RNA at the surface of phase-separated condensates impacts their size and number

Cochard, Audrey; Mg, Navarro; Kashida, Shunnichi; Kress, Michel; Weil, Dominique; Gueroui, Zoher

doi:10.1101/2021.06.22.449254

Cited by 6 publications

(1 citation statement)

References 97 publications

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“…Of the DFDs that populated a FRET-positive state, the filamentous DFDs were strongly biased towards those with discontinuous DAmFRET profiles (Figure S2C, chi-square contingency test, p<0.0001). All of the eight DFDs with diffuse fluorescence despite forming FRET-positive species lacked a nucleation barrier, suggesting their assembly is limited finite oligomers or emulsions (44)(45)(46)(47)(48).…”

Section: A Subset Of Dfds Are Supersaturablementioning

confidence: 99%

Protein supersaturation powers innate immune signaling

Gama

Miller

Lange

et al. 2023

Preprint

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The response of cells to existential threats such as virus invasion often involves semi-crystalline polymerization of certain signaling proteins, but the highly ordered nature of the polymers has no known function. We hypothesized that the undiscovered function is kinetic in nature, emerging from the nucleation barrier to the underlying phase transition, rather than the material polymers themselves. We explored this idea using fluorescence microscopy and Distributed Amphifluoric FRET (DAmFRET) to characterize the phase behavior of all 116 members of the death fold domain (DFD) superfamily, the largest group of putative polymer modules in human immune signaling. A subset of them polymerized in a nucleation-limited manner able to digitize cell state. These were enriched for the highly connected hubs of the DFD protein-protein interaction network. Full-length (F.L) signalosome adaptors retained this activity. We then designed and carried out a comprehensive nucleating interaction screen to map the pathways of signaling through the network. The results recapitulated known signaling pathways including a recently discovered link between the different cell death subroutines of pyroptosis and extrinsic apoptosis. We went on to validate this nucleating interaction in vivo. In the process, we discovered that the inflammasome is powered by constitutive supersaturation of the adaptor protein, ASC, implying that innate immune cells are thermodynamically fated for inflammatory cell death. Finally, we showed that supersaturation in the extrinsic apoptosis pathway commits cells to die, whereas the lack of supersaturation in the intrinsic apoptosis pathway permits cells to recover. Our results collectively suggest that innate immunity comes at the cost of occasional spontaneous cell death, and uncover a physical basis for the progressive nature of age-associated inflammation.

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Section: A Subset Of Dfds Are Supersaturablementioning

confidence: 99%

Protein supersaturation powers innate immune signaling

Gama

Miller

Lange

et al. 2023

Preprint

View full text Add to dashboard Cite

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Nucleobase Clustering Contributes to the Formation and Hollowing of Repeat-Expansion RNA Condensate

Gong

et al. 2022

J. Am. Chem. Soc.

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RNA molecules with repeat expansion sequences can phase separate into gel-like condensate, and this process may lead to neurodegenerative diseases. Here we report that in the presence of Mg 2+ ion, RNA molecules containing 20CAG repeats coacervate into filled droplets or hollowed condensate. Using hyperspectral stimulated Raman spectroscopy, we show that RNA coacervation is accompanied by the stacking and clustering of nucleobases, while forfeiting the canonical base-paired structure. At an increasing RNA/Mg 2+ ratio, the RNA droplets first expand in sizes, and then shrink and adopt hollow vesicle-like structures. Significantly, for both large and vesicle-like droplets, the nucleobase-clustered structure is more prominent at the rim than at the center, accounting for the rigidification of RNA droplets. Thus, our finding has broad implications for the general aging processes of RNA-containing membrane-less organelles.

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