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

• Published in: Nature chemistry 2022-10, Vol.14 (10), p.1110-1117
• Main Authors: Choi, Saehyun, Meyer, McCauley O., Bevilacqua, Philip C., Keating, Christine D.
• Format: Article
• Language: English
• Subjects: 631/92/552; 639/638/298/923/1028; 639/638/92/56; Analytical Chemistry; Binding sites; Biochemistry; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Coexistence; Double-stranded RNA; Droplets; Hybridization; Inorganic Chemistry; Intracellular; Liquid phases; Multiphase; Organelles; Organic Chemistry; Peptides; Phase separation; Physical Chemistry; Ribonucleic acid; RNA; Thermodynamic equilibrium; Thermodynamics
• ISSN: 1755-4330; 1755-4349
• DOI: 10.1038/s41557-022-00980-7

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. The biochemical roles and mechanisms of multiphase membraneless organelles are not yet well understood. Now, multiphase peptide droplets have been shown to sort RNA based on whether it is single- or double-stranded, as well as impact RNA duplexation through in-droplet thermodynamic equilibria. This work provides insight into possible primitive mechanisms for multicompartment intracellular condensates and can aid in the design of functional artificial membraneless organelles.