Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization

  • Cell. 2020 Apr 16;181(2):306-324.e28. doi: 10.1016/j.cell.2020.03.050.
David W Sanders  1 ,  Nancy Kedersha  2 ,  Daniel S W Lee  1 ,  Amy R Strom  1 ,  Victoria Drake  1 ,  Joshua A Riback  1 ,  Dan Bracha  1 ,  Jorine M Eeftens  1 ,  Allana Iwanicki  1 ,  Alicia Wang  1 ,  Ming-Tzo Wei  1 ,  Gena Whitney  1 ,  Shawn M Lyons  3 ,  Paul Anderson  2 ,  William M Jacobs  4 ,  Pavel Ivanov  2 ,  Clifford P Brangwynne  5
Affiliations
  • 1. Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
  • 2. Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
  • 3. Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA.
  • 4. Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
  • 5. Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton, NJ 08544, USA. Electronic address: [email protected].
PMID: 32302570 DOI: 10.1016/j.cell.2020.03.050
Abstract

Liquid-liquid phase separation (LLPS) mediates formation of membraneless condensates such as those associated with RNA processing, but the rules that dictate their assembly, substructure, and coexistence with Other liquid-like compartments remain elusive. Here, we address the biophysical mechanism of this multiphase organization using quantitative reconstitution of cytoplasmic stress granules (SGs) with attached P-bodies in human cells. Protein-interaction networks can be viewed as interconnected complexes (nodes) of RNA-binding domains (RBDs), whose integrated RNA-binding capacity determines whether LLPS occurs upon RNA influx. Surprisingly, both RBD-RNA specificity and disordered segments of key proteins are non-essential, but modulate multiphase condensation. Instead, stoichiometry-dependent competition between protein networks for connecting nodes determines SG and P-body composition and miscibility, while competitive binding of unconnected proteins disengages networks and prevents LLPS. Inspired by patchy colloid theory, we propose a general framework by which competing networks give rise to compositionally specific and tunable condensates, while relative linkage between nodes underlies multiphase organization.

Keywords
G3BP; P-bodies; RNA binding; UBAP2L; USP10; condensates; membraneless organelles; multiphase; phase separation; stress granules.