Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

By T. Nott, E. Petsalaki, P. Farber, D. Jervis, E. Fussner, A. Plochowietz, Timothy D. Craggs, D. Bazett-Jones, Tony Pawson, Julie D. Forman-Kay and 1 more. Molecules and Cells, 2015

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Summary Cells chemically isolate molecules in compartments to both facilitate and regulate their interactions. In addition to membrane-encapsulated compartments, cells can form proteinaceous and membraneless organelles, including nucleoli, Cajal and PML bodies, and stress granules. The principles that determine when and why these structures form have remained elusive. Here, we demonstrate that the disordered tails of Ddx4, a primary constituent of nuage or germ granules, form phase-separated organelles both in live cells and in vitro. These bodies are stabilized by patterned electrostatic interactions that are highly sensitive to temperature, ionic strength, arginine methylation, and splicing. Sequence determinants are used to identify proteins found in both membraneless organelles and cell adhesion. Moreover, the bodies provide an alternative solvent environment that can concentrate single-stranded DNA but largely exclude double-stranded DNA. We propose that phase separation of disordered proteins containing weakly interacting blocks is a general mechanism for forming regulated, membraneless organelles.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d65ac611b5a266c8b392baacb2b9de6e3627e591

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Citations in the corpus

Spatiotemporal control of intracellular phase transitions using light-activated optoDroplets (2016, neutral): “We find similar results upon fusing the C-terminal IDR of the ALS-related RNA binding protein HNRNPA1 (optoHNRNPA1), or the N-terminal IDR of DDX4 (optoDDX4), both of which have been reported to drive liquid-liquid phase separation ((Nott et al., 2015), (Molliex et al., 2015))(Fig.”
Phase separation in biology; functional organization of a higher order (2016, methodology): “Interestingly, low complexity sequences and disorder [47, 48, 50, 56] are overrepresented in proteins shown to phase separate in vitro.”
Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity (2017, methodology): “In the E1 + E3 + water ternary system, we estimated χij values using surface-tension scaling24 (Supplementary equations (6)– (15)) and FH approximations to generate a ternary phase diagram (Supplementary equations (16)–(20)).”
A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins (2018, positive): “However, there are numerous examples of non-prion-like intrinsically disordered regions that drive phase separation such as DDX4, LAF-1 and FIB1 (Elbaum-Garfinkle et al., 2015; Feric et al., 2016; Nott et al., 2015).”
Intrinsically Disordered Proteins and Their “Mysterious” (Meta)Physics (2019, background): “These very large (detectable by lightmicroscope), highly dynamic (but stable), and liquid-like assemblages are formed via the intracellular liquidliquid demixing phase separations [186–189] and originate due to the colocalization of molecules at high concentrations within a small cellular or nuclear”
Sequence determinants of protein phase behavior from a coarse-grained model (2017, methodology): “These 4 organelles include processing bodies [4], stress granules [3, 5–7] and germ granules [8, 9] 5 in the cytoplasm, and nucleoli [10] and nuclear speckles [11] in the nucleus.”
The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics (2015, background): “However, it is estimated that as many as 30% (39) of proteins in the human genome have regions of intrinsic disorder, and IDPs appear to be involved in a range of biological functions, owing to their flexible conformations and binding promiscuity.”
CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins (2017, background): “These clusters are required to drive phase separation (27) (see Fig.”
Coactivator condensation at super-enhancers links phase separation and gene control (2018, background): “Within these condensates, BRD4 andMED1 exhibit apparent diffusion coefficients similar to those previously reported for other proteins in phase-separated condensates in vivo (36, 37).”
Residue-by-residue view of in vitro FUS granules that bind the C-terminal domain of RNA polymerase II (2015, positive): “Similar phase separation has been observed for a variety of sequences, including highly charged proteins such as Ddx4, which bear little sequence composition resemblance to FUS.”
Formation and Maturation of Phase Separated Liquid Droplets by RNA Binding Proteins (2015, background): “The IDR of Ddx4, a protein that resides in maternal mRNP granules referred to as nuage, was shown to undergo LLPS in vitro and in cells in a salt- and temperature-dependent manner (Nott et al., 2015).”