Project description:Loc1 RIP-chip Experimental procedure: C-terminally TAP-tagged Loc1p from yeast S. cerevisiae was purified from 1 L of cells grown in YPD medium as previously described (Gerber et al. 2004, PLoS Biol. 2, E79). Untagged control cells (BY4741) cells served as a negative control. cDNA was synthesized from 3 μg of total RNA derived from the extract and 500 ng of affinity-isolated RNA and labeled with Cy3 and Cy5 fluorescent dyes, respectively. Samples were mixed and hybridized to cDNA microarrays. Publication: Niedner-Boblenz A. et al. 2024, Nucleic Acids Res, in press. Title: Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation Abstract: RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro- and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA- and DNA-related processes by concentrating them in membrane-less organelles. The general function and wide distribution of PUN motifs across species suggests that in an ancient “RNA world” PUN-like motifs may have supported the correct folding of early ribozymes.
