Molecular Crowding Tunes Material States of Ribonucleoprotein Condensates.

biomolecules Article Molecular Crowding Tunes Material States of Ribonucleoprotein Condensates Taranpreet Kaur 1 , Ibraheem Alshareedah 1 , Wei Wang 1 , Jason Ngo 1 , Mahdi Muhammad Moosa 2 and Priya R. Banerjee 1, * 1 2 * Department of Physics, University at Buffalo, SUNY, NY 14260, USA; (T.K.); (I.A.); (W.W.); (J.N.) Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Correspondence: Received: 31 December 2018; Accepted: 5 February 2019; Published: 19 February 2019



 Abstract: Ribonucleoprotein (RNP) granules are membraneless liquid condensates that dynamically form, dissolve, and mature into a gel-like state in response to a changing cellular environment. RNP condensation is largely governed by promiscuous attractive inter-chain interactions mediated by low-complexity domains (LCDs). Using an archetypal disordered RNP, fused in sarcoma (FUS), here we study how molecular crowding impacts the RNP liquid condensation. We observe that the liquid–liquid coexistence boundary of FUS is lowered by polymer crowders, consistent with an excluded volume model. With increasing bulk crowder concentration, the RNP partition increases and the diffusion rate decreases in the condensed phase. Furthermore, we show that RNP condensates undergo substantial hardening wherein protein-dense droplets transition from viscous fluid to viscoelastic gel-like states in a crowder concentration-dependent manner. Utilizing two distinct LCDs that broadly represent commonly occurring sequence motifs driving RNP phase transitions, we reveal that the impact of crowding is largely independent of LCD charge and sequence patterns. These results are consistent with a thermodynamic model of crowder-mediated depletion interaction, which suggests that inter-RNP attraction is enhanced by molecular crowding. The depletion force is likely to play a key role in tuning the physical properties of RNP condensates within the crowded cellular space. Keywords: membraneless organelles; optical tweezer; liquid–liquid phase separation; protein diffusion; depletion interaction; entropic force; low-complexity sequences; intrinsically disordered proteins 1. Introduction Ribonucleoprotein (RNP) granules or particles are a diverse group of subcellular compartments that are utilized by eukaryotic cells to spatiotemporally organize various biomolecular processes. These non-membranous assemblies, also termed as membraneless organelles (MLOs), dynamically form, dissolve, and tune their physicochemical microenvironment in response to changing cellular cues [1–3]. RNP granules are enriched in proteins with low-complexity domains (LCDs) that are structurally disordered [4–6], and are assumed to be formed by RNP liquid–liquid phase separation (LLPS) [7]. LLPS is a spontaneous physical process that results in the formation of co-existing liquid phases of varying densities from a homogeneous solution [2,8]. At the molecular level, low-affinity multivalent interactions amongst different LCDs and their partner nucleic acids provide the necessary energetic input to drive the LLPS of RNPs [9]. Furthermore, LCD-mediated promiscuous interactions can act synergistically with sequence-specific interactions in many RNPs, thereby shaping their global Biomolecules 2019, 9, 71; doi:10.3390/biom9020071 www.mdpi.com/journal/biomolecules Biomolecules 2019, 9, 71 2 of 17 phase behavior [10]. Experimentally, it was observed that these promiscuous interactions are tuned by several cellular physicochemical perturbations (e.g., pH, salt concentration, and non-specific interactions with biomacromolecules) [10–14]. Unlike in typically utilized in vitro experimental conditions, in cellulo environments are crowded by a plethora of macromolecules that are ubiquitous within the cellular milieu [15]. To effectively capture biomolecular dynamics in a crowded cellular environment, in vitro studies utilizing recombinant proteins employ buffer systems containing inert biocompatible polymers as crowding agents. One of the most widely used crowders is polyethylene glycol (PEG), a neutral hydrophilic polymer with numerous applications in crystallography, biotechnology, and medicine [16–19]. Macromolecular crowding by PEG and similar polymer agents imparts a significant excluded volume effect (i.e., a space occupied by one molecule cannot be accessed by another) and results in alterations of molecular and mesoscale properties of biomolecules. For example, molecular crowding was shown to affect protein conformation [20–23], RNA folding [24], conformational dynamics of intrinsically disordered proteins [25], energetics of protein self-association [26–28], molecular recognition [29], and LLPS of globular proteins [30–33]. However, how macromolecular crowding alters disordered RNP condensation remains underexplored. The well-established excluded-volume model of colloid–polymer mixtures predicts that the addition of a polymer chain to a neutral colloidal suspension will trigger inter-colloid attraction [34]. The underlying driving force, known as the depletion interaction, is originated due to a net entropy gain by the system via maximizing the free volume available to the polymer chains. For globular protein–crowder mixtures, this depletion interaction can induce various phase transition processes, including protein crystallization [35]. In a similar vein, for RNP systems containing low-complexity “sticky” domains, a considerable impact of macromolecular crowding on their phase transition is expected [36]. This idea is supported by multiple recent observations such as (i) crowding induces homotypic LLPS of the nucleolar phosphoprotein Npm1 in vitro [37], (ii) PEG induces a robust liquid phase transition of the Alzheimer’s disease-linked protein Tau [38], and (iii) macromolecular crowding results in a substantial decrease in protein concentration required for inducing hnRNPA1 phase separation [39,40]. However, it remains unknown whether molecular crowding impacts the fluid dynamics of RNP condensates. The material properties of intracellular RNP granules are important determinants of their function in intracellular storage and signaling [1,41]. Notably, many RNP condensates are competent to mature into a fiber-like state, which is implicated in several neurological diseases [11,42–45]. While the roles of LCD sequence compositions and charge patterns in controlling mesoscale dynamics of the RNP condensates have been the subject of some recent investigations [46,47], little is known regarding the effect of generalized thermodynamic forces such as crowding on RNP condensation. Here we conduct an experimental study to evaluate the impact of macromolecular crowding on the RNP liquid–liquid coexistence boundary, condensate fluidity in the micron-scale, and transport property by RNP diffusion in the nano-scale. Utilizing an archetypal RNP, fused in sarcoma (FUS), as well as representatives of the tw (...truncated)