PhaSePro: the database of proteins driving liquid–liquid phase separation

Abstract

Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromolecules. Since the first discoveries of certain proteins being able to drive LLPS, it emerged as a general mechanism for the effective organization of cellular space that is exploited in all kingdoms of life. While numerous experimental studies report novel cases, the computational identification of LLPS drivers is lagging behind, and many open questions remain about the sequence determinants, composition, regulation and biological relevance of the resulting condensates. Our limited ability to overcome these issues is largely due to the lack of a dedicated LLPS database. Therefore, here we introduce PhaSePro (https://phasepro.elte.hu), an openly accessible, comprehensive, manually curated database of experimentally validated LLPS driver proteins/protein regions. It not only provides a wealth of information on such systems, but improves the standardization of data by introducing novel LLPS-specific controlled vocabularies. PhaSePro can be accessed through an appealing, user-friendly interface and thus has definite potential to become the central resource in this dynamically developing field.

Single molecule microscopy reveals key physical features of repair foci in living cells

“…In human cells, Herpes Simplex Virus appears to share many properties commonly attributed to LLPS, but SPT measurements have recently shown that they are formed through a distinct compartmentalization mechanism 54 . As the list of proteins that can undergo phase separation is growing in the literature 56,57 , it will be essential to confirm the nature of sub-compartments using in vivo single molecule approaches. It also becomes necessary to define solid criteria and observables at the microscopic level to distinguish between different models (Heltberg et al, in preparation) and to develop alternative models of membrane-less sub-compartments.…”

A guide to regulation of the formation of biomolecular condensates

“…As this interaction is crucial for LLPS, only short SynGAP isoforms can form MLOs. Similar motif–domain interactions are common in LLPS , and AS has been shown to specifically target them in several cases, such as GRB2, a component of the phase‐separated LAT signalosome . The short isoform, called GRB3‐3, lacks a functional SH2 domain, inhibiting the binding of phosphorylated Tyr crucial for signalosome formation with LAT .…”

“…A large number of studies have addressed the identity of constituent proteins (and RNA), the conditions of the formation of MLOs and their physical properties. As a result, many ‘phase‐separating’ proteins have been identified, ranging from 120 (PhaSePro ) to 9300 (DrLLPS ). These contradicting numbers raise the issue of specificity and probably highlight the fact that only a small fraction of phase‐separating proteins (scaffolds) actually drive phase separation, while many of them (clients) only get recruited into the droplets once they have formed .…”

Learning of Signaling Networks: Molecular Mechanisms

“…Further, protein kinase C βII-induced upregulation and mitochondrial translocation of the adaptor protein, p66SHC, was associated with the formation of hyperglycemic molecular memory of human aortic endothelial cells ( Figure 2 [30]). Protein translocation may also occur between subcompartments of a cellular organelle, such as in the nucleus or in the form of the formation of biomolecular condensates by liquid-liquid phase separation [31]. Protein translocation establishes a whole set of novel protein-protein interactions, increasing their edge weights in signaling networks.…”