RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins

Abstract

Biomolecular condensates formed via liquid–liquid phase separation (LLPS) play a crucial role in the spatiotemporal organization of the cell material. Nucleic acids can act as critical modulators in the stability of these protein condensates. To unveil the role of RNA length in regulating the stability of RNA binding protein (RBP) condensates, we present a multiscale computational strategy that exploits the advantages of a sequence-dependent coarse-grained representation of proteins and a minimal coarse-grained model wherein proteins are described as patchy colloids. We find that for a constant nucleotide/protein ratio, the protein fused in sarcoma (FUS), which can phase separate on its own—i.e., via homotypic interactions—only exhibits a mild dependency on the RNA strand length. In contrast, the 25-repeat proline-arginine peptide (PR25), which does not undergo LLPS on its own at physiological conditions but instead exhibits complex coacervation with RNA—i.e., via heterotypic interactions—shows a strong dependence on the length of the RNA strands. Our minimal patchy particle simulations suggest that the strikingly different effect of RNA length on homotypic LLPS versus RBP–RNA complex coacervation is general. Phase separation is RNA-length dependent whenever the relative contribution of heterotypic interactions sustaining LLPS is comparable or higher than those stemming from protein homotypic interactions. Taken together, our results contribute to illuminate the intricate physicochemical mechanisms that influence the stability of RBP condensates through RNA inclusion.

Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it

“…The stability and viscoelastic properties of RNA-binding protein condensates is expected to be sensitively affected by the presence of RNA in an intricate manner that likely depends on RNA concentration, structure, sequence, and chain length [20, 21, 86, 111, 130, 131]. For instance, while short single-stranded disordered RNA strands (∼50 nucleotides) can severely reduce droplet viscosity (e.g.…”

Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it

“…The stability and viscoelastic properties of RNA-binding protein condensates is expected to be sensitively affected by the presence of RNA in an intricate manner that likely depends on RNA concentration, structure, sequence, and chain length 20,21,87,111,131,132 . For instance, while short single-stranded disordered RNA strands (~50 nucleotides) can severely reduce droplet viscosity (e.g.…”

Landscape of biomolecular condensates in heat stress responses

“…Due to its efficient dynamics, LLPS is assumed to enable biomolecular condensates in plants to assemble and disassemble in a very intricate manner as required by the cell, including heat stress ( Posey et al., 2018 ; Peran and Mittag, 2020 ; Emenecker et al., 2021 ). The mechanism of LLPS critically depends on i) the concentrations of macromolecules, such as proteins, DNA, and RNA; ii) cellular conditions, including pH, temperature, and salt concentration; and iii) post-translational modifications (PTMs), such as phosphorylation, glycosylation, methylation, and acetylation ( Brangwynne et al., 2015 ; Bah and Forman-Kay, 2016 ; Banani et al., 2017 ; Emenecker et al., 2021 ; Sanchez-Burgos et al., 2022 ).…”