Integration of Data from Liquid-Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers.

Nazanin Farahi,Peter Tompa,Shoshana J Wodak,Rita Pancsa,Tamas Lazar

doi:10.3390/ijms22063017

Abstract

Liquid–liquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles, representing functionally specialized liquid-like cellular condensates formed by proteins and nucleic acids. Integrating the data on LLPS-associated proteins from dedicated databases revealed only modest agreement between them and yielded a high-confidence dataset of 89 human LLPS drivers. Analysis of the supporting evidence for our dataset uncovered a systematic and potentially concerning difference between protein concentrations used in a good fraction of the in vitro LLPS experiments, a key parameter that governs the phase behavior, and the proteomics-derived cellular abundance levels of the corresponding proteins. Closer scrutiny of the underlying experimental data enabled us to offer a sound rationale for this systematic difference, which draws on our current understanding of the cellular organization of the proteome and the LLPS process. In support of this rationale, we find that genes coding for our human LLPS drivers tend to be dosage-sensitive, suggesting that their cellular availability is tightly regulated to preserve their functional role in direct or indirect relation to condensate formation. Our analysis offers guideposts for increasing agreement between in vitro and in vivo studies, probing the roles of proteins in LLPS.

Highlights

An important recent discovery in the field of molecular cell biology is that the formation of biomolecular condensates in living cells is driven by a reversible process called liquid–liquid phase separation (LLPS) [1]
Interpretation of LLPS Experiments to Define the Roles of Proteins in the Formation and Integrity of membraneless organelles (MLOs)
Consolidating the data on the LLPS driver/scaffold proteins from 3 recently published databases dedicated to archiving information on proteins associated with the formation of liquid condensates in living cells enabled us to derive a high confidence dataset of 89 human LLPS driver proteins supported by physiologically relevant experiments

Summary

Introduction

An important recent discovery in the field of molecular cell biology is that the formation of biomolecular condensates in living cells is driven by a reversible process called liquid–liquid phase separation (LLPS) [1] These condensates, the so-called membraneless organelles (MLOs), represent distinct liquid phases selectively enriched in certain macromolecules and fulfill essential cellular functions under normal conditions and in response to stress [2,3,4,5]. The functional benefits of MLOs do not directly derive from the individual role of their constituent molecules but emerge from their collective behavior [3,4,9,10,11,12,13] This recently recognized process is considered as a fundamental mechanism employed by living cells to cost-efficiently [5] organize and reorganize cellular space and material according to functional needs [3,14,15,16]. The latter often contain long filaments resembling amyloid fibers, involved in many neurodegenerative diseases [25] such as amyotrophic lateral sclerosis [26,27], frontotemporal dementia [28], and Alzheimer’s disease [29,30,31], drawing attention to the potential pathological roles of liquid condensates

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Results

Conclusion