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Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles

Abstract

Liquid–liquid phase separation has emerged as an important means of intracellular RNA compartmentalization. Some membraneless organelles host two or more compartments serving different putative biochemical roles. The mechanisms for, and functional consequences of, this subcompartmentalization are not yet well understood. Here we show that adjacent phases of decapeptide-based multiphase model membraneless organelles differ markedly in their interactions with RNA. Single- and double-stranded RNAs preferentially accumulate in different phases within the same droplet, and one phase is more destabilizing for RNA duplexes than the other. Single-phase peptide droplets did not capture this behaviour. Phase coexistence introduces new thermodynamic equilibria that alter RNA duplex stability and RNA sorting by hybridization state. These effects require neither biospecific RNA-binding sites nor full-length proteins. As such, they are more general and point to primitive versions of mechanisms operating in extant biology that could aid understanding and enable the design of functional artificial membraneless organelles.

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Fig. 1: Formation of multi- and single-phase oligopeptide coacervates.
Fig. 2: Partitioning of RNA in single- and multiphase peptide coacervates.
Fig. 3: Comparison of RNA duplex stability in single- and multiphase peptide coacervates.
Fig. 4: Estimated local concentrations of ssRNA and dsRNA in each coacervate phase after equilibration of added dsRNA.
Fig. 5: Coupling of partitioning and dissociation equilibria in multiphase coacervate droplets dictates the distribution of ssRNAs and dsRNAs.

Data availability

All data supporting the findings of this study are available within the Article and its Supplementary Information, and also from the corresponding authors upon request. Source data are provided with this Paper.

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Acknowledgements

This work was supported by the NASA Exobiology programme grant no. 80NSSC17K0034 (S.C., M.O.M., P.C.B. and C.D.K.). S.C. was also supported by Future Investigators in NASA Earth and Space Science and Technology (FINESST) under grant no. 80NSSC19K1531 and no. 80NSSC22K0553. We thank F. Pir Cakmak and H. Fares for helpful discussions, and T. Mal for help with NMR analysis.

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M.O.M. performed the radiolabelled RNA partitioning experiments. S.C. performed all other experiments. All authors conceived and designed the experiments and analysed the data. S.C. and C.D.K. wrote the manuscript, with input from P.C.B. and M.O.M.

Corresponding authors

Correspondence to Philip C. Bevilacqua or Christine D. Keating.

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Nature Chemistry thanks Pilong Li and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–18, Discussions 1–7 and Tables 1–17.

Supplementary Data 1

Calculation of radiolabelled RNA partitioning in coacervate phases.

Source data

Source Data Fig. 1

Estimated labelled peptide concentration for all trials.

Source Data Fig. 2

Estimated RNA concentration for all trials.

Source Data Fig. 3

FRET values and its intensities for all trials.

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Choi, S., Meyer, M.O., Bevilacqua, P.C. et al. Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles. Nat. Chem. (2022). https://doi.org/10.1038/s41557-022-00980-7

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