying two endosomal RBPs Rrm4 and the small glycine-rich RBP Grp1 revealed that both RBPs bound predominantly in the 3´ UTR of thousands of shared cargo mRNAs. In addition, Rrm4 recognised specific landmark sites of translation such as the start and stop codon, suggesting an intimate connection of mRNA transport and translation. Apparently, Rrm4 uses a tailormade transport strategy for different sets of target mRNAs. This special binding behaviour allowed the identification of functional units, for example, the majority of mRNAs encoding subunits of the mitochondrial ATPase were bound precisely at the stop codon. This uncovers a novel link between endosomal mRNA transport and mitochondrial biology. In essence, we provide first insights into the positional organisation of RNA-binding proteins during mRNA transport.
Publications
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(2019) The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO reports 20 (1) e46588
Olgeiser, Lilli; Haag, Carl; Boerner, Susan; Ule, Jernej; Busch, Anke; Koepke, Janine; König, Julian; Feldbrügge, Michael; Zarnack, Kathi
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(2015) Membrane-coupled mRNA trafficking in fungi. Annu. Rev. Microbiol. 69: 265-281
C. Haag, B. Steuten, and M. Feldbrügge
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(2018) mRNA transport in fungal top models. WIREs RNA. 9: e1453
D. Niessing, R.P. Jansen, T. Pohlmann and M. Feldbrügge
