No abstract

Membrane-less organelles are cellular structures which arise through the phenomenon of phase separation. This process enables compartmentalization of specific sets of macromolecules (e.g., proteins, nucleic acids), thereby regulating cellular processes by increasing local concentration, and modulating the structure and dynamics of their constituents. Understanding the connection between structure, material properties and function of membrane-less organelles requires inter-disciplinary approaches, which address length and timescales that span several orders of magnitude (e.g., Ångstroms to micrometer, picoseconds to hours). In this review, we discuss the wide variety of methods that have been applied to characterize the morphology, rheology, structure and dynamics of membrane-less organelles and their components, in vitro and in live cells.

Abbreviations: Acute myeloid leukemia (AML), dense phase (DP), fluorescence recovery after photobleaching (FRAP), fusion oncoprotein (FO), Gibbs free energy of transfer (ΔG Tr ), Gle2binding-sequence (GLEBS), human CD34-positive hematopoietic stem and progenitor cells (hCD34+ cells), immunofluorescence (IF), intrinsically disordered region (IDR), light phase (LP), lineage-negative hematopoietic stem and progenitor cells (lin-HSPCs), liquid-liquid phase separation (LLPS), mEGFP-tagged NHA9 (G-NHA9), mobile fraction (M f ), monomeric enhanced green fluorescent protein (mEGFP), nuclear pore complex (NPC), NUP98-HOXA9 (NHA9), partition coefficient (K p ), patient-derived xenograft (PDX), Pearson correlation coefficient (PCC), Principal component analysis (PCA), RNA sequencing (RNA-seq), and saturation concentration (C sat ).

The nucleolus, the site for ribosome biogenesis contains hundreds of proteins and several types of RNA. The functions of many non-ribosomal nucleolar proteins are poorly understood, including Surfeit locus protein 6 (SURF6), an essential disordered protein with roles in ribosome biogenesis and cell proliferation. SURF6 co-localizes with Nucleophosmin (NPM1), a highly abundant protein that mediates the liquid-like features of the granular component region of the nucleolus through phase separation. Here, we show that electrostatically-driven interactions between disordered regions of NPM1 and SURF6 drive liquid-liquid phase separation. We demonstrate that co-existing heterotypic (NPM1-SURF6) and homotypic (NPM1-NPM1) scaffolding interactions within NPM1-SURF6 liquid-phase droplets dynamically and seamlessly interconvert in response to variations in molecular crowding and protein concentrations. We propose a mechanism wherein NPM1-dependent nucleolar scaffolds are modulated by non-ribosomal proteins through active rearrangements of interaction networks that can possibly contribute to the directionality of ribosomal biogenesis within the liquid-like nucleolus.

Summary Protein folding and aggregation inevitably compete with one another. This competition is even keener for proteins with frustrated landscapes, such as those rich in β-structure. Interestingly, despite their rugged energy landscapes and high β-sheet content, intracellular lipid-binding proteins (iLBPs) appear to successfully avoid aggregation, as they are not implicated in aggregation diseases. In this study, we used a canonical iLBP, cellular retinoic acid-binding protein 1 (CRABP1), to better understand how folding is favored over aggregation. Analysis of folding kinetics of point mutants reveals that the folding pathway of CRABP1 involves early barrel closure. This folding mechanism protects sequences in CRABP1 that comprise cores of aggregates as identified by NMR. The amino acid conservation pattern in other iLBPs suggests that early barrel closure may be a general strategy for successful folding and minimization of aggregation. We suggest that folding mechanisms more broadly may incorporate steps that disfavor aggregation.