Who's In and Who's Out-Compositional Control of Biomolecular Condensates

Abstract

Biomolecular condensates are two- and three-dimensional compartments in eukaryotic cells that concentrate specific collections of molecules without an encapsulating membrane. Many condensates behave as dynamic liquids and appear to form through liquid-liquid phase separation driven by weak, multivalent interactions between macromolecules. In this review, we discuss current models and data regarding the control of condensate composition, and we describe our current understanding of the composition of representative condensates including PML nuclear bodies, P-bodies, stress granules, the nucleolus, and two-dimensional membrane localized LAT and nephrin clusters. Specific interactions, such as interactions between modular binding domains, weaker interactions between intrinsically disorder regions and nucleic acid base pairing, and nonspecific interactions, such as electrostatic interactions and hydrophobic interactions, influence condensate composition. Understanding how specific condensate composition is determined is essential to understanding condensates as biochemical entities and ultimately discerning their cellular and organismic functions.

Keywords: LAT cluster; PML nuclear body; biomolecular condensate; composition; phase separation.

Figure 1.

A unified model of condensate composition A model condensate formed from a protein scaffold with multivalent RNA binding domains (RBDs - grey) linked to an IDR (black) and an RNA scaffold with multiple RBD recognition elements (yellow) and specific secondary structure elements. Client protein recruitment is dependent on both the number of RBDs and the sequence of the IDR. Different IDR sequences are represented by the different colors of the client proteins. Client RNA recruitment is dependent on the RNA secondary structure and valency of RBD recognition elements (orange). For more detailed description of model, see the text.

Figure 2.

Compositional control of condensates formed from scaffolds with modular domains (A) Model of client recruitment with different scaffold stoichiometries. Client recruitment is dependent on the availability of binding sites on the scaffolds and the valency of the clients. (B) Droplets were formed with 6 μM of a (SUMO)₉-(SIM)₈ scaffold containing Ulp1 cleavage sites after only the two N-terminal SUMOs and were equilibrated with 50 nM of GFP-(SIM)₂ (Client 1, green) and RFP-(SUMO)₂ (Client 2, magenta). At time 0, 10 nM of Ulp1 was added. Pseudocolored images of the merged fluorescent signals from the two clients are shown. Figure reproduced with permission from [40].