Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation

• Published in: Nature communications 2018-02, Vol.9 (1), p.842-13, Article 842
• Main Authors: Mitrea, Diana M., Cika, Jaclyn A., Stanley, Christopher B., Nourse, Amanda, Onuchic, Paulo L., Banerjee, Priya R., Phillips, Aaron H., Park, Cheon-Gil, Deniz, Ashok A., Kriwacki, Richard W.
• Format: Article
• Language: English
• Subjects: 101/6; 14/19; 45/70; 631/535/1261; 631/57/2265; 631/57/2269; 631/57/2272/2273; 631/57/2272/2276; 82/80; 82/83; 96/33; 96/34; Arginine; BASIC BIOLOGICAL SCIENCES; Binding Sites; Biosynthesis; Cell Nucleolus - chemistry; Cell Nucleolus - metabolism; Cell Nucleolus - ultrastructure; Cloning, Molecular; Confocal microscopy; Escherichia coli - genetics; Escherichia coli - metabolism; Fluorescence; Gene Expression; Genetic Vectors - chemistry; Genetic Vectors - metabolism; Humanities and Social Sciences; Humans; intrinsically disordered proteins; Intrinsically Disordered Proteins - chemistry; Intrinsically Disordered Proteins - genetics; Intrinsically Disordered Proteins - metabolism; Kinetics; Mathematical analysis; Matrix methods; Microscopy; Models, Molecular; molecular conformation; multidisciplinary; Mutation; Nuclear Proteins - chemistry; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; Nucleoli; Nucleophosmin; Organelle Biogenesis; Phase separation; Phase Transition; Protein Binding; Protein Interaction Domains and Motifs; Proteins; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; Ribonucleic acid; Ribosomes - genetics; Ribosomes - metabolism; RNA; rRNA; SAXS; Science; Science (multidisciplinary); single-molecule biophysics; Static Electricity; supramolecular assembly; Ultracentrifugation; Valency
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-03255-3

Nucleophosmin (NPM1) is an abundant, oligomeric protein in the granular component of the nucleolus with roles in ribosome biogenesis. Pentameric NPM1 undergoes liquid–liquid phase separation (LLPS) via heterotypic interactions with nucleolar components, including ribosomal RNA (rRNA) and proteins which display multivalent arginine-rich linear motifs (R-motifs), and is integral to the liquid-like nucleolar matrix. Here we show that NPM1 can also undergo LLPS via homotypic interactions between its polyampholytic intrinsically disordered regions, a mechanism that opposes LLPS via heterotypic interactions. Using a combination of biophysical techniques, including confocal microscopy, SAXS, analytical ultracentrifugation, and single-molecule fluorescence, we describe how conformational changes within NPM1 control valency and switching between the different LLPS mechanisms. We propose that this newly discovered interplay between multiple LLPS mechanisms may influence the direction of vectorial pre-ribosomal particle assembly within, and exit from the nucleolus as part of the ribosome biogenesis process. The nucleolus is a membrane-less organelle formed through liquid–liquid phase separation (LLPS). Here the authors use biophysical methods and show that the nucleolar protein nucleophosmin (NPM1) also undergoes LLPS through homotypic, inter-NPM1 interactions and discuss implications for the ribosome biogenesis process.