What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?

Abstract

Exciting recent work has highlighted that numerous cellular compartments lack encapsulating lipid bilayers (often called "membraneless organelles"), and that their structure and function are central to the regulation of key biological processes, including transcription, RNA splicing, translation, and more. These structures have been described as "biomolecular condensates" to underscore that biomolecules can be significantly concentrated in them. Many condensates, including RNA granules and processing bodies, are enriched in proteins and nucleic acids. Biomolecular condensates exhibit a range of material states from liquid- to gel-like, with the physical process of liquid-liquid phase separation implicated in driving or contributing to their formation. To date, in vitro studies of phase separation have provided mechanistic insights into the formation and function of condensates. However, the link between the often micron-sized in vitro condensates with nanometer-sized cellular correlates has not been well established. Consequently, questions have arisen as to whether cellular structures below the optical resolution limit can be considered biomolecular condensates. Similarly, the distinction between condensates and discrete dynamic hub complexes is debated. Here we discuss the key features that define biomolecular condensates to help understand behaviors of structures containing and generating RNA.

Keywords: dynamic hub; phase separation; ribonucleoprotein particle; simulation.

FIGURE 1.

Scales of biomolecular condensates and component biomolecules. Left (expanded view). (Top row from left to right) Elastin-like peptide (ELP) condensates as characterized by molecular dynamics simulations to be ∼6 nm in diameter (Rauscher and Pomès 2017); single mRNA molecule (1 kb or 1000 nt), ∼10 nm radius of gyration (R_g) (Yoffe et al. 2008; Gopal et al. 2012; Borodavka et al. 2016); RNP condensate, such as of a mRNA transport granule, composed of a single mRNA with some RBPs, ∼100 nm diameter (Batish et al. 2012); mediator-RNA Pol II foci, containing growing RNA chains and multiple components of the transcriptional machinery, ∼300 nm in diameter (Cho et al. 2018). (Bottom row from left to right) 35-residue elastin-like peptide (ELP), R_g ∼ 1 nm; 400-residue intrinsically disordered protein region (IDR), R_g ∼ 3.5 nm; 1000-residue IDR, R_g ∼ 6 nm; megadalton (MDa) protein complexes, ∼10 to 30 nm diameters (depending on geometry). (Right) Comparison of the scales of the condensates on the top row to the nucleolus, ∼1000 to 3000 nm in diameter.