scholarly journals Starvation-induced proteasome assemblies in the nucleus link amino acid supply to apoptosis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Maxime Uriarte ◽  
Nadine Sen Nkwe ◽  
Roch Tremblay ◽  
Oumaima Ahmed ◽  
Clémence Messmer ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Phase Separation ◽  
Amino Acid ◽  
Liquid Phase ◽  
Mammalian Cells ◽  
Proteasome Inhibition ◽  
Eukaryotic Cells ◽  
Amino Acid Deprivation ◽  
Common Response ◽  
Liquid Liquid Phase Separation

AbstractEukaryotic cells have evolved highly orchestrated protein catabolic machineries responsible for the timely and selective disposal of proteins and organelles, thereby ensuring amino acid recycling. However, how protein degradation is coordinated with amino acid supply and protein synthesis has remained largely elusive. Here we show that the mammalian proteasome undergoes liquid-liquid phase separation in the nucleus upon amino acid deprivation. We termed these proteasome condensates SIPAN (Starvation-Induced Proteasome Assemblies in the Nucleus) and show that these are a common response of mammalian cells to amino acid deprivation. SIPAN undergo fusion events, rapidly exchange proteasome particles with the surrounding milieu and quickly dissolve following amino acid replenishment. We further show that: (i) SIPAN contain K48-conjugated ubiquitin, (ii) proteasome inhibition accelerates SIPAN formation, (iii) deubiquitinase inhibition prevents SIPAN resolution and (iv) RAD23B proteasome shuttling factor is required for SIPAN formation. Finally, SIPAN formation is associated with decreased cell survival and p53-mediated apoptosis, which might contribute to tissue fitness in diverse pathophysiological conditions.

scholarly journals Liquid–liquid phase separation in human health and diseases

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Bin Wang ◽  
Lei Zhang ◽  
Tong Dai ◽  
Ziran Qin ◽  
Huasong Lu ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Human Health ◽  
Essential Role ◽  
Current Knowledge ◽  
Vital Role ◽  
Liquid Phase Separation ◽  
Eukaryotic Cells ◽  
Liquid Liquid Phase Separation

AbstractEmerging evidence suggests that liquid–liquid phase separation (LLPS) represents a vital and ubiquitous phenomenon underlying the formation of membraneless organelles in eukaryotic cells (also known as biomolecular condensates or droplets). Recent studies have revealed evidences that indicate that LLPS plays a vital role in human health and diseases. In this review, we describe our current understanding of LLPS and summarize its physiological functions. We further describe the role of LLPS in the development of human diseases. Additionally, we review the recently developed methods for studying LLPS. Although LLPS research is in its infancy—but is fast-growing—it is clear that LLPS plays an essential role in the development of pathophysiological conditions. This highlights the need for an overview of the recent advances in the field to translate our current knowledge regarding LLPS into therapeutic discoveries.

scholarly journals Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence

2020 ◽  
Author(s):  
Simon M. Lichtinger ◽  
Adiran Garaizar ◽  
Rosana Collepardo-Guevara ◽  
Aleks Reinhardt
Keyword(s):  
Phase Separation ◽  
Amino Acid ◽  
Liquid Phase ◽  
Amino Acid Sequence ◽  
Amino Acid Sequences ◽  
Liquid Phase Separation ◽  
Computational Method ◽  
Coarse Grained ◽  
Intrinsically Disordered ◽  
Liquid Liquid Phase Separation

AbstractRationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid-liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose an innovative computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We apply it to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction. We find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence: the critical temperature can be enhanced by increasing the frequency of hydrophobic and aromatic residues, by changing the charge patterning, or by a combination of both. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the composition of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.

scholarly journals Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation

2020 ◽  
Author(s):  
A-M Ladouceur ◽  
B Parmar ◽  
S Biedzinski ◽  
J Wall ◽  
SG Tope ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Rna Polymerase ◽  
Tree Of Life ◽  
Liquid Phase Separation ◽  
Eukaryotic Cells ◽  
Bacterial Cells ◽  
Intracellular Organization ◽  
Universal Mechanism ◽  
Liquid Liquid Phase Separation

AbstractOnce described as mere “bags of enzymes”, bacterial cells are in fact highly organized, with many macromolecules exhibiting non-uniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid-liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in E. coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and suggests that this process serves as a universal mechanism for intracellular organization across the tree of life.SignificanceBacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid-liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid-liquid phase separation is a universal mechanism for intracellular organization that extends across the tree of life.

scholarly journals Solubility Parameters of Amino Acids on Liquid–Liquid Phase Separation and Aggregation of Proteins

2021 ◽  
Vol 9 ◽  
Author(s):  
Akira Nomoto ◽  
Suguru Nishinami ◽  
Kentaro Shiraki
Keyword(s):  
Amino Acids ◽  
Phase Separation ◽  
Amino Acid ◽  
Liquid Phase ◽  
Aromatic Amino Acids ◽  
Liquid Phase Separation ◽  
Solubility Parameters ◽  
Liquid Liquid Phase Separation

The solution properties of amino acids determine the folding, aggregation, and liquid–liquid phase separation (LLPS) behaviors of proteins. Various indices of amino acids, such as solubility, hydropathy, and conformational parameter, describe the behaviors of protein folding and solubility both in vitro and in vivo. However, understanding the propensity of LLPS and aggregation is difficult due to the multiple interactions among different amino acids. Here, the solubilities of aromatic amino acids (SAs) were investigated in solution containing 20 types of amino acids as amino acid solvents. The parameters of SAs in amino acid solvents (PSASs) were varied and dependent on the type of the solvent. Specifically, Tyr and Trp had the highest positive values while Glu and Asp had the lowest. The PSAS values represent soluble and insoluble interactions, which collectively are the driving force underlying the formation of droplets and aggregates. Interestingly, the PSAS of a soluble solvent reflected the affinity between amino acids and aromatic rings, while that of an insoluble solvent reflected the affinity between amino acids and water. These findings suggest that the PSAS can distinguish amino acids that contribute to droplet and aggregate formation, and provide a deeper understanding of LLPS and aggregation of proteins.

scholarly journals Multi-Step Ubiquitin Decoding Mechanism for Proteasomal Degradation

2020 ◽  
Vol 13 (6) ◽  
pp. 128
Author(s):  
Hikaru Tsuchiya ◽  
Akinori Endo ◽  
Yasushi Saeki
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Structural Diversity ◽  
Proteasomal Degradation ◽  
26S Proteasome ◽  
Eukaryotic Cells ◽  
Present Evidence ◽  
Major Function ◽  
Chain Lengths ◽  
Liquid Liquid Phase Separation

The 26S proteasome is a 2.5-MDa protease complex responsible for the selective and ATP-dependent degradation of ubiquitylated proteins in eukaryotic cells. Proteasome-mediated protein degradation accounts for ~70% of all cellular proteolysis under basal conditions, and thereby any dysfunction can lead to drastic changes in cell homeostasis. A major function of ubiquitylation is to target proteins for proteasomal degradation. Accompanied by deciphering the structural diversity of ubiquitin chains with eight linkages and chain lengths, the ubiquitin code for proteasomal degradation has been expanding beyond the best-characterized Lys48-linked ubiquitin chains. Whereas polyubiquitylated proteins can be directly recognized by the proteasome, in several cases, these proteins need to be extracted or segregated by the conserved ATPases associated with diverse cellular activities (AAA)-family ATPase p97/valosin-containing protein (VCP) complex and escorted to the proteasome by ubiquitin-like (UBL)–ubiquitin associated (UBA) proteins; these are called substrate-shuttling factors. Furthermore, proteasomes are highly mobile and are appropriately spatiotemporally regulated in response to different cellular environments and stresses. In this review, we highlight an emerging key link between p97, shuttling factors, and proteasome for efficient proteasomal degradation. We also present evidence that proteasome-containing nuclear foci form by liquid–liquid phase separation under acute hyperosmotic stress.

scholarly journals Liquid-liquid phase separation of light-inducible transcription factors increases transcription activation in mammalian cells and mice

2021 ◽  
Vol 7 (1) ◽  
pp. eabd3568
Author(s):  
Nils Schneider ◽  
Franz-Georg Wieland ◽  
Deqiang Kong ◽  
Alexandra A. M. Fischer ◽  
Maximilian Hörner ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Phase Separation ◽  
Liquid Phase ◽  
Mammalian Cells ◽  
Liquid Phase Separation ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Gene Switches ◽  
Liquid Liquid Phase Separation

Light-inducible gene switches represent a key strategy for the precise manipulation of cellular events in fundamental and applied research. However, the performance of widely used gene switches is limited due to low tissue penetrance and possible phototoxicity of the light stimulus. To overcome these limitations, we engineer optogenetic synthetic transcription factors to undergo liquid-liquid phase separation in close spatial proximity to promoters. Phase separation of constitutive and optogenetic synthetic transcription factors was achieved by incorporation of intrinsically disordered regions. Supported by a quantitative mathematical model, we demonstrate that engineered transcription factor droplets form at target promoters and increase gene expression up to fivefold. This increase in performance was observed in multiple mammalian cells lines as well as in mice following in situ transfection. The results of this work suggest that the introduction of intrinsically disordered domains is a simple yet effective means to boost synthetic transcription factor activity.

scholarly journals Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence

2021 ◽  
Vol 17 (8) ◽  
pp. e1009328
Author(s):  
Simon M. Lichtinger ◽  
Adiran Garaizar ◽  
Rosana Collepardo-Guevara ◽  
Aleks Reinhardt
Keyword(s):  
Phase Separation ◽  
Amino Acid ◽  
Liquid Phase ◽  
Amino Acid Sequence ◽  
Amino Acid Sequences ◽  
Liquid Phase Separation ◽  
Computational Method ◽  
Coarse Grained ◽  
Intrinsically Disordered ◽  
Liquid Liquid Phase Separation

Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid–liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose a computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We validate the predicted critical solution temperatures of the mutated sequences with ABSINTH, a more accurate all-atom model. We apply the algorithm to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction, and we find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the make-up of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.

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